RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux lgw01-48 3.13.0-85-generic #129-Ubuntu SMP Thu Mar 17 20:50:15 UTC 2016 x86_64 Buildd toolchain package versions: launchpad-buildd_139 python-lpbuildd_139 sbuild_0.65.2-1ubuntu2~ubuntu14.04.1~ppa8 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.04.1 bzr_2.6.0+bzr6593-1ubuntu1.5 git-build-recipe_0.3~git201603101733.90b6821~ubuntu14.04.2 git_1:1.9.1-1ubuntu0.3 dpkg-dev_1.17.5ubuntu5.6 python-debian_0.1.27ubuntu1~ubuntu14.04.1~ppa1 qemu-user-static_2.0.0+dfsg-2ubuntu1.22. Syncing the system clock with the buildd NTP service... 3 May 23:22:12 ntpdate[1664]: adjust time server 10.211.37.1 offset 0.002397 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-9686715', '/home/buildd/filecache-default/9af1b65e710cc0b334e8c9a330a1d817d2c021bb'] Unpacking chroot for build PACKAGEBUILD-9686715 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-9686715'] Mounting chroot for build PACKAGEBUILD-9686715 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-9686715', 'deb http://ftpmaster.internal/ubuntu yakkety main universe', 'deb http://ftpmaster.internal/ubuntu yakkety-security main universe', 'deb http://ftpmaster.internal/ubuntu yakkety-updates main universe', 'deb http://ftpmaster.internal/ubuntu yakkety-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-9686715 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-9686715', 'i386'] Updating debian chroot for build PACKAGEBUILD-9686715 Get:1 http://ftpmaster.internal/ubuntu yakkety InRelease [247 kB] Get:2 http://ftpmaster.internal/ubuntu yakkety-security InRelease [92.2 kB] Get:3 http://ftpmaster.internal/ubuntu yakkety-updates InRelease [92.2 kB] Get:4 http://ftpmaster.internal/ubuntu yakkety-proposed InRelease [95.7 kB] Get:5 http://ftpmaster.internal/ubuntu yakkety/main i386 Packages [1198 kB] Get:6 http://ftpmaster.internal/ubuntu yakkety/main Translation-en [568 kB] Get:7 http://ftpmaster.internal/ubuntu yakkety/universe i386 Packages [7601 kB] Get:8 http://ftpmaster.internal/ubuntu yakkety/universe Translation-en [4413 kB] Get:9 http://ftpmaster.internal/ubuntu yakkety-security/main i386 Packages [64 B] Get:10 http://ftpmaster.internal/ubuntu yakkety-security/main Translation-en [64 B] Get:11 http://ftpmaster.internal/ubuntu yakkety-security/universe i386 Packages [64 B] Get:12 http://ftpmaster.internal/ubuntu yakkety-security/universe Translation-en [64 B] Get:13 http://ftpmaster.internal/ubuntu yakkety-updates/main i386 Packages [64 B] Get:14 http://ftpmaster.internal/ubuntu yakkety-updates/main Translation-en [64 B] Get:15 http://ftpmaster.internal/ubuntu yakkety-updates/universe i386 Packages [64 B] Get:16 http://ftpmaster.internal/ubuntu yakkety-updates/universe Translation-en [64 B] Get:17 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 Packages [60.4 kB] Get:18 http://ftpmaster.internal/ubuntu yakkety-proposed/main Translation-en [33.1 kB] Get:19 http://ftpmaster.internal/ubuntu yakkety-proposed/universe i386 Packages [329 kB] Get:20 http://ftpmaster.internal/ubuntu yakkety-proposed/universe Translation-en [179 kB] Fetched 14.9 MB in 7s (2080 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libpng16-16 The following packages will be upgraded: apt apt-transport-https bash binutils bzip2 cpp-5 debconf dmsetup dpkg dpkg-dev g++-5 gcc-5 gcc-5-base gcc-6-base grep hostname init init-system-helpers initscripts libapt-pkg5.0 libasan2 libatomic1 libbz2-1.0 libcc1-0 libcilkrts5 libdevmapper1.02.1 libdpkg-perl libgcc-5-dev libgcc1 libgcrypt20 libgomp1 libgpg-error0 libitm1 libmpx0 libperl5.22 libpng12-0 libquadmath0 librtmp1 libsasl2-2 libsasl2-modules-db libselinux1 libsemanage-common libsemanage1 libsepol1 libslang2 libstdc++-5-dev libstdc++6 libsystemd0 libtasn1-6 libubsan0 libudev1 libusb-0.1-4 linux-libc-dev make optipng perl perl-base perl-modules-5.22 policyrcd-script-zg2 systemd systemd-sysv sysv-rc sysvinit-utils tar tzdata zlib1g 66 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 95.1 MB of archives. After this operation, 185 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu yakkety/main i386 bash i386 4.3-14ubuntu2 [591 kB] Get:2 http://ftpmaster.internal/ubuntu yakkety/main i386 dpkg i386 1.18.4ubuntu2 [2113 kB] Get:3 http://ftpmaster.internal/ubuntu yakkety/main i386 grep i386 2.25-1 [157 kB] Get:4 http://ftpmaster.internal/ubuntu yakkety/main i386 hostname i386 3.17ubuntu1 [11.9 kB] Get:5 http://ftpmaster.internal/ubuntu yakkety/main i386 perl-modules-5.22 all 5.22.2-1 [2642 kB] Get:6 http://ftpmaster.internal/ubuntu yakkety/main i386 libperl5.22 i386 5.22.2-1 [3014 kB] Get:7 http://ftpmaster.internal/ubuntu yakkety/main i386 perl i386 5.22.2-1 [237 kB] Get:8 http://ftpmaster.internal/ubuntu yakkety/main i386 perl-base i386 5.22.2-1 [1369 kB] Get:9 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 bzip2 i386 1.0.6-8build1 [32.5 kB] Get:10 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libbz2-1.0 i386 1.0.6-8build1 [30.9 kB] Get:11 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 zlib1g i386 1:1.2.8.dfsg-2ubuntu5 [52.1 kB] Get:12 http://ftpmaster.internal/ubuntu yakkety/main i386 init-system-helpers all 1.31ubuntu1 [31.9 kB] Get:13 http://ftpmaster.internal/ubuntu yakkety/main i386 init i386 1.31ubuntu1 [4564 B] Get:14 http://ftpmaster.internal/ubuntu yakkety/main i386 tar i386 1.28-2.2 [221 kB] Get:15 http://ftpmaster.internal/ubuntu yakkety/main i386 gcc-6-base i386 6.1.1-0ubuntu12 [16.0 kB] Get:16 http://ftpmaster.internal/ubuntu yakkety/main i386 libgcc1 i386 1:6.1.1-0ubuntu12 [46.9 kB] Get:17 http://ftpmaster.internal/ubuntu yakkety/main i386 libstdc++6 i386 6.1.1-0ubuntu12 [433 kB] Get:18 http://ftpmaster.internal/ubuntu yakkety/main i386 libapt-pkg5.0 i386 1.2.11 [736 kB] Get:19 http://ftpmaster.internal/ubuntu yakkety/main i386 apt i386 1.2.11 [1054 kB] Get:20 http://ftpmaster.internal/ubuntu yakkety/main i386 debconf all 1.5.59ubuntu1 [136 kB] Get:21 http://ftpmaster.internal/ubuntu yakkety/main i386 sysvinit-utils i386 2.88dsf-59.3ubuntu5 [22.0 kB] Get:22 http://ftpmaster.internal/ubuntu yakkety/main i386 sysv-rc all 2.88dsf-59.3ubuntu5 [18.2 kB] Get:23 http://ftpmaster.internal/ubuntu yakkety/main i386 initscripts i386 2.88dsf-59.3ubuntu5 [24.5 kB] Get:24 http://ftpmaster.internal/ubuntu yakkety/main i386 libgpg-error0 i386 1.22-1 [37.3 kB] Get:25 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libselinux1 i386 2.5-2 [70.4 kB] Get:26 http://ftpmaster.internal/ubuntu yakkety/main i386 libsystemd0 i386 229-5ubuntu1 [228 kB] Get:27 http://ftpmaster.internal/ubuntu yakkety/main i386 systemd i386 229-5ubuntu1 [3682 kB] Get:28 http://ftpmaster.internal/ubuntu yakkety/main i386 systemd-sysv i386 229-5ubuntu1 [17.7 kB] Get:29 http://ftpmaster.internal/ubuntu yakkety/main i386 libudev1 i386 229-5ubuntu1 [63.5 kB] Get:30 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libdevmapper1.02.1 i386 2:1.02.122-1ubuntu1 [154 kB] Get:31 http://ftpmaster.internal/ubuntu yakkety/main i386 libgcrypt20 i386 1.7.0-2 [372 kB] Get:32 http://ftpmaster.internal/ubuntu yakkety/main i386 libsepol1 i386 2.5-1 [236 kB] Get:33 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libsemanage-common all 2.5-1 [6800 B] Get:34 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libsemanage1 i386 2.5-1 [88.3 kB] Get:35 http://ftpmaster.internal/ubuntu yakkety/main i386 libusb-0.1-4 i386 2:0.1.12-29 [17.7 kB] Get:36 http://ftpmaster.internal/ubuntu yakkety/main i386 tzdata all 2016d-2 [168 kB] Get:37 http://ftpmaster.internal/ubuntu yakkety/main i386 libslang2 i386 2.3.0-2.3ubuntu1 [416 kB] Get:38 http://ftpmaster.internal/ubuntu yakkety/main i386 libtasn1-6 i386 4.8-1 [44.8 kB] Get:39 http://ftpmaster.internal/ubuntu yakkety/main i386 apt-transport-https i386 1.2.11 [27.6 kB] Get:40 http://ftpmaster.internal/ubuntu yakkety/main i386 libpng16-16 i386 1.6.21-4 [181 kB] Get:41 http://ftpmaster.internal/ubuntu yakkety/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-1 [58.1 kB] Get:42 http://ftpmaster.internal/ubuntu yakkety/main i386 libsasl2-modules-db i386 2.1.26.dfsg1-15 [15.4 kB] Get:43 http://ftpmaster.internal/ubuntu yakkety/main i386 libsasl2-2 i386 2.1.26.dfsg1-15 [51.8 kB] Get:44 http://ftpmaster.internal/ubuntu yakkety/main i386 binutils i386 2.26-8ubuntu3 [2482 kB] Get:45 http://ftpmaster.internal/ubuntu yakkety/main i386 libgomp1 i386 6.1.1-0ubuntu12 [79.9 kB] Get:46 http://ftpmaster.internal/ubuntu yakkety/main i386 libitm1 i386 6.1.1-0ubuntu12 [31.2 kB] Get:47 http://ftpmaster.internal/ubuntu yakkety/main i386 libatomic1 i386 6.1.1-0ubuntu12 [9918 B] Get:48 http://ftpmaster.internal/ubuntu yakkety/main i386 libasan2 i386 5.3.1-16ubuntu3 [271 kB] Get:49 http://ftpmaster.internal/ubuntu yakkety/main i386 libubsan0 i386 6.1.1-0ubuntu12 [120 kB] Get:50 http://ftpmaster.internal/ubuntu yakkety/main i386 libcilkrts5 i386 6.1.1-0ubuntu12 [45.8 kB] Get:51 http://ftpmaster.internal/ubuntu yakkety/main i386 libmpx0 i386 5.3.1-16ubuntu3 [11.1 kB] Get:52 http://ftpmaster.internal/ubuntu yakkety/main i386 libquadmath0 i386 6.1.1-0ubuntu12 [204 kB] Get:53 http://ftpmaster.internal/ubuntu yakkety/main i386 g++-5 i386 5.3.1-16ubuntu3 [30.4 MB] Get:54 http://ftpmaster.internal/ubuntu yakkety/main i386 gcc-5 i386 5.3.1-16ubuntu3 [8403 kB] Get:55 http://ftpmaster.internal/ubuntu yakkety/main i386 libstdc++-5-dev i386 5.3.1-16ubuntu3 [1437 kB] Get:56 http://ftpmaster.internal/ubuntu yakkety/main i386 libgcc-5-dev i386 5.3.1-16ubuntu3 [2242 kB] Get:57 http://ftpmaster.internal/ubuntu yakkety/main i386 libcc1-0 i386 6.1.1-0ubuntu12 [33.0 kB] Get:58 http://ftpmaster.internal/ubuntu yakkety/main i386 cpp-5 i386 5.3.1-16ubuntu3 [28.4 MB] Get:59 http://ftpmaster.internal/ubuntu yakkety/main i386 gcc-5-base i386 5.3.1-16ubuntu3 [17.4 kB] Get:60 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 dmsetup i386 2:1.02.122-1ubuntu1 [72.9 kB] Get:61 http://ftpmaster.internal/ubuntu yakkety/main i386 dpkg-dev all 1.18.4ubuntu2 [584 kB] Get:62 http://ftpmaster.internal/ubuntu yakkety/main i386 libdpkg-perl all 1.18.4ubuntu2 [195 kB] Get:63 http://ftpmaster.internal/ubuntu yakkety/main i386 make i386 4.1-9 [154 kB] Get:64 http://ftpmaster.internal/ubuntu yakkety/universe i386 libpng12-0 i386 1.2.54-6ubuntu1 [122 kB] Get:65 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 linux-libc-dev i386 4.4.0-22.38 [840 kB] Get:66 http://ftpmaster.internal/ubuntu yakkety/main i386 optipng i386 0.7.6-1build1 [86.3 kB] Get:67 http://ftpmaster.internal/ubuntu yakkety/main i386 policyrcd-script-zg2 all 0.1-3 [5610 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 95.1 MB in 10s (9394 kB/s) (Reading database ... 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Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up libgpg-error0:i386 (1.22-1) ... Processing triggers for systemd (229-4ubuntu4) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12148 files and directories currently installed.) Preparing to unpack .../libselinux1_2.5-2_i386.deb ... Unpacking libselinux1:i386 (2.5-2) over (2.4-3build2) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up libselinux1:i386 (2.5-2) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12148 files and directories currently installed.) Preparing to unpack .../libsystemd0_229-5ubuntu1_i386.deb ... Unpacking libsystemd0:i386 (229-5ubuntu1) over (229-4ubuntu4) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up libsystemd0:i386 (229-5ubuntu1) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12145 files and directories currently installed.) Preparing to unpack .../tzdata_2016d-2_all.deb ... Unpacking tzdata (2016d-2) over (2016d-0ubuntu0.16.04) ... Preparing to unpack .../libslang2_2.3.0-2.3ubuntu1_i386.deb ... Unpacking libslang2:i386 (2.3.0-2.3ubuntu1) over (2.3.0-2ubuntu1) ... Preparing to unpack .../libtasn1-6_4.8-1_i386.deb ... Unpacking libtasn1-6:i386 (4.8-1) over (4.7-3) ... Preparing to unpack .../apt-transport-https_1.2.11_i386.deb ... Unpacking apt-transport-https (1.2.11) over (1.2.10ubuntu1) ... Selecting previously unselected package libpng16-16:i386. Preparing to unpack .../libpng16-16_1.6.21-4_i386.deb ... Unpacking libpng16-16:i386 (1.6.21-4) ... Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d.1-1_i386.deb ... Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d.1-1) over (2.4+20151223.gitfa8646d-1build1) ... Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-15_i386.deb ... Unpacking libsasl2-modules-db:i386 (2.1.26.dfsg1-15) over (2.1.26.dfsg1-14build1) ... Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-15_i386.deb ... Unpacking libsasl2-2:i386 (2.1.26.dfsg1-15) over (2.1.26.dfsg1-14build1) ... Preparing to unpack .../binutils_2.26-8ubuntu3_i386.deb ... Unpacking binutils (2.26-8ubuntu3) over (2.26-8ubuntu2) ... Preparing to unpack .../libgomp1_6.1.1-0ubuntu12_i386.deb ... 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Unpacking libquadmath0:i386 (6.1.1-0ubuntu12) over (5.3.1-14ubuntu2) ... Preparing to unpack .../g++-5_5.3.1-16ubuntu3_i386.deb ... Unpacking g++-5 (5.3.1-16ubuntu3) over (5.3.1-14ubuntu2) ... Preparing to unpack .../gcc-5_5.3.1-16ubuntu3_i386.deb ... Unpacking gcc-5 (5.3.1-16ubuntu3) over (5.3.1-14ubuntu2) ... Preparing to unpack .../libstdc++-5-dev_5.3.1-16ubuntu3_i386.deb ... Unpacking libstdc++-5-dev:i386 (5.3.1-16ubuntu3) over (5.3.1-14ubuntu2) ... Preparing to unpack .../libgcc-5-dev_5.3.1-16ubuntu3_i386.deb ... Unpacking libgcc-5-dev:i386 (5.3.1-16ubuntu3) over (5.3.1-14ubuntu2) ... Preparing to unpack .../libcc1-0_6.1.1-0ubuntu12_i386.deb ... Unpacking libcc1-0:i386 (6.1.1-0ubuntu12) over (5.3.1-14ubuntu2) ... Preparing to unpack .../cpp-5_5.3.1-16ubuntu3_i386.deb ... Unpacking cpp-5 (5.3.1-16ubuntu3) over (5.3.1-14ubuntu2) ... Preparing to unpack .../gcc-5-base_5.3.1-16ubuntu3_i386.deb ... Unpacking gcc-5-base:i386 (5.3.1-16ubuntu3) over (5.3.1-14ubuntu2) ... Preparing to unpack .../dmsetup_2%3a1.02.122-1ubuntu1_i386.deb ... Unpacking dmsetup (2:1.02.122-1ubuntu1) over (2:1.02.110-1ubuntu10) ... Preparing to unpack .../dpkg-dev_1.18.4ubuntu2_all.deb ... Unpacking dpkg-dev (1.18.4ubuntu2) over (1.18.4ubuntu1) ... Preparing to unpack .../libdpkg-perl_1.18.4ubuntu2_all.deb ... Unpacking libdpkg-perl (1.18.4ubuntu2) over (1.18.4ubuntu1) ... Preparing to unpack .../archives/make_4.1-9_i386.deb ... Unpacking make (4.1-9) over (4.1-6) ... Preparing to unpack .../libpng12-0_1.2.54-6ubuntu1_i386.deb ... Unpacking libpng12-0:i386 (1.2.54-6ubuntu1) over (1.2.54-1ubuntu1) ... Preparing to unpack .../linux-libc-dev_4.4.0-22.38_i386.deb ... Unpacking linux-libc-dev:i386 (4.4.0-22.38) over (4.4.0-21.37) ... Preparing to unpack .../optipng_0.7.6-1build1_i386.deb ... Unpacking optipng (0.7.6-1build1) over (0.7.6-1) ... Preparing to unpack .../policyrcd-script-zg2_0.1-3_all.deb ... Unpacking policyrcd-script-zg2 (0.1-3) over (0.1-2) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up perl-modules-5.22 (5.22.2-1) ... Setting up libperl5.22:i386 (5.22.2-1) ... Setting up perl (5.22.2-1) ... Setting up bzip2 (1.0.6-8build1) ... Setting up sysv-rc (2.88dsf-59.3ubuntu5) ... Setting up initscripts (2.88dsf-59.3ubuntu5) ... Installing new version of config file /etc/init.d/ondemand ... Setting up tzdata (2016d-2) ... Current default time zone: 'Etc/UTC' Local time is now: Tue May 3 23:23:03 UTC 2016. Universal Time is now: Tue May 3 23:23:03 UTC 2016. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libslang2:i386 (2.3.0-2.3ubuntu1) ... Setting up libtasn1-6:i386 (4.8-1) ... Setting up apt-transport-https (1.2.11) ... Setting up libpng16-16:i386 (1.6.21-4) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-1) ... Setting up libsasl2-modules-db:i386 (2.1.26.dfsg1-15) ... Setting up libsasl2-2:i386 (2.1.26.dfsg1-15) ... Setting up binutils (2.26-8ubuntu3) ... Setting up libgomp1:i386 (6.1.1-0ubuntu12) ... Setting up libitm1:i386 (6.1.1-0ubuntu12) ... Setting up libatomic1:i386 (6.1.1-0ubuntu12) ... Setting up gcc-5-base:i386 (5.3.1-16ubuntu3) ... Setting up libasan2:i386 (5.3.1-16ubuntu3) ... Setting up libubsan0:i386 (6.1.1-0ubuntu12) ... Setting up libcilkrts5:i386 (6.1.1-0ubuntu12) ... Setting up libmpx0:i386 (5.3.1-16ubuntu3) ... Setting up libquadmath0:i386 (6.1.1-0ubuntu12) ... Setting up cpp-5 (5.3.1-16ubuntu3) ... Setting up libcc1-0:i386 (6.1.1-0ubuntu12) ... Setting up libgcc-5-dev:i386 (5.3.1-16ubuntu3) ... Setting up gcc-5 (5.3.1-16ubuntu3) ... Setting up libstdc++-5-dev:i386 (5.3.1-16ubuntu3) ... Setting up g++-5 (5.3.1-16ubuntu3) ... Setting up dmsetup (2:1.02.122-1ubuntu1) ... Setting up libdpkg-perl (1.18.4ubuntu2) ... Setting up make (4.1-9) ... Setting up dpkg-dev (1.18.4ubuntu2) ... Setting up libpng12-0:i386 (1.2.54-6ubuntu1) ... Setting up linux-libc-dev:i386 (4.4.0-22.38) ... Setting up optipng (0.7.6-1build1) ... Setting up policyrcd-script-zg2 (0.1-3) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Processing triggers for systemd (229-5ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-9686715', 'i386', 'yakkety-proposed', '-c', 'chroot:autobuild', '--arch=i386', '--dist=yakkety-proposed', '--purge=never', '--nolog', 'r-base_3.3.0-1.dsc'] Initiating build PACKAGEBUILD-9686715 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 3.13.0-85-generic #129-Ubuntu SMP Thu Mar 17 20:50:15 UTC 2016 i686 sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on lgw01-48.buildd ╔══════════════════════════════════════════════════════════════════════════════╗ ║ r-base 3.3.0-1 (i386) 03 May 2016 23:23 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: r-base Version: 3.3.0-1 Source Version: 3.3.0-1 Distribution: yakkety-proposed Machine Architecture: amd64 Host Architecture: i386 Build Architecture: i386 I: NOTICE: Log filtering will replace 'build/r-base-asNdei/r-base-3.3.0' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/r-base-asNdei' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-9686715/chroot-autobuild' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Local sources ───────────── r-base_3.3.0-1.dsc exists in .; copying to chroot Check architectures ─────────────────── Check dependencies ────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-kOMLHw/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/«BUILDDIR»/resolver-kOMLHw/apt_archive ./ InRelease Get:2 copy:/«BUILDDIR»/resolver-kOMLHw/apt_archive ./ Release [2119 B] Ign:3 copy:/«BUILDDIR»/resolver-kOMLHw/apt_archive ./ Release.gpg Get:4 copy:/«BUILDDIR»/resolver-kOMLHw/apt_archive ./ Sources [208 B] Get:5 copy:/«BUILDDIR»/resolver-kOMLHw/apt_archive ./ Packages [526 B] Fetched 2853 B in 0s (235 kB/s) Reading package lists... W: The repository 'copy:/«BUILDDIR»/resolver-kOMLHw/apt_archive ./ Release' is not signed. Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 770 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Get:1 copy:/«BUILDDIR»/resolver-kOMLHw/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 770 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 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Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), gcc (>= 4:4.1.0), g++ (>= 4:4.1.0), gfortran (>= 4:4.1.0), libblas-dev, liblapack-dev (>= 3.1.1), tcl8.6-dev, tk8.6-dev, bison, groff-base, libncurses5-dev, libreadline-dev, debhelper (>= 7.2.3), texinfo (>= 4.1-2), libbz2-dev, liblzma-dev, libpcre3-dev, libcurl4-openssl-dev | libcurl4-dev, xdg-utils, zlib1g-dev, libpng-dev, libjpeg-dev, libx11-dev, libxt-dev, x11proto-core-dev, libpango1.0-dev, libcairo2-dev, libtiff5-dev, xvfb, xauth, xfonts-base, texlive-base, texlive-latex-base, texlive-generic-recommended, texlive-fonts-recommended, texlive-fonts-extra, texlive-extra-utils, texlive-latex-recommended, texlive-latex-extra, default-jdk, mpack, bash-completion Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), gcc (>= 4:4.1.0), g++ (>= 4:4.1.0), gfortran (>= 4:4.1.0), libblas-dev, liblapack-dev (>= 3.1.1), tcl8.6-dev, tk8.6-dev, bison, groff-base, libncurses5-dev, libreadline-dev, debhelper (>= 7.2.3), texinfo (>= 4.1-2), libbz2-dev, liblzma-dev, libpcre3-dev, libcurl4-openssl-dev | libcurl4-dev, xdg-utils, zlib1g-dev, libpng-dev, libjpeg-dev, libx11-dev, libxt-dev, x11proto-core-dev, libpango1.0-dev, libcairo2-dev, libtiff5-dev, xvfb, xauth, xfonts-base, texlive-base, texlive-latex-base, texlive-generic-recommended, texlive-fonts-recommended, texlive-fonts-extra, texlive-extra-utils, texlive-latex-recommended, texlive-latex-extra, default-jdk, mpack, bash-completion dpkg-deb: building package 'sbuild-build-depends-r-base-dummy' in '/«BUILDDIR»/resolver-IOnagW/apt_archive/sbuild-build-depends-r-base-dummy.deb'. Ign:1 copy:/«BUILDDIR»/resolver-IOnagW/apt_archive ./ InRelease Get:2 copy:/«BUILDDIR»/resolver-IOnagW/apt_archive ./ Release [2119 B] Ign:3 copy:/«BUILDDIR»/resolver-IOnagW/apt_archive ./ Release.gpg Get:4 copy:/«BUILDDIR»/resolver-IOnagW/apt_archive ./ Sources [685 B] Get:5 copy:/«BUILDDIR»/resolver-IOnagW/apt_archive ./ Packages [932 B] Fetched 3736 B in 0s (0 B/s) Reading package lists... W: The repository 'copy:/«BUILDDIR»/resolver-IOnagW/apt_archive ./ Release' is not signed. Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install r-base build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bash-completion bison bsdmainutils ca-certificates-java debhelper default-jdk default-jdk-headless default-jre default-jre-headless dh-autoreconf dh-strip-nondeterminism file fontconfig fontconfig-config fonts-cabin fonts-comfortaa fonts-crosextra-caladea fonts-crosextra-carlito fonts-dejavu-core fonts-dejavu-extra fonts-ebgaramond fonts-ebgaramond-extra fonts-font-awesome fonts-freefont-otf fonts-freefont-ttf fonts-gfs-artemisia fonts-gfs-complutum fonts-gfs-didot fonts-gfs-neohellenic fonts-gfs-olga fonts-gfs-solomos fonts-junicode fonts-lato fonts-linuxlibertine fonts-lobster fonts-lobstertwo fonts-oflb-asana-math fonts-roboto-hinted fonts-sil-gentium fonts-sil-gentium-basic fonts-sil-gentiumplus fonts-stix gettext gettext-base gfortran gfortran-5 gir1.2-freedesktop gir1.2-glib-2.0 gir1.2-pango-1.0 groff-base icu-devtools intltool-debian java-common libarchive-zip-perl libasound2 libasound2-data libasprintf0v5 libasyncns0 libatk1.0-0 libatk1.0-data libavahi-client3 libavahi-common-data libavahi-common3 libbison-dev libblas-common libblas-dev libblas3 libbsd0 libbz2-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev libcroco3 libcups2 libcupsfilters1 libcupsimage2 libcurl3 libcurl4-openssl-dev libdatrie1 libdbus-1-3 libdrm-amdgpu1 libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libflac8 libfontconfig1 libfontconfig1-dev libfontenc1 libfreetype6 libfreetype6-dev libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgfortran-5-dev libgfortran3 libgif7 libgirepository-1.0-1 libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libgraphite2-3 libgraphite2-dev libgs9 libgs9-common libgtk2.0-0 libgtk2.0-common libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libice-dev libice6 libicu-dev libicu57 libijs-0.35 libjbig-dev libjbig0 libjbig2dec0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjson-c3 libkpathsea6 liblapack-dev liblapack3 liblcms2-2 libllvm3.8 liblzma-dev liblzo2-2 libmagic1 libncurses5-dev libnspr4 libnss3 libnss3-nssdb libogg0 libpango-1.0-0 libpango1.0-dev libpangocairo-1.0-0 libpangoft2-1.0-0 libpangoxft-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpcsclite1 libpipeline1 libpixman-1-0 libpixman-1-dev libpng-dev libpoppler58 libpotrace0 libptexenc1 libpthread-stubs0-dev libpulse0 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline-dev libreadline6-dev libsigsegv2 libsm-dev libsm6 libsndfile1 libsynctex1 libtcl8.6 libtexlua52 libtexluajit2 libtext-unidecode-perl libthai-data libthai0 libtiff5 libtiff5-dev libtiffxx5 libtimedate-perl libtinfo-dev libtk8.6 libtool libunistring0 libvorbis0a libvorbisenc2 libwrap0 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-render0-dev libxcb-shm0 libxcb-shm0-dev libxcb-sync1 libxcb1 libxcb1-dev libxcomposite1 libxcursor1 libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes3 libxfont1 libxft-dev libxft2 libxi6 libxinerama1 libxkbfile1 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml2 libxmu6 libxmuu1 libxpm4 libxrandr2 libxrender-dev libxrender1 libxshmfence1 libxss-dev libxss1 libxt-dev libxt6 libxtst6 libxxf86vm1 libzzip-0-13 m4 man-db mime-support mpack openjdk-8-jdk openjdk-8-jdk-headless openjdk-8-jre openjdk-8-jre-headless pkg-config po-debconf poppler-data preview-latex-style python python-minimal python2.7 python2.7-minimal shared-mime-info t1utils tcl8.6 tcl8.6-dev tex-common texinfo texlive-base texlive-binaries texlive-extra-utils texlive-fonts-extra texlive-fonts-recommended texlive-generic-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6 tk8.6-dev ttf-adf-accanthis ttf-adf-gillius ttf-adf-universalis ucf x11-common x11-xkb-utils x11proto-core-dev x11proto-input-dev x11proto-kb-dev x11proto-render-dev x11proto-scrnsaver-dev x11proto-xext-dev xauth xdg-utils xfonts-base xfonts-encodings xfonts-utils xkb-data xorg-sgml-doctools xserver-common xtrans-dev xvfb zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc bison-doc wamerican | wordlist whois vacation dh-make default-java-plugin fontforge gettext-doc gfortran-multilib gfortran-doc gfortran-5-multilib gfortran-5-doc libgfortran3-dbg groff libasound2-plugins alsa-utils liblapack-doc-man liblapack-doc libcairo2-doc cups-common libcurl4-doc libcurl3-dbg libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssl-dev libglib2.0-doc fonts-droid texlive-lang-cjk librsvg2-common gvfs libice-doc icu-doc liblcms2-utils liblzma-doc ncurses-doc imagemagick libpango1.0-doc pciutils pcscd pulseaudio readline-doc libsm-doc libtool-doc gcj-jdk libxcb-doc libxext-doc libxt-doc less www-browser mail-transport-agent inews openjdk-8-demo openjdk-8-source visualvm icedtea-8-plugin openjdk-8-jre-jamvm libnss-mdns fonts-ipafont-gothic fonts-ipafont-mincho ttf-wqy-microhei | ttf-wqy-zenhei fonts-indic libmail-box-perl poppler-utils ghostscript fonts-japanese-mincho | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-nanum python-doc python-tk python2.7-doc binfmt-support tcl-tclreadline tcl8.6-doc texinfo-doc-nonfree perl-tk gv | postscript-viewer xpdf-reader | pdf-viewer dvipng dvidvi xindy fragmaster purifyeps lacheck chktex latexmk latexdiff cm-super python-pygments libfile-which-perl libspreadsheet-parseexcel-perl texlive-pstricks libtcltk-ruby dot2tex prerex tk8.6-doc gvfs-bin Recommended packages: curl | wget | lynx-cur libasprintf-dev libgettextpo-dev bzip2-doc dbus libtxc-dxtn-s2tc0 | libtxc-dxtn0 xdg-user-dirs hicolor-icon-theme libgtk2.0-bin libpng-tools libltdl-dev tcpd libx11-doc libxml-sax-expat-perl xml-core libgnome-2-0 libgnomevfs2-0 libgconf-2-4 libmail-sendmail-perl lmodern ruby wish libyaml-tiny-perl ghostscript libfile-homedir-perl ruby | ruby-interpreter texlive-fonts-extra-doc texlive-fonts-recommended-doc tipa tex-gyre texlive-latex-base-doc texlive-latex-extra-doc prosper texlive-latex-recommended-doc texlive-pictures-doc tk xterm | x-terminal-emulator libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bash-completion bison bsdmainutils ca-certificates-java debhelper default-jdk default-jdk-headless default-jre default-jre-headless dh-autoreconf dh-strip-nondeterminism file fontconfig fontconfig-config fonts-cabin fonts-comfortaa fonts-crosextra-caladea fonts-crosextra-carlito fonts-dejavu-core fonts-dejavu-extra fonts-ebgaramond fonts-ebgaramond-extra fonts-font-awesome fonts-freefont-otf fonts-freefont-ttf fonts-gfs-artemisia fonts-gfs-complutum fonts-gfs-didot fonts-gfs-neohellenic fonts-gfs-olga fonts-gfs-solomos fonts-junicode fonts-lato fonts-linuxlibertine fonts-lobster fonts-lobstertwo fonts-oflb-asana-math fonts-roboto-hinted fonts-sil-gentium fonts-sil-gentium-basic fonts-sil-gentiumplus fonts-stix gettext gettext-base gfortran gfortran-5 gir1.2-freedesktop gir1.2-glib-2.0 gir1.2-pango-1.0 groff-base icu-devtools intltool-debian java-common libarchive-zip-perl libasound2 libasound2-data libasprintf0v5 libasyncns0 libatk1.0-0 libatk1.0-data libavahi-client3 libavahi-common-data libavahi-common3 libbison-dev libblas-common libblas-dev libblas3 libbsd0 libbz2-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev libcroco3 libcups2 libcupsfilters1 libcupsimage2 libcurl3 libcurl4-openssl-dev libdatrie1 libdbus-1-3 libdrm-amdgpu1 libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libflac8 libfontconfig1 libfontconfig1-dev libfontenc1 libfreetype6 libfreetype6-dev libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgfortran-5-dev libgfortran3 libgif7 libgirepository-1.0-1 libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libgraphite2-3 libgraphite2-dev libgs9 libgs9-common libgtk2.0-0 libgtk2.0-common libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libice-dev libice6 libicu-dev libicu57 libijs-0.35 libjbig-dev libjbig0 libjbig2dec0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjson-c3 libkpathsea6 liblapack-dev liblapack3 liblcms2-2 libllvm3.8 liblzma-dev liblzo2-2 libmagic1 libncurses5-dev libnspr4 libnss3 libnss3-nssdb libogg0 libpango-1.0-0 libpango1.0-dev libpangocairo-1.0-0 libpangoft2-1.0-0 libpangoxft-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpcsclite1 libpipeline1 libpixman-1-0 libpixman-1-dev libpng-dev libpoppler58 libpotrace0 libptexenc1 libpthread-stubs0-dev libpulse0 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline-dev libreadline6-dev libsigsegv2 libsm-dev libsm6 libsndfile1 libsynctex1 libtcl8.6 libtexlua52 libtexluajit2 libtext-unidecode-perl libthai-data libthai0 libtiff5 libtiff5-dev libtiffxx5 libtimedate-perl libtinfo-dev libtk8.6 libtool libunistring0 libvorbis0a libvorbisenc2 libwrap0 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-render0-dev libxcb-shm0 libxcb-shm0-dev libxcb-sync1 libxcb1 libxcb1-dev libxcomposite1 libxcursor1 libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes3 libxfont1 libxft-dev libxft2 libxi6 libxinerama1 libxkbfile1 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml2 libxmu6 libxmuu1 libxpm4 libxrandr2 libxrender-dev libxrender1 libxshmfence1 libxss-dev libxss1 libxt-dev libxt6 libxtst6 libxxf86vm1 libzzip-0-13 m4 man-db mime-support mpack openjdk-8-jdk openjdk-8-jdk-headless openjdk-8-jre openjdk-8-jre-headless pkg-config po-debconf poppler-data preview-latex-style python python-minimal python2.7 python2.7-minimal sbuild-build-depends-r-base-dummy shared-mime-info t1utils tcl8.6 tcl8.6-dev tex-common texinfo texlive-base texlive-binaries texlive-extra-utils texlive-fonts-extra texlive-fonts-recommended texlive-generic-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6 tk8.6-dev ttf-adf-accanthis ttf-adf-gillius ttf-adf-universalis ucf x11-common x11-xkb-utils x11proto-core-dev x11proto-input-dev x11proto-kb-dev x11proto-render-dev x11proto-scrnsaver-dev x11proto-xext-dev xauth xdg-utils xfonts-base xfonts-encodings xfonts-utils xkb-data xorg-sgml-doctools xserver-common xtrans-dev xvfb zlib1g-dev 0 upgraded, 309 newly installed, 0 to remove and 0 not upgraded. Need to get 503 MB of archives. After this operation, 1735 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-r-base-dummy Authentication warning overridden. Get:1 copy:/«BUILDDIR»/resolver-IOnagW/apt_archive ./ sbuild-build-depends-r-base-dummy 0.invalid.0 [1180 B] Get:2 http://ftpmaster.internal/ubuntu yakkety/main i386 bash-completion all 1:2.1-4.2ubuntu2 [152 kB] Get:3 http://ftpmaster.internal/ubuntu yakkety/main i386 libxau6 i386 1:1.0.8-1 [8352 B] Get:4 http://ftpmaster.internal/ubuntu yakkety/main i386 libxdmcp6 i386 1:1.1.2-1.1 [11.4 kB] Get:5 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb1 i386 1.11.1-1ubuntu1 [44.1 kB] Get:6 http://ftpmaster.internal/ubuntu yakkety/main i386 libx11-data all 2:1.6.3-1ubuntu2 [113 kB] Get:7 http://ftpmaster.internal/ubuntu yakkety/main i386 libx11-6 i386 2:1.6.3-1ubuntu2 [592 kB] Get:8 http://ftpmaster.internal/ubuntu yakkety/main i386 libxext6 i386 2:1.3.3-1 [31.6 kB] Get:9 http://ftpmaster.internal/ubuntu yakkety/main i386 groff-base i386 1.22.3-7 [1160 kB] Get:10 http://ftpmaster.internal/ubuntu yakkety/main i386 bsdmainutils i386 9.0.6ubuntu3 [175 kB] Get:11 http://ftpmaster.internal/ubuntu yakkety/main i386 libpipeline1 i386 1.4.1-2 [26.5 kB] Get:12 http://ftpmaster.internal/ubuntu yakkety/main i386 man-db i386 2.7.5-1 [865 kB] Get:13 http://ftpmaster.internal/ubuntu yakkety/main i386 fonts-dejavu-core all 2.35-1 [1039 kB] Get:14 http://ftpmaster.internal/ubuntu yakkety/main i386 fonts-freefont-ttf all 20120503-4 [4140 kB] Get:15 http://ftpmaster.internal/ubuntu yakkety/main i386 ucf all 3.0036 [52.9 kB] Get:16 http://ftpmaster.internal/ubuntu yakkety/main i386 fontconfig-config all 2.11.94-0ubuntu1 [49.9 kB] Get:17 http://ftpmaster.internal/ubuntu yakkety/main i386 libexpat1 i386 2.1.1-1 [74.3 kB] Get:18 http://ftpmaster.internal/ubuntu yakkety/main i386 libfreetype6 i386 2.6.3-3ubuntu1 [335 kB] Get:19 http://ftpmaster.internal/ubuntu yakkety/main i386 libfontconfig1 i386 2.11.94-0ubuntu1 [140 kB] Get:20 http://ftpmaster.internal/ubuntu yakkety/main i386 fontconfig i386 2.11.94-0ubuntu1 [177 kB] Get:21 http://ftpmaster.internal/ubuntu yakkety/main i386 fonts-lato all 2.0-1 [2693 kB] Get:22 http://ftpmaster.internal/ubuntu yakkety/main i386 libasyncns0 i386 0.8-5build1 [12.7 kB] Get:23 http://ftpmaster.internal/ubuntu yakkety/main i386 x11-common all 1:7.7+13ubuntu3 [22.4 kB] Get:24 http://ftpmaster.internal/ubuntu yakkety/main i386 libice6 i386 2:1.0.9-1 [38.2 kB] Get:25 http://ftpmaster.internal/ubuntu yakkety/main i386 libjpeg-turbo8 i386 1.4.2-0ubuntu3 [117 kB] Get:26 http://ftpmaster.internal/ubuntu yakkety/main i386 liblcms2-2 i386 2.6-3ubuntu2 [147 kB] Get:27 http://ftpmaster.internal/ubuntu yakkety/main i386 liblzo2-2 i386 2.08-1.2 [52.7 kB] Get:28 http://ftpmaster.internal/ubuntu yakkety/main i386 libogg0 i386 1.3.2-1 [16.2 kB] Get:29 http://ftpmaster.internal/ubuntu yakkety/main i386 libpcrecpp0v5 i386 2:8.38-3.1 [16.0 kB] Get:30 http://ftpmaster.internal/ubuntu yakkety/main i386 libsm6 i386 2:1.2.2-1 [14.8 kB] Get:31 http://ftpmaster.internal/ubuntu yakkety/main i386 libunistring0 i386 0.9.3-5.2ubuntu1 [277 kB] Get:32 http://ftpmaster.internal/ubuntu yakkety/main i386 libwrap0 i386 7.6.q-25 [45.8 kB] Get:33 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcomposite1 i386 1:0.4.4-1 [7594 B] Get:34 http://ftpmaster.internal/ubuntu yakkety/main i386 libxfixes3 i386 1:5.0.1-2 [11.4 kB] Get:35 http://ftpmaster.internal/ubuntu yakkety/main i386 libxrender1 i386 1:0.9.9-0ubuntu1 [19.2 kB] Get:36 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcursor1 i386 1:1.1.14-1 [22.8 kB] Get:37 http://ftpmaster.internal/ubuntu yakkety/main i386 libxdamage1 i386 1:1.1.4-2 [6812 B] Get:38 http://ftpmaster.internal/ubuntu yakkety/main i386 libfontenc1 i386 1:1.1.3-1 [14.0 kB] Get:39 http://ftpmaster.internal/ubuntu yakkety/main i386 libxfont1 i386 1:1.5.1-1 [97.3 kB] Get:40 http://ftpmaster.internal/ubuntu yakkety/main i386 libxft2 i386 2.3.2-1 [35.5 kB] Get:41 http://ftpmaster.internal/ubuntu yakkety/main i386 libxinerama1 i386 2:1.1.3-1 [7900 B] Get:42 http://ftpmaster.internal/ubuntu yakkety/main i386 libxpm4 i386 1:3.5.11-1 [32.1 kB] Get:43 http://ftpmaster.internal/ubuntu yakkety/main i386 libxshmfence1 i386 1.2-1 [5164 B] Get:44 http://ftpmaster.internal/ubuntu yakkety/main i386 libxss1 i386 1:1.2.2-1 [8566 B] Get:45 http://ftpmaster.internal/ubuntu yakkety/main i386 libxtst6 i386 2:1.2.2-1 [13.8 kB] Get:46 http://ftpmaster.internal/ubuntu yakkety/main i386 libxxf86vm1 i386 1:1.1.4-1 [11.3 kB] Get:47 http://ftpmaster.internal/ubuntu yakkety/main i386 libzzip-0-13 i386 0.13.62-3 [27.5 kB] Get:48 http://ftpmaster.internal/ubuntu yakkety/main i386 java-common all 0.56ubuntu2 [7742 B] Get:49 http://ftpmaster.internal/ubuntu yakkety/main i386 default-jre-headless i386 2:1.8-56ubuntu2 [4376 B] Get:50 http://ftpmaster.internal/ubuntu yakkety/main i386 libnspr4 i386 2:4.11-1ubuntu1 [121 kB] Get:51 http://ftpmaster.internal/ubuntu yakkety/main i386 libnss3-nssdb all 2:3.21-1ubuntu4 [10.6 kB] Get:52 http://ftpmaster.internal/ubuntu yakkety/main i386 libnss3 i386 2:3.21-1ubuntu4 [1187 kB] Get:53 http://ftpmaster.internal/ubuntu yakkety/main i386 ca-certificates-java all 20160321 [12.9 kB] Get:54 http://ftpmaster.internal/ubuntu yakkety/main i386 libavahi-common-data i386 0.6.32~rc+dfsg-1ubuntu2 [21.7 kB] Get:55 http://ftpmaster.internal/ubuntu yakkety/main i386 libavahi-common3 i386 0.6.32~rc+dfsg-1ubuntu2 [23.5 kB] Get:56 http://ftpmaster.internal/ubuntu yakkety/main i386 libdbus-1-3 i386 1.10.6-1ubuntu3 [173 kB] Get:57 http://ftpmaster.internal/ubuntu yakkety/main i386 libavahi-client3 i386 0.6.32~rc+dfsg-1ubuntu2 [27.1 kB] Get:58 http://ftpmaster.internal/ubuntu yakkety/main i386 libcups2 i386 2.1.3-5 [212 kB] Get:59 http://ftpmaster.internal/ubuntu yakkety/main i386 libjpeg8 i386 8c-2ubuntu8 [2188 B] Get:60 http://ftpmaster.internal/ubuntu yakkety/main i386 libpcsclite1 i386 1.8.14-1ubuntu1 [22.9 kB] Get:61 http://ftpmaster.internal/ubuntu yakkety/main i386 libxi6 i386 2:1.7.6-1 [31.3 kB] Get:62 http://ftpmaster.internal/ubuntu yakkety/main i386 openjdk-8-jre-headless i386 8u91-b14-2ubuntu1 [26.5 MB] Get:63 http://ftpmaster.internal/ubuntu yakkety/main i386 poppler-data all 0.4.7-7 [1495 kB] Get:64 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libpython2.7-minimal i386 2.7.11-8 [336 kB] Get:65 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 python2.7-minimal i386 2.7.11-8 [1357 kB] Get:66 http://ftpmaster.internal/ubuntu yakkety/main i386 python-minimal i386 2.7.11-1 [28.2 kB] Get:67 http://ftpmaster.internal/ubuntu yakkety/main i386 mime-support all 3.59ubuntu1 [31.0 kB] Get:68 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libpython2.7-stdlib i386 2.7.11-8 [1873 kB] Get:69 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 python2.7 i386 2.7.11-8 [220 kB] Get:70 http://ftpmaster.internal/ubuntu yakkety/main i386 libpython-stdlib i386 2.7.11-1 [7664 B] Get:71 http://ftpmaster.internal/ubuntu yakkety/main i386 python i386 2.7.11-1 [137 kB] Get:72 http://ftpmaster.internal/ubuntu yakkety/main i386 libjbig0 i386 2.1-3.1 [27.0 kB] Get:73 http://ftpmaster.internal/ubuntu yakkety/main i386 libmagic1 i386 1:5.25-2ubuntu1 [222 kB] Get:74 http://ftpmaster.internal/ubuntu yakkety/main i386 file i386 1:5.25-2ubuntu1 [21.1 kB] Get:75 http://ftpmaster.internal/ubuntu yakkety/main i386 libbsd0 i386 0.8.2-1 [45.2 kB] Get:76 http://ftpmaster.internal/ubuntu yakkety/main i386 xkb-data all 2.16-1ubuntu1 [305 kB] Get:77 http://ftpmaster.internal/ubuntu yakkety/main i386 libasprintf0v5 i386 0.19.7-2ubuntu3 [6462 B] Get:78 http://ftpmaster.internal/ubuntu yakkety/main i386 gettext-base i386 0.19.7-2ubuntu3 [48.8 kB] Get:79 http://ftpmaster.internal/ubuntu yakkety/main i386 libglib2.0-0 i386 2.48.0-1ubuntu4 [1183 kB] Get:80 http://ftpmaster.internal/ubuntu yakkety/main i386 libgirepository-1.0-1 i386 1.46.0-3ubuntu1 [97.4 kB] Get:81 http://ftpmaster.internal/ubuntu yakkety/main i386 gir1.2-glib-2.0 i386 1.46.0-3ubuntu1 [127 kB] Get:82 http://ftpmaster.internal/ubuntu yakkety/main i386 libdrm2 i386 2.4.67-1 [30.8 kB] Get:83 http://ftpmaster.internal/ubuntu yakkety/main i386 libedit2 i386 3.1-20150325-1ubuntu2 [80.9 kB] Get:84 http://ftpmaster.internal/ubuntu yakkety/main i386 libelf1 i386 0.165-3ubuntu1 [48.7 kB] Get:85 http://ftpmaster.internal/ubuntu yakkety/main i386 libglib2.0-data all 2.48.0-1ubuntu4 [131 kB] Get:86 http://ftpmaster.internal/ubuntu yakkety/main i386 libicu57 i386 57.1-1 [7806 kB] Get:87 http://ftpmaster.internal/ubuntu yakkety/main i386 libxml2 i386 2.9.3+dfsg1-1build1 [729 kB] Get:88 http://ftpmaster.internal/ubuntu yakkety/main i386 libxmuu1 i386 2:1.1.2-2 [9988 B] Get:89 http://ftpmaster.internal/ubuntu yakkety/main i386 shared-mime-info i386 1.6-1 [406 kB] Get:90 http://ftpmaster.internal/ubuntu yakkety/main i386 xauth i386 1:1.0.9-1ubuntu2 [23.0 kB] Get:91 http://ftpmaster.internal/ubuntu yakkety/main i386 libsigsegv2 i386 2.10-5 [14.3 kB] Get:92 http://ftpmaster.internal/ubuntu yakkety/main i386 m4 i386 1.4.17-5 [195 kB] Get:93 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 autoconf all 2.69-10 [321 kB] Get:94 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 autotools-dev all 20160430.1 [39.6 kB] Get:95 http://ftpmaster.internal/ubuntu yakkety/main i386 automake all 1:1.15-4ubuntu1 [510 kB] Get:96 http://ftpmaster.internal/ubuntu yakkety/main i386 autopoint all 0.19.7-2ubuntu3 [406 kB] Get:97 http://ftpmaster.internal/ubuntu yakkety/main i386 libbison-dev i386 2:3.0.4.dfsg-1 [338 kB] Get:98 http://ftpmaster.internal/ubuntu yakkety/main i386 bison i386 2:3.0.4.dfsg-1 [256 kB] Get:99 http://ftpmaster.internal/ubuntu yakkety/main i386 libcroco3 i386 0.6.11-1 [87.8 kB] Get:100 http://ftpmaster.internal/ubuntu yakkety/main i386 gettext i386 0.19.7-2ubuntu3 [1085 kB] Get:101 http://ftpmaster.internal/ubuntu yakkety/main i386 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:102 http://ftpmaster.internal/ubuntu yakkety/main i386 po-debconf all 1.0.19 [234 kB] Get:103 http://ftpmaster.internal/ubuntu yakkety/main i386 libarchive-zip-perl all 1.57-1 [84.0 kB] Get:104 http://ftpmaster.internal/ubuntu yakkety/main i386 libfile-stripnondeterminism-perl all 0.016-1 [11.0 kB] Get:105 http://ftpmaster.internal/ubuntu yakkety/main i386 libtimedate-perl all 2.3000-2 [37.5 kB] Get:106 http://ftpmaster.internal/ubuntu yakkety/main i386 dh-strip-nondeterminism all 0.016-1 [4858 B] Get:107 http://ftpmaster.internal/ubuntu yakkety/main i386 libtool all 2.4.6-0.1 [193 kB] Get:108 http://ftpmaster.internal/ubuntu yakkety/main i386 dh-autoreconf all 12 [15.8 kB] Get:109 http://ftpmaster.internal/ubuntu yakkety/main i386 debhelper all 9.20160403ubuntu1 [711 kB] Get:110 http://ftpmaster.internal/ubuntu yakkety/main i386 libgtk2.0-common all 2.24.30-1ubuntu1 [123 kB] Get:111 http://ftpmaster.internal/ubuntu yakkety/main i386 libatk1.0-data all 2.20.0-1 [17.5 kB] Get:112 http://ftpmaster.internal/ubuntu yakkety/main i386 libatk1.0-0 i386 2.20.0-1 [58.1 kB] Get:113 http://ftpmaster.internal/ubuntu yakkety/main i386 libpixman-1-0 i386 0.33.6-1 [237 kB] Get:114 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb-render0 i386 1.11.1-1ubuntu1 [12.2 kB] Get:115 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb-shm0 i386 1.11.1-1ubuntu1 [5754 B] Get:116 http://ftpmaster.internal/ubuntu yakkety/main i386 libcairo2 i386 1.14.6-1build1 [613 kB] Get:117 http://ftpmaster.internal/ubuntu yakkety/main i386 libtiff5 i386 4.0.6-1 [154 kB] Get:118 http://ftpmaster.internal/ubuntu yakkety/main i386 libgdk-pixbuf2.0-common all 2.34.0-1ubuntu1 [10.3 kB] Get:119 http://ftpmaster.internal/ubuntu yakkety/main i386 libgdk-pixbuf2.0-0 i386 2.34.0-1ubuntu1 [170 kB] Get:120 http://ftpmaster.internal/ubuntu yakkety/main i386 libthai-data all 0.1.24-2 [131 kB] Get:121 http://ftpmaster.internal/ubuntu yakkety/main i386 libdatrie1 i386 0.2.10-2 [18.8 kB] Get:122 http://ftpmaster.internal/ubuntu yakkety/main i386 libthai0 i386 0.1.24-2 [18.5 kB] Get:123 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libpango-1.0-0 i386 1.40.1-1 [155 kB] Get:124 http://ftpmaster.internal/ubuntu yakkety/main i386 libgraphite2-3 i386 1.3.6-1ubuntu1 [73.3 kB] Get:125 http://ftpmaster.internal/ubuntu yakkety/main i386 libharfbuzz0b i386 1.2.6-2 [188 kB] Get:126 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libpangoft2-1.0-0 i386 1.40.1-1 [36.3 kB] Get:127 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libpangocairo-1.0-0 i386 1.40.1-1 [22.5 kB] Get:128 http://ftpmaster.internal/ubuntu yakkety/main i386 libxrandr2 i386 2:1.5.0-1 [19.1 kB] Get:129 http://ftpmaster.internal/ubuntu yakkety/main i386 libgtk2.0-0 i386 2.24.30-1ubuntu1 [1904 kB] Get:130 http://ftpmaster.internal/ubuntu yakkety/main i386 libglapi-mesa i386 11.2.1-1ubuntu1 [23.0 kB] Get:131 http://ftpmaster.internal/ubuntu yakkety/main i386 libx11-xcb1 i386 2:1.6.3-1ubuntu2 [8944 B] Get:132 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb-dri2-0 i386 1.11.1-1ubuntu1 [7292 B] Get:133 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb-dri3-0 i386 1.11.1-1ubuntu1 [5392 B] Get:134 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb-glx0 i386 1.11.1-1ubuntu1 [22.3 kB] Get:135 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb-present0 i386 1.11.1-1ubuntu1 [5396 B] Get:136 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb-sync1 i386 1.11.1-1ubuntu1 [8702 B] Get:137 http://ftpmaster.internal/ubuntu yakkety/main i386 libdrm-amdgpu1 i386 2.4.67-1 [19.5 kB] Get:138 http://ftpmaster.internal/ubuntu yakkety/main i386 libpciaccess0 i386 0.13.4-1 [20.3 kB] Get:139 http://ftpmaster.internal/ubuntu yakkety/main i386 libdrm-intel1 i386 2.4.67-1 [59.7 kB] Get:140 http://ftpmaster.internal/ubuntu yakkety/main i386 libdrm-nouveau2 i386 2.4.67-1 [18.2 kB] Get:141 http://ftpmaster.internal/ubuntu yakkety/main i386 libdrm-radeon1 i386 2.4.67-1 [23.1 kB] Get:142 http://ftpmaster.internal/ubuntu yakkety/main i386 libllvm3.8 i386 1:3.8-2ubuntu3 [11.5 MB] Get:143 http://ftpmaster.internal/ubuntu yakkety/main i386 libgl1-mesa-dri i386 11.2.1-1ubuntu1 [4950 kB] Get:144 http://ftpmaster.internal/ubuntu yakkety/main i386 libgl1-mesa-glx i386 11.2.1-1ubuntu1 [135 kB] Get:145 http://ftpmaster.internal/ubuntu yakkety/main i386 libasound2-data all 1.1.0-1 [29.9 kB] Get:146 http://ftpmaster.internal/ubuntu yakkety/main i386 libasound2 i386 1.1.0-1 [371 kB] Get:147 http://ftpmaster.internal/ubuntu yakkety/main i386 libgif7 i386 5.1.4-0.1 [31.9 kB] Get:148 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libjson-c3 i386 0.12-3 [23.5 kB] Get:149 http://ftpmaster.internal/ubuntu yakkety/main i386 libflac8 i386 1.3.1-4 [154 kB] Get:150 http://ftpmaster.internal/ubuntu yakkety/main i386 libvorbis0a i386 1.3.5-3 [85.7 kB] Get:151 http://ftpmaster.internal/ubuntu yakkety/main i386 libvorbisenc2 i386 1.3.5-3 [64.5 kB] Get:152 http://ftpmaster.internal/ubuntu yakkety/main i386 libsndfile1 i386 1.0.25-10 [157 kB] Get:153 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libpulse0 i386 1:8.0-2ubuntu1 [252 kB] Get:154 http://ftpmaster.internal/ubuntu yakkety/main i386 openjdk-8-jre i386 8u91-b14-2ubuntu1 [70.8 kB] Get:155 http://ftpmaster.internal/ubuntu yakkety/main i386 default-jre i386 2:1.8-56ubuntu2 [980 B] Get:156 http://ftpmaster.internal/ubuntu yakkety/main i386 openjdk-8-jdk-headless i386 8u91-b14-2ubuntu1 [8167 kB] Get:157 http://ftpmaster.internal/ubuntu yakkety/main i386 default-jdk-headless i386 2:1.8-56ubuntu2 [976 B] Get:158 http://ftpmaster.internal/ubuntu yakkety/main i386 openjdk-8-jdk i386 8u91-b14-2ubuntu1 [429 kB] Get:159 http://ftpmaster.internal/ubuntu yakkety/main i386 default-jdk i386 2:1.8-56ubuntu2 [962 B] Get:160 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-cabin all 1.5-2 [140 kB] Get:161 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-comfortaa all 2.003-1 [131 kB] Get:162 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-crosextra-caladea all 20130214-1 [82.3 kB] Get:163 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-crosextra-carlito all 20130920-1 [742 kB] Get:164 http://ftpmaster.internal/ubuntu yakkety/main i386 fonts-dejavu-extra all 2.35-1 [1749 kB] Get:165 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-ebgaramond all 0.015+git20130628-3 [651 kB] Get:166 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-ebgaramond-extra all 0.015+git20130628-3 [933 kB] Get:167 http://ftpmaster.internal/ubuntu yakkety/main i386 fonts-font-awesome all 4.6.1~dfsg-1 [541 kB] Get:168 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-freefont-otf all 20120503-4 [3068 kB] Get:169 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-gfs-artemisia all 1.1-5 [260 kB] Get:170 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-gfs-complutum all 1.1-6 [41.6 kB] Get:171 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-gfs-didot all 1.1-6 [278 kB] Get:172 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-gfs-neohellenic all 1.1-6 [215 kB] Get:173 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-gfs-olga all 1.1-5 [33.4 kB] Get:174 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-gfs-solomos all 1.1-5 [40.7 kB] Get:175 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-junicode all 0.7.8-2 [642 kB] Get:176 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-linuxlibertine all 5.3.0-2 [1688 kB] Get:177 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-lobster all 2.0-2 [38.7 kB] Get:178 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-lobstertwo all 2.0-2 [92.7 kB] Get:179 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-oflb-asana-math all 000.907-6 [246 kB] Get:180 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-roboto-hinted all 2:0~20160106-1 [2942 kB] Get:181 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-sil-gentium all 20081126:1.03-1 [247 kB] Get:182 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-sil-gentium-basic all 1.1-7 [379 kB] Get:183 http://ftpmaster.internal/ubuntu yakkety/universe i386 fonts-sil-gentiumplus all 5.000-1 [2805 kB] Get:184 http://ftpmaster.internal/ubuntu yakkety/main i386 libgfortran3 i386 6.1.1-0ubuntu12 [263 kB] Get:185 http://ftpmaster.internal/ubuntu yakkety/main i386 libgfortran-5-dev i386 5.3.1-16ubuntu3 [277 kB] Get:186 http://ftpmaster.internal/ubuntu yakkety/main i386 gfortran-5 i386 5.3.1-16ubuntu3 [29.2 MB] Get:187 http://ftpmaster.internal/ubuntu yakkety/main i386 gfortran i386 4:5.3.1-1ubuntu1 [1282 B] Get:188 http://ftpmaster.internal/ubuntu yakkety/main i386 gir1.2-freedesktop i386 1.46.0-3ubuntu1 [5732 B] Get:189 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libpangoxft-1.0-0 i386 1.40.1-1 [16.0 kB] Get:190 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 gir1.2-pango-1.0 i386 1.40.1-1 [21.4 kB] Get:191 http://ftpmaster.internal/ubuntu yakkety/main i386 icu-devtools i386 57.1-1 [165 kB] Get:192 http://ftpmaster.internal/ubuntu yakkety/main i386 libblas-common i386 3.6.0-2ubuntu2 [5338 B] Get:193 http://ftpmaster.internal/ubuntu yakkety/main i386 libblas3 i386 3.6.0-2ubuntu2 [130 kB] Get:194 http://ftpmaster.internal/ubuntu yakkety/main i386 libblas-dev i386 3.6.0-2ubuntu2 [129 kB] Get:195 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libbz2-dev i386 1.0.6-8build1 [28.6 kB] Get:196 http://ftpmaster.internal/ubuntu yakkety/main i386 libcairo-gobject2 i386 1.14.6-1build1 [16.7 kB] Get:197 http://ftpmaster.internal/ubuntu yakkety/main i386 libcairo-script-interpreter2 i386 1.14.6-1build1 [58.5 kB] Get:198 http://ftpmaster.internal/ubuntu yakkety/main i386 libexpat1-dev i386 2.1.1-1 [116 kB] Get:199 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 zlib1g-dev i386 1:1.2.8.dfsg-2ubuntu5 [167 kB] Get:200 http://ftpmaster.internal/ubuntu yakkety/main i386 libpng-dev i386 1.6.21-4 [143 kB] Get:201 http://ftpmaster.internal/ubuntu yakkety/main i386 libfreetype6-dev i386 2.6.3-3ubuntu1 [5185 kB] Get:202 http://ftpmaster.internal/ubuntu yakkety/main i386 pkg-config i386 0.29.1-0ubuntu1 [45.8 kB] Get:203 http://ftpmaster.internal/ubuntu yakkety/main i386 libfontconfig1-dev i386 2.11.94-0ubuntu1 [662 kB] Get:204 http://ftpmaster.internal/ubuntu yakkety/main i386 xorg-sgml-doctools all 1:1.11-1 [12.9 kB] Get:205 http://ftpmaster.internal/ubuntu yakkety/main i386 x11proto-core-dev all 7.0.28-2ubuntu1 [254 kB] Get:206 http://ftpmaster.internal/ubuntu yakkety/main i386 libxau-dev i386 1:1.0.8-1 [10.2 kB] Get:207 http://ftpmaster.internal/ubuntu yakkety/main i386 libxdmcp-dev i386 1:1.1.2-1.1 [25.0 kB] Get:208 http://ftpmaster.internal/ubuntu yakkety/main i386 x11proto-input-dev all 2.3.1-1 [118 kB] Get:209 http://ftpmaster.internal/ubuntu yakkety/main i386 x11proto-kb-dev all 1.0.7-0ubuntu1 [224 kB] Get:210 http://ftpmaster.internal/ubuntu yakkety/main i386 xtrans-dev all 1.3.5-1 [70.5 kB] Get:211 http://ftpmaster.internal/ubuntu yakkety/main i386 libpthread-stubs0-dev i386 0.3-4 [4054 B] Get:212 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb1-dev i386 1.11.1-1ubuntu1 [76.3 kB] Get:213 http://ftpmaster.internal/ubuntu yakkety/main i386 libx11-dev i386 2:1.6.3-1ubuntu2 [663 kB] Get:214 http://ftpmaster.internal/ubuntu yakkety/main i386 x11proto-render-dev all 2:0.11.1-2 [20.1 kB] Get:215 http://ftpmaster.internal/ubuntu yakkety/main i386 libxrender-dev i386 1:0.9.9-0ubuntu1 [24.9 kB] Get:216 http://ftpmaster.internal/ubuntu yakkety/main i386 x11proto-xext-dev all 7.3.0-1 [212 kB] Get:217 http://ftpmaster.internal/ubuntu yakkety/main i386 libxext-dev i386 2:1.3.3-1 [82.8 kB] Get:218 http://ftpmaster.internal/ubuntu yakkety/main i386 libice-dev i386 2:1.0.9-1 [42.4 kB] Get:219 http://ftpmaster.internal/ubuntu yakkety/main i386 libsm-dev i386 2:1.2.2-1 [15.1 kB] Get:220 http://ftpmaster.internal/ubuntu yakkety/main i386 libpixman-1-dev i386 0.33.6-1 [261 kB] Get:221 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb-render0-dev i386 1.11.1-1ubuntu1 [15.6 kB] Get:222 http://ftpmaster.internal/ubuntu yakkety/main i386 libxcb-shm0-dev i386 1.11.1-1ubuntu1 [6628 B] Get:223 http://ftpmaster.internal/ubuntu yakkety/main i386 libglib2.0-bin i386 2.48.0-1ubuntu4 [41.1 kB] Get:224 http://ftpmaster.internal/ubuntu yakkety/main i386 libpcre16-3 i386 2:8.38-3.1 [144 kB] Get:225 http://ftpmaster.internal/ubuntu yakkety/main i386 libpcre32-3 i386 2:8.38-3.1 [136 kB] Get:226 http://ftpmaster.internal/ubuntu yakkety/main i386 libpcre3-dev i386 2:8.38-3.1 [530 kB] Get:227 http://ftpmaster.internal/ubuntu yakkety/main i386 libglib2.0-dev i386 2.48.0-1ubuntu4 [1422 kB] Get:228 http://ftpmaster.internal/ubuntu yakkety/main i386 libcairo2-dev i386 1.14.6-1build1 [629 kB] Get:229 http://ftpmaster.internal/ubuntu yakkety/main i386 libcupsfilters1 i386 1.8.3-2ubuntu4 [84.2 kB] Get:230 http://ftpmaster.internal/ubuntu yakkety/main i386 libcupsimage2 i386 2.1.3-5 [16.8 kB] Get:231 http://ftpmaster.internal/ubuntu yakkety/main i386 libcurl3 i386 7.47.0-1ubuntu2 [207 kB] Get:232 http://ftpmaster.internal/ubuntu yakkety/main i386 libcurl4-openssl-dev i386 7.47.0-1ubuntu2 [291 kB] Get:233 http://ftpmaster.internal/ubuntu yakkety/main i386 libgraphite2-dev i386 1.3.6-1ubuntu1 [14.6 kB] Get:234 http://ftpmaster.internal/ubuntu yakkety/main i386 libijs-0.35 i386 0.35-12 [16.0 kB] Get:235 http://ftpmaster.internal/ubuntu yakkety/main i386 libjbig2dec0 i386 0.12+20150918-1build1 [58.0 kB] Get:236 http://ftpmaster.internal/ubuntu yakkety/main i386 libpaper1 i386 1.1.24+nmu4ubuntu1 [13.8 kB] Get:237 http://ftpmaster.internal/ubuntu yakkety/main i386 libgs9-common all 9.18~dfsg~0-0ubuntu5 [2982 kB] Get:238 http://ftpmaster.internal/ubuntu yakkety/main i386 libgs9 i386 9.18~dfsg~0-0ubuntu5 [2154 kB] Get:239 http://ftpmaster.internal/ubuntu yakkety/main i386 libharfbuzz-icu0 i386 1.2.6-2 [5378 B] Get:240 http://ftpmaster.internal/ubuntu yakkety/main i386 libharfbuzz-gobject0 i386 1.2.6-2 [10.3 kB] Get:241 http://ftpmaster.internal/ubuntu yakkety/main i386 libicu-dev i386 57.1-1 [15.3 MB] Get:242 http://ftpmaster.internal/ubuntu yakkety/main i386 libharfbuzz-dev i386 1.2.6-2 [240 kB] Get:243 http://ftpmaster.internal/ubuntu yakkety/main i386 libjpeg-turbo8-dev i386 1.4.2-0ubuntu3 [263 kB] Get:244 http://ftpmaster.internal/ubuntu yakkety/main i386 libjpeg8-dev i386 8c-2ubuntu8 [1546 B] Get:245 http://ftpmaster.internal/ubuntu yakkety/main i386 libjpeg-dev i386 8c-2ubuntu8 [1544 B] Get:246 http://ftpmaster.internal/ubuntu yakkety/main i386 libkpathsea6 i386 2015.20160222.37495-1build1 [58.6 kB] Get:247 http://ftpmaster.internal/ubuntu yakkety/main i386 liblapack3 i386 3.6.0-2ubuntu2 [1764 kB] Get:248 http://ftpmaster.internal/ubuntu yakkety/main i386 liblapack-dev i386 3.6.0-2ubuntu2 [1691 kB] Get:249 http://ftpmaster.internal/ubuntu yakkety/main i386 libtinfo-dev i386 6.0+20160213-1ubuntu1 [76.4 kB] Get:250 http://ftpmaster.internal/ubuntu yakkety/main i386 libncurses5-dev i386 6.0+20160213-1ubuntu1 [177 kB] Get:251 http://ftpmaster.internal/ubuntu yakkety/main i386 libxft-dev i386 2.3.2-1 [43.6 kB] Get:252 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libpango1.0-dev i386 1.40.1-1 [284 kB] Get:253 http://ftpmaster.internal/ubuntu yakkety/main i386 libpaper-utils i386 1.1.24+nmu4ubuntu1 [8298 B] Get:254 http://ftpmaster.internal/ubuntu yakkety/main i386 libpoppler58 i386 0.41.0-0ubuntu2 [790 kB] Get:255 http://ftpmaster.internal/ubuntu yakkety/main i386 libpotrace0 i386 1.13-2 [16.8 kB] Get:256 http://ftpmaster.internal/ubuntu yakkety/main i386 libptexenc1 i386 2015.20160222.37495-1build1 [35.1 kB] Get:257 http://ftpmaster.internal/ubuntu yakkety/main i386 libreadline6-dev i386 6.3-8ubuntu2 [126 kB] Get:258 http://ftpmaster.internal/ubuntu yakkety/main i386 libreadline-dev i386 6.3-8ubuntu2 [988 B] Get:259 http://ftpmaster.internal/ubuntu yakkety/main i386 libsynctex1 i386 2015.20160222.37495-1build1 [43.7 kB] Get:260 http://ftpmaster.internal/ubuntu yakkety/main i386 libtcl8.6 i386 8.6.5+dfsg-2 [932 kB] Get:261 http://ftpmaster.internal/ubuntu yakkety/main i386 libtexlua52 i386 2015.20160222.37495-1build1 [99.8 kB] Get:262 http://ftpmaster.internal/ubuntu yakkety/main i386 libtexluajit2 i386 2015.20160222.37495-1build1 [226 kB] Get:263 http://ftpmaster.internal/ubuntu yakkety/universe i386 libtext-unidecode-perl all 1.27-1 [103 kB] Get:264 http://ftpmaster.internal/ubuntu yakkety/main i386 libjbig-dev i386 2.1-3.1 [24.1 kB] Get:265 http://ftpmaster.internal/ubuntu yakkety/main i386 liblzma-dev i386 5.1.1alpha+20120614-2ubuntu2 [139 kB] Get:266 http://ftpmaster.internal/ubuntu yakkety/main i386 libtiffxx5 i386 4.0.6-1 [6208 B] Get:267 http://ftpmaster.internal/ubuntu yakkety/main i386 libtiff5-dev i386 4.0.6-1 [284 kB] Get:268 http://ftpmaster.internal/ubuntu yakkety/main i386 libtk8.6 i386 8.6.5-1 [729 kB] Get:269 http://ftpmaster.internal/ubuntu yakkety/main i386 libxt6 i386 1:1.1.5-0ubuntu1 [164 kB] Get:270 http://ftpmaster.internal/ubuntu yakkety/main i386 libxmu6 i386 2:1.1.2-2 [48.4 kB] Get:271 http://ftpmaster.internal/ubuntu yakkety/main i386 libxaw7 i386 2:1.0.13-1 [182 kB] Get:272 http://ftpmaster.internal/ubuntu yakkety/main i386 libxkbfile1 i386 1:1.0.9-0ubuntu1 [68.8 kB] Get:273 http://ftpmaster.internal/ubuntu yakkety/main i386 libxml-namespacesupport-perl all 1.11-1 [13.2 kB] Get:274 http://ftpmaster.internal/ubuntu yakkety/main i386 libxml-sax-base-perl all 1.07-1 [21.5 kB] Get:275 http://ftpmaster.internal/ubuntu yakkety/main i386 libxml-sax-perl all 0.99+dfsg-2ubuntu1 [64.6 kB] Get:276 http://ftpmaster.internal/ubuntu yakkety/main i386 libxml-libxml-perl i386 2.0123+dfsg-1build1 [332 kB] Get:277 http://ftpmaster.internal/ubuntu yakkety/main i386 x11proto-scrnsaver-dev all 1.2.2-1 [25.0 kB] Get:278 http://ftpmaster.internal/ubuntu yakkety/main i386 libxss-dev i386 1:1.2.2-1 [12.7 kB] Get:279 http://ftpmaster.internal/ubuntu yakkety/main i386 libxt-dev i386 1:1.1.5-0ubuntu1 [395 kB] Get:280 http://ftpmaster.internal/ubuntu yakkety/universe i386 mpack i386 1.6-8 [39.3 kB] Get:281 http://ftpmaster.internal/ubuntu yakkety/main i386 tex-common all 6.05 [545 kB] Get:282 http://ftpmaster.internal/ubuntu yakkety/main i386 preview-latex-style all 11.88-1.1ubuntu1 [184 kB] Get:283 http://ftpmaster.internal/ubuntu yakkety/main i386 t1utils i386 1.39-2 [54.6 kB] Get:284 http://ftpmaster.internal/ubuntu yakkety/main i386 tcl8.6 i386 8.6.5+dfsg-2 [14.3 kB] Get:285 http://ftpmaster.internal/ubuntu yakkety/main i386 tcl8.6-dev i386 8.6.5+dfsg-2 [963 kB] Get:286 http://ftpmaster.internal/ubuntu yakkety/universe i386 texinfo i386 6.1.0.dfsg.1-6 [743 kB] Get:287 http://ftpmaster.internal/ubuntu yakkety/main i386 texlive-binaries i386 2015.20160222.37495-1build1 [7552 kB] Get:288 http://ftpmaster.internal/ubuntu yakkety/main i386 xdg-utils all 1.1.1-1ubuntu1 [59.9 kB] Get:289 http://ftpmaster.internal/ubuntu yakkety/main i386 texlive-base all 2015.20160320-1 [18.2 MB] Get:290 http://ftpmaster.internal/ubuntu yakkety/main i386 texlive-latex-base all 2015.20160320-1 [849 kB] Get:291 http://ftpmaster.internal/ubuntu yakkety/main i386 texlive-extra-utils all 2015.20160320-1 [11.9 MB] Get:292 http://ftpmaster.internal/ubuntu yakkety/main i386 fonts-stix all 1.1.1-4 [591 kB] Get:293 http://ftpmaster.internal/ubuntu yakkety/universe i386 ttf-adf-gillius all 0.20090423-2 [400 kB] Get:294 http://ftpmaster.internal/ubuntu yakkety/universe i386 ttf-adf-universalis all 0.20090423-2 [221 kB] Get:295 http://ftpmaster.internal/ubuntu yakkety/universe i386 ttf-adf-accanthis all 0.20090423-2 [401 kB] Get:296 http://ftpmaster.internal/ubuntu yakkety/universe i386 texlive-fonts-extra all 2015.20160320-1 [233 MB] Get:297 http://ftpmaster.internal/ubuntu yakkety/universe i386 texlive-fonts-recommended all 2015.20160320-1 [5695 kB] Get:298 http://ftpmaster.internal/ubuntu yakkety/main i386 texlive-generic-recommended all 2015.20160320-1 [2860 kB] Get:299 http://ftpmaster.internal/ubuntu yakkety/main i386 texlive-latex-recommended all 2015.20160320-1 [13.0 MB] Get:300 http://ftpmaster.internal/ubuntu yakkety/main i386 texlive-pictures all 2015.20160320-1 [3737 kB] Get:301 http://ftpmaster.internal/ubuntu yakkety/universe i386 texlive-latex-extra all 2015.20160320-1 [10.3 MB] Get:302 http://ftpmaster.internal/ubuntu yakkety/main i386 tk8.6 i386 8.6.5-1 [12.2 kB] Get:303 http://ftpmaster.internal/ubuntu yakkety/main i386 tk8.6-dev i386 8.6.5-1 [755 kB] Get:304 http://ftpmaster.internal/ubuntu yakkety/main i386 x11-xkb-utils i386 7.7+2 [157 kB] Get:305 http://ftpmaster.internal/ubuntu yakkety/main i386 xfonts-encodings all 1:1.0.4-2 [573 kB] Get:306 http://ftpmaster.internal/ubuntu yakkety/main i386 xfonts-utils i386 1:7.7+3 [75.2 kB] Get:307 http://ftpmaster.internal/ubuntu yakkety/main i386 xfonts-base all 1:1.0.4+nmu1 [5914 kB] Get:308 http://ftpmaster.internal/ubuntu yakkety/main i386 xserver-common all 2:1.18.3-1ubuntu3 [26.5 kB] Get:309 http://ftpmaster.internal/ubuntu yakkety/universe i386 xvfb i386 2:1.18.3-1ubuntu3 [828 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 503 MB in 36s (13.7 MB/s) Selecting previously unselected package bash-completion. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12158 files and directories currently installed.) Preparing to unpack .../bash-completion_1%3a2.1-4.2ubuntu2_all.deb ... Unpacking bash-completion (1:2.1-4.2ubuntu2) ... Replaced by files in installed package apt (1.2.11) ... Selecting previously unselected package libxau6:i386. Preparing to unpack .../libxau6_1%3a1.0.8-1_i386.deb ... Unpacking libxau6:i386 (1:1.0.8-1) ... Selecting previously unselected package libxdmcp6:i386. 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Preparing to unpack .../bsdmainutils_9.0.6ubuntu3_i386.deb ... Unpacking bsdmainutils (9.0.6ubuntu3) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../libpipeline1_1.4.1-2_i386.deb ... Unpacking libpipeline1:i386 (1.4.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.7.5-1_i386.deb ... Unpacking man-db (2.7.5-1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../fonts-dejavu-core_2.35-1_all.deb ... Unpacking fonts-dejavu-core (2.35-1) ... Selecting previously unselected package fonts-freefont-ttf. Preparing to unpack .../fonts-freefont-ttf_20120503-4_all.deb ... Unpacking fonts-freefont-ttf (20120503-4) ... Selecting previously unselected package ucf. Preparing to unpack .../archives/ucf_3.0036_all.deb ... Moving old data out of the way Unpacking ucf (3.0036) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../fontconfig-config_2.11.94-0ubuntu1_all.deb ... Unpacking fontconfig-config (2.11.94-0ubuntu1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.1.1-1_i386.deb ... Unpacking libexpat1:i386 (2.1.1-1) ... Selecting previously unselected package libfreetype6:i386. Preparing to unpack .../libfreetype6_2.6.3-3ubuntu1_i386.deb ... Unpacking libfreetype6:i386 (2.6.3-3ubuntu1) ... Selecting previously unselected package libfontconfig1:i386. Preparing to unpack .../libfontconfig1_2.11.94-0ubuntu1_i386.deb ... Unpacking libfontconfig1:i386 (2.11.94-0ubuntu1) ... Selecting previously unselected package fontconfig. Preparing to unpack .../fontconfig_2.11.94-0ubuntu1_i386.deb ... Unpacking fontconfig (2.11.94-0ubuntu1) ... Selecting previously unselected package fonts-lato. Preparing to unpack .../fonts-lato_2.0-1_all.deb ... Unpacking fonts-lato (2.0-1) ... Selecting previously unselected package libasyncns0:i386. Preparing to unpack .../libasyncns0_0.8-5build1_i386.deb ... Unpacking libasyncns0:i386 (0.8-5build1) ... Selecting previously unselected package x11-common. Preparing to unpack .../x11-common_1%3a7.7+13ubuntu3_all.deb ... Unpacking x11-common (1:7.7+13ubuntu3) ... Selecting previously unselected package libice6:i386. Preparing to unpack .../libice6_2%3a1.0.9-1_i386.deb ... Unpacking libice6:i386 (2:1.0.9-1) ... Selecting previously unselected package libjpeg-turbo8:i386. Preparing to unpack .../libjpeg-turbo8_1.4.2-0ubuntu3_i386.deb ... Unpacking libjpeg-turbo8:i386 (1.4.2-0ubuntu3) ... Selecting previously unselected package liblcms2-2:i386. Preparing to unpack .../liblcms2-2_2.6-3ubuntu2_i386.deb ... Unpacking liblcms2-2:i386 (2.6-3ubuntu2) ... Selecting previously unselected package liblzo2-2:i386. Preparing to unpack .../liblzo2-2_2.08-1.2_i386.deb ... Unpacking liblzo2-2:i386 (2.08-1.2) ... Selecting previously unselected package libogg0:i386. Preparing to unpack .../libogg0_1.3.2-1_i386.deb ... Unpacking libogg0:i386 (1.3.2-1) ... Selecting previously unselected package libpcrecpp0v5:i386. Preparing to unpack .../libpcrecpp0v5_2%3a8.38-3.1_i386.deb ... Unpacking libpcrecpp0v5:i386 (2:8.38-3.1) ... Selecting previously unselected package libsm6:i386. Preparing to unpack .../libsm6_2%3a1.2.2-1_i386.deb ... Unpacking libsm6:i386 (2:1.2.2-1) ... Selecting previously unselected package libunistring0:i386. Preparing to unpack .../libunistring0_0.9.3-5.2ubuntu1_i386.deb ... Unpacking libunistring0:i386 (0.9.3-5.2ubuntu1) ... Selecting previously unselected package libwrap0:i386. Preparing to unpack .../libwrap0_7.6.q-25_i386.deb ... Unpacking libwrap0:i386 (7.6.q-25) ... Selecting previously unselected package libxcomposite1:i386. Preparing to unpack .../libxcomposite1_1%3a0.4.4-1_i386.deb ... Unpacking libxcomposite1:i386 (1:0.4.4-1) ... Selecting previously unselected package libxfixes3:i386. Preparing to unpack .../libxfixes3_1%3a5.0.1-2_i386.deb ... Unpacking libxfixes3:i386 (1:5.0.1-2) ... Selecting previously unselected package libxrender1:i386. Preparing to unpack .../libxrender1_1%3a0.9.9-0ubuntu1_i386.deb ... Unpacking libxrender1:i386 (1:0.9.9-0ubuntu1) ... Selecting previously unselected package libxcursor1:i386. Preparing to unpack .../libxcursor1_1%3a1.1.14-1_i386.deb ... Unpacking libxcursor1:i386 (1:1.1.14-1) ... Selecting previously unselected package libxdamage1:i386. Preparing to unpack .../libxdamage1_1%3a1.1.4-2_i386.deb ... Unpacking libxdamage1:i386 (1:1.1.4-2) ... Selecting previously unselected package libfontenc1:i386. Preparing to unpack .../libfontenc1_1%3a1.1.3-1_i386.deb ... Unpacking libfontenc1:i386 (1:1.1.3-1) ... Selecting previously unselected package libxfont1:i386. Preparing to unpack .../libxfont1_1%3a1.5.1-1_i386.deb ... Unpacking libxfont1:i386 (1:1.5.1-1) ... Selecting previously unselected package libxft2:i386. Preparing to unpack .../libxft2_2.3.2-1_i386.deb ... Unpacking libxft2:i386 (2.3.2-1) ... Selecting previously unselected package libxinerama1:i386. Preparing to unpack .../libxinerama1_2%3a1.1.3-1_i386.deb ... Unpacking libxinerama1:i386 (2:1.1.3-1) ... Selecting previously unselected package libxpm4:i386. Preparing to unpack .../libxpm4_1%3a3.5.11-1_i386.deb ... Unpacking libxpm4:i386 (1:3.5.11-1) ... Selecting previously unselected package libxshmfence1:i386. Preparing to unpack .../libxshmfence1_1.2-1_i386.deb ... Unpacking libxshmfence1:i386 (1.2-1) ... Selecting previously unselected package libxss1:i386. Preparing to unpack .../libxss1_1%3a1.2.2-1_i386.deb ... Unpacking libxss1:i386 (1:1.2.2-1) ... Selecting previously unselected package libxtst6:i386. Preparing to unpack .../libxtst6_2%3a1.2.2-1_i386.deb ... Unpacking libxtst6:i386 (2:1.2.2-1) ... Selecting previously unselected package libxxf86vm1:i386. Preparing to unpack .../libxxf86vm1_1%3a1.1.4-1_i386.deb ... Unpacking libxxf86vm1:i386 (1:1.1.4-1) ... Selecting previously unselected package libzzip-0-13:i386. Preparing to unpack .../libzzip-0-13_0.13.62-3_i386.deb ... Unpacking libzzip-0-13:i386 (0.13.62-3) ... Selecting previously unselected package java-common. Preparing to unpack .../java-common_0.56ubuntu2_all.deb ... Unpacking java-common (0.56ubuntu2) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../default-jre-headless_2%3a1.8-56ubuntu2_i386.deb ... Unpacking default-jre-headless (2:1.8-56ubuntu2) ... Selecting previously unselected package libnspr4:i386. Preparing to unpack .../libnspr4_2%3a4.11-1ubuntu1_i386.deb ... Unpacking libnspr4:i386 (2:4.11-1ubuntu1) ... Selecting previously unselected package libnss3-nssdb. Preparing to unpack .../libnss3-nssdb_2%3a3.21-1ubuntu4_all.deb ... Unpacking libnss3-nssdb (2:3.21-1ubuntu4) ... Selecting previously unselected package libnss3:i386. 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Setting up fonts-dejavu-core (2.35-1) ... Setting up fonts-freefont-ttf (20120503-4) ... Setting up ucf (3.0036) ... Setting up fontconfig-config (2.11.94-0ubuntu1) ... Setting up libexpat1:i386 (2.1.1-1) ... Setting up libfreetype6:i386 (2.6.3-3ubuntu1) ... Setting up libfontconfig1:i386 (2.11.94-0ubuntu1) ... Setting up fontconfig (2.11.94-0ubuntu1) ... Regenerating fonts cache... done. Setting up fonts-lato (2.0-1) ... Setting up libasyncns0:i386 (0.8-5build1) ... Setting up x11-common (1:7.7+13ubuntu3) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libice6:i386 (2:1.0.9-1) ... Setting up libjpeg-turbo8:i386 (1.4.2-0ubuntu3) ... Setting up liblcms2-2:i386 (2.6-3ubuntu2) ... Setting up liblzo2-2:i386 (2.08-1.2) ... Setting up libogg0:i386 (1.3.2-1) ... Setting up libpcrecpp0v5:i386 (2:8.38-3.1) ... 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Setting up libdrm-radeon1:i386 (2.4.67-1) ... Setting up libllvm3.8:i386 (1:3.8-2ubuntu3) ... Setting up libgl1-mesa-dri:i386 (11.2.1-1ubuntu1) ... Setting up libgl1-mesa-glx:i386 (11.2.1-1ubuntu1) ... update-alternatives: using /usr/lib/i386-linux-gnu/mesa/ld.so.conf to provide /etc/ld.so.conf.d/i386-linux-gnu_GL.conf (i386-linux-gnu_gl_conf) in auto mode Setting up libasound2-data (1.1.0-1) ... Setting up libasound2:i386 (1.1.0-1) ... Setting up libgif7:i386 (5.1.4-0.1) ... Setting up libjson-c3:i386 (0.12-3) ... Setting up libflac8:i386 (1.3.1-4) ... Setting up libvorbis0a:i386 (1.3.5-3) ... Setting up libvorbisenc2:i386 (1.3.5-3) ... Setting up libsndfile1:i386 (1.0.25-10) ... Setting up libpulse0:i386 (1:8.0-2ubuntu1) ... Setting up fonts-cabin (1.5-2) ... Setting up fonts-comfortaa (2.003-1) ... Setting up fonts-crosextra-caladea (20130214-1) ... Setting up fonts-crosextra-carlito (20130920-1) ... Setting up fonts-dejavu-extra (2.35-1) ... Setting up fonts-ebgaramond (0.015+git20130628-3) ... Setting up fonts-ebgaramond-extra (0.015+git20130628-3) ... Setting up fonts-font-awesome (4.6.1~dfsg-1) ... Setting up fonts-freefont-otf (20120503-4) ... Setting up fonts-gfs-artemisia (1.1-5) ... Setting up fonts-gfs-complutum (1.1-6) ... Setting up fonts-gfs-didot (1.1-6) ... Setting up fonts-gfs-neohellenic (1.1-6) ... Setting up fonts-gfs-olga (1.1-5) ... Setting up fonts-gfs-solomos (1.1-5) ... Setting up fonts-junicode (0.7.8-2) ... Setting up fonts-linuxlibertine (5.3.0-2) ... Setting up fonts-lobster (2.0-2) ... Setting up fonts-lobstertwo (2.0-2) ... Setting up fonts-oflb-asana-math (000.907-6) ... Setting up fonts-roboto-hinted (2:0~20160106-1) ... Setting up fonts-sil-gentium (20081126:1.03-1) ... Setting up fonts-sil-gentium-basic (1.1-7) ... Setting up fonts-sil-gentiumplus (5.000-1) ... Setting up libgfortran3:i386 (6.1.1-0ubuntu12) ... Setting up libgfortran-5-dev:i386 (5.3.1-16ubuntu3) ... Setting up gfortran-5 (5.3.1-16ubuntu3) ... Setting up gfortran (4:5.3.1-1ubuntu1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up gir1.2-freedesktop:i386 (1.46.0-3ubuntu1) ... Setting up libpangoxft-1.0-0:i386 (1.40.1-1) ... Setting up gir1.2-pango-1.0:i386 (1.40.1-1) ... Setting up icu-devtools (57.1-1) ... Setting up libblas-common (3.6.0-2ubuntu2) ... Setting up libblas3 (3.6.0-2ubuntu2) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up libblas-dev (3.6.0-2ubuntu2) ... update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode Setting up libbz2-dev:i386 (1.0.6-8build1) ... Setting up libcairo-gobject2:i386 (1.14.6-1build1) ... Setting up libcairo-script-interpreter2:i386 (1.14.6-1build1) ... Setting up libexpat1-dev:i386 (2.1.1-1) ... Setting up zlib1g-dev:i386 (1:1.2.8.dfsg-2ubuntu5) ... Setting up libpng-dev:i386 (1.6.21-4) ... Setting up libfreetype6-dev:i386 (2.6.3-3ubuntu1) ... Setting up pkg-config (0.29.1-0ubuntu1) ... Setting up libfontconfig1-dev:i386 (2.11.94-0ubuntu1) ... Setting up xorg-sgml-doctools (1:1.11-1) ... Setting up x11proto-core-dev (7.0.28-2ubuntu1) ... Setting up libxau-dev:i386 (1:1.0.8-1) ... Setting up libxdmcp-dev:i386 (1:1.1.2-1.1) ... Setting up x11proto-input-dev (2.3.1-1) ... Setting up x11proto-kb-dev (1.0.7-0ubuntu1) ... Setting up xtrans-dev (1.3.5-1) ... Setting up libpthread-stubs0-dev:i386 (0.3-4) ... Setting up libxcb1-dev:i386 (1.11.1-1ubuntu1) ... Setting up libx11-dev:i386 (2:1.6.3-1ubuntu2) ... Setting up x11proto-render-dev (2:0.11.1-2) ... Setting up libxrender-dev:i386 (1:0.9.9-0ubuntu1) ... Setting up x11proto-xext-dev (7.3.0-1) ... Setting up libxext-dev:i386 (2:1.3.3-1) ... Setting up libice-dev:i386 (2:1.0.9-1) ... Setting up libsm-dev:i386 (2:1.2.2-1) ... Setting up libpixman-1-dev (0.33.6-1) ... Setting up libxcb-render0-dev:i386 (1.11.1-1ubuntu1) ... Setting up libxcb-shm0-dev:i386 (1.11.1-1ubuntu1) ... Setting up libglib2.0-bin (2.48.0-1ubuntu4) ... Setting up libpcre16-3:i386 (2:8.38-3.1) ... Setting up libpcre32-3:i386 (2:8.38-3.1) ... Setting up libpcre3-dev:i386 (2:8.38-3.1) ... Setting up libglib2.0-dev (2.48.0-1ubuntu4) ... Setting up libcairo2-dev (1.14.6-1build1) ... Setting up libcupsfilters1:i386 (1.8.3-2ubuntu4) ... Setting up libcupsimage2:i386 (2.1.3-5) ... Setting up libcurl3:i386 (7.47.0-1ubuntu2) ... Setting up libcurl4-openssl-dev:i386 (7.47.0-1ubuntu2) ... Setting up libgraphite2-dev (1.3.6-1ubuntu1) ... Setting up libijs-0.35:i386 (0.35-12) ... Setting up libjbig2dec0 (0.12+20150918-1build1) ... Setting up libpaper1:i386 (1.1.24+nmu4ubuntu1) ... Creating config file /etc/papersize with new version Setting up libgs9-common (9.18~dfsg~0-0ubuntu5) ... update-alternatives: using /usr/share/ghostscript/9.18 to provide /usr/share/ghostscript/current (ghostscript-current) in auto mode Setting up libgs9:i386 (9.18~dfsg~0-0ubuntu5) ... Setting up libharfbuzz-icu0:i386 (1.2.6-2) ... Setting up libharfbuzz-gobject0:i386 (1.2.6-2) ... Setting up libicu-dev (57.1-1) ... Setting up libharfbuzz-dev:i386 (1.2.6-2) ... Setting up libjpeg-turbo8-dev:i386 (1.4.2-0ubuntu3) ... Setting up libjpeg8-dev:i386 (8c-2ubuntu8) ... Setting up libjpeg-dev:i386 (8c-2ubuntu8) ... Setting up libkpathsea6:i386 (2015.20160222.37495-1build1) ... Setting up liblapack3 (3.6.0-2ubuntu2) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up liblapack-dev (3.6.0-2ubuntu2) ... update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode Setting up libtinfo-dev:i386 (6.0+20160213-1ubuntu1) ... Setting up libncurses5-dev:i386 (6.0+20160213-1ubuntu1) ... Setting up libxft-dev (2.3.2-1) ... Setting up libpango1.0-dev (1.40.1-1) ... Setting up libpaper-utils (1.1.24+nmu4ubuntu1) ... Setting up libpoppler58:i386 (0.41.0-0ubuntu2) ... Setting up libpotrace0 (1.13-2) ... Setting up libptexenc1:i386 (2015.20160222.37495-1build1) ... Setting up libreadline6-dev:i386 (6.3-8ubuntu2) ... Setting up libreadline-dev:i386 (6.3-8ubuntu2) ... Setting up libsynctex1:i386 (2015.20160222.37495-1build1) ... Setting up libtcl8.6:i386 (8.6.5+dfsg-2) ... Setting up libtexlua52:i386 (2015.20160222.37495-1build1) ... Setting up libtexluajit2:i386 (2015.20160222.37495-1build1) ... Setting up libtext-unidecode-perl (1.27-1) ... Setting up libjbig-dev:i386 (2.1-3.1) ... Setting up liblzma-dev:i386 (5.1.1alpha+20120614-2ubuntu2) ... Setting up libtiffxx5:i386 (4.0.6-1) ... Setting up libtiff5-dev:i386 (4.0.6-1) ... Setting up libtk8.6:i386 (8.6.5-1) ... Setting up libxt6:i386 (1:1.1.5-0ubuntu1) ... Setting up libxmu6:i386 (2:1.1.2-2) ... Setting up libxaw7:i386 (2:1.0.13-1) ... Setting up libxkbfile1:i386 (1:1.0.9-0ubuntu1) ... Setting up libxml-namespacesupport-perl (1.11-1) ... Setting up libxml-sax-base-perl (1.07-1) ... Setting up libxml-sax-perl (0.99+dfsg-2ubuntu1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxml-libxml-perl (2.0123+dfsg-1build1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up x11proto-scrnsaver-dev (1.2.2-1) ... Setting up libxss-dev:i386 (1:1.2.2-1) ... Setting up libxt-dev:i386 (1:1.1.5-0ubuntu1) ... Setting up mpack (1.6-8) ... Setting up tex-common (6.05) ... update-language: texlive-base not installed and configured, doing nothing! Setting up preview-latex-style (11.88-1.1ubuntu1) ... Setting up t1utils (1.39-2) ... Setting up tcl8.6 (8.6.5+dfsg-2) ... Setting up tcl8.6-dev:i386 (8.6.5+dfsg-2) ... Setting up texinfo (6.1.0.dfsg.1-6) ... Running mktexlsr. This may take some time. ... done. Setting up texlive-binaries (2015.20160222.37495-1build1) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up xdg-utils (1.1.1-1ubuntu1) ... Setting up fonts-stix (1.1.1-4) ... Setting up ttf-adf-gillius (0.20090423-2) ... Setting up ttf-adf-universalis (0.20090423-2) ... Setting up ttf-adf-accanthis (0.20090423-2) ... Setting up tk8.6 (8.6.5-1) ... Setting up tk8.6-dev:i386 (8.6.5-1) ... Setting up x11-xkb-utils (7.7+2) ... Setting up xfonts-encodings (1:1.0.4-2) ... Setting up xfonts-utils (1:7.7+3) ... Setting up xfonts-base (1:1.0.4+nmu1) ... Setting up xserver-common (2:1.18.3-1ubuntu3) ... Setting up xvfb (2:1.18.3-1ubuntu3) ... Processing triggers for tex-common (6.05) ... update-language: texlive-base not installed and configured, doing nothing! texlive-base is not ready, skipping fmtutil --all call Setting up texlive-base (2015.20160320-1) ... /usr/bin/tl-paper: setting paper size for dvips to a4. /usr/bin/tl-paper: setting paper size for dvipdfmx to a4. /usr/bin/tl-paper: setting paper size for xdvi to a4. /usr/bin/tl-paper: setting paper size for pdftex to a4. Processing triggers for tex-common (6.05) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Setting up texlive-fonts-extra (2015.20160320-1) ... Setting up texlive-fonts-recommended (2015.20160320-1) ... Setting up texlive-generic-recommended (2015.20160320-1) ... Setting up texlive-latex-base (2015.20160320-1) ... Processing triggers for tex-common (6.05) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Setting up texlive-latex-recommended (2015.20160320-1) ... Setting up texlive-pictures (2015.20160320-1) ... Setting up texlive-extra-utils (2015.20160320-1) ... Processing triggers for tex-common (6.05) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Setting up texlive-latex-extra (2015.20160320-1) ... Processing triggers for tex-common (6.05) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Setting up libnss3-nssdb (2:3.21-1ubuntu4) ... Setting up dh-autoreconf (12) ... Setting up libnss3:i386 (2:3.21-1ubuntu4) ... Setting up openjdk-8-jre-headless:i386 (8u91-b14-2ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode OpenJDK Server VM warning: ignoring option PermSize=128m; support was removed in 8.0 Setting up ca-certificates-java (20160321) ... Adding debian:DigiCert_Global_Root_G2.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:NetLock_Business_=Class_B=_Root.pem Adding debian:Sonera_Class_1_Root_CA.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:ComSign_CA.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:GeoTrust_Global_CA_2.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Certigna.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:RSA_Security_2048_v3.pem Adding debian:StartCom_Certification_Authority_G2.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:EC-ACC.pem Adding debian:ApplicationCA_-_Japanese_Government.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:Camerfirma_Chambers_of_Commerce_Root.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:S-TRUST_Authentication_and_Encryption_Root_CA_2005_PN.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Certification_Authority_of_WoSign_G2.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:WellsSecure_Public_Root_Certificate_Authority.pem Adding debian:Juur-SK.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:Camerfirma_Global_Chambersign_Root.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G2.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:StartCom_Certification_Authority.pem Adding debian:AddTrust_External_Root.pem Adding debian:NetLock_Notary_=Class_A=_Root.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:EBG_Elektronik_Sertifika_Hizmet_Sağlayıcısı.pem Adding debian:AffirmTrust_Premium.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:Swisscom_Root_CA_2.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:China_Internet_Network_Information_Center_EV_Certificates_Root.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:Equifax_Secure_Global_eBusiness_CA.pem Adding debian:NetLock_Express_=Class_C=_Root.pem Adding debian:WoSign_China.pem Adding debian:AddTrust_Low-Value_Services_Root.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:Security_Communication_EV_RootCA1.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:AffirmTrust_Networking.pem Adding debian:Taiwan_GRCA.pem Adding debian:TC_TrustCenter_Class_3_CA_II.pem Adding debian:ACEDICOM_Root.pem Adding debian:AddTrust_Qualified_Certificates_Root.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:CNNIC_ROOT.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:PSCProcert.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:ACCVRAIZ1.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G3.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:Visa_eCommerce_Root.pem Adding debian:TÜBİTAK_UEKAE_Kök_Sertifika_Hizmet_Sağlayıcısı_-_Sürüm_3.pem Adding debian:UTN_USERFirst_Hardware_Root_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G2.pem Adding debian:AC_Raíz_Certicámara_S.A..pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:NetLock_Qualified_=Class_QA=_Root.pem Adding debian:Certinomis_-_Root_CA.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:DST_ACES_CA_X6.pem Adding debian:Secure_Global_CA.pem Adding debian:S-TRUST_Universal_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G2.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2007.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:CA_Disig_Root_R1.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G3.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:Root_CA_Generalitat_Valenciana.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:Comodo_Trusted_Services_root.pem Adding debian:Certum_Root_CA.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority.pem Adding debian:IGC_A.pem Adding debian:SwissSign_Platinum_CA_-_G2.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:StartCom_Certification_Authority_2.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:Certinomis_-_Autorité_Racine.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H6.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:CA_WoSign_ECC_Root.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:UTN_USERFirst_Email_Root_CA.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:Comodo_Secure_Services_root.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:Equifax_Secure_eBusiness_CA_1.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H5.pem Adding debian:Equifax_Secure_CA.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_2.pem Adding debian:CA_Disig.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:SecureTrust_CA.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:Swisscom_Root_EV_CA_2.pem Adding debian:Buypass_Class_2_CA_1.pem Adding debian:AddTrust_Public_Services_Root.pem Adding debian:Staat_der_Nederlanden_Root_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:DST_Root_CA_X3.pem Adding debian:Microsec_e-Szigno_Root_CA.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:Swisscom_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:WoSign.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:QuoVadis_Root_CA.pem done. Setting up default-jre-headless (2:1.8-56ubuntu2) ... Setting up debhelper (9.20160403ubuntu1) ... Setting up openjdk-8-jre:i386 (8u91-b14-2ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/jre/bin/policytool to provide /usr/bin/policytool (policytool) in auto mode Setting up default-jre (2:1.8-56ubuntu2) ... Setting up openjdk-8-jdk-headless:i386 (8u91-b14-2ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/idlj to provide /usr/bin/idlj (idlj) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/wsimport to provide /usr/bin/wsimport (wsimport) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jsadebugd to provide /usr/bin/jsadebugd (jsadebugd) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/native2ascii to provide /usr/bin/native2ascii (native2ascii) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/javah to provide /usr/bin/javah (javah) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/extcheck to provide /usr/bin/extcheck (extcheck) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/schemagen to provide /usr/bin/schemagen (schemagen) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/xjc to provide /usr/bin/xjc (xjc) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jhat to provide /usr/bin/jhat (jhat) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/wsgen to provide /usr/bin/wsgen (wsgen) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode Setting up default-jdk-headless (2:1.8-56ubuntu2) ... Setting up openjdk-8-jdk:i386 (8u91-b14-2ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/appletviewer to provide /usr/bin/appletviewer (appletviewer) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-i386/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up default-jdk (2:1.8-56ubuntu2) ... Setting up sbuild-build-depends-r-base-dummy (0.invalid.0) ... Setting up dh-strip-nondeterminism (0.016-1) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Processing triggers for systemd (229-5ubuntu1) ... Processing triggers for ca-certificates (20160104ubuntu1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.13.0-85-generic amd64 (i686) Toolchain package versions: binutils_2.26-8ubuntu3 dpkg-dev_1.18.4ubuntu2 g++-5_5.3.1-16ubuntu3 gcc-5_5.3.1-16ubuntu3 libc6-dev_2.23-0ubuntu3 libstdc++-5-dev_5.3.1-16ubuntu3 libstdc++6_6.1.1-0ubuntu12 linux-libc-dev_4.4.0-22.38 Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.2.11 apt-transport-https_1.2.11 autoconf_2.69-10 automake_1:1.15-4ubuntu1 autopoint_0.19.7-2ubuntu3 autotools-dev_20160430.1 base-files_9.6ubuntu1 base-passwd_3.5.39 bash_4.3-14ubuntu2 bash-completion_1:2.1-4.2ubuntu2 binutils_2.26-8ubuntu3 bison_2:3.0.4.dfsg-1 bsdmainutils_9.0.6ubuntu3 bsdutils_1:2.27.1-6ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8build1 ca-certificates_20160104ubuntu1 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readline-common_6.3-8ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-base-dummy_0.invalid.0 sed_4.2.2-7 sensible-utils_0.0.9 shared-mime-info_1.6-1 systemd_229-5ubuntu1 systemd-sysv_229-5ubuntu1 sysv-rc_2.88dsf-59.3ubuntu5 sysvinit-utils_2.88dsf-59.3ubuntu5 t1utils_1.39-2 tar_1.28-2.2 tcl8.6_8.6.5+dfsg-2 tcl8.6-dev_8.6.5+dfsg-2 tex-common_6.05 texinfo_6.1.0.dfsg.1-6 texlive-base_2015.20160320-1 texlive-binaries_2015.20160222.37495-1build1 texlive-extra-utils_2015.20160320-1 texlive-fonts-extra_2015.20160320-1 texlive-fonts-recommended_2015.20160320-1 texlive-generic-recommended_2015.20160320-1 texlive-latex-base_2015.20160320-1 texlive-latex-extra_2015.20160320-1 texlive-latex-recommended_2015.20160320-1 texlive-pictures_2015.20160320-1 tk8.6_8.6.5-1 tk8.6-dev_8.6.5-1 ttf-adf-accanthis_0.20090423-2 ttf-adf-gillius_0.20090423-2 ttf-adf-universalis_0.20090423-2 tzdata_2016d-2 ubuntu-keyring_2012.05.19 ucf_3.0036 util-linux_2.27.1-6ubuntu3 x11-common_1:7.7+13ubuntu3 x11-xkb-utils_7.7+2 x11proto-core-dev_7.0.28-2ubuntu1 x11proto-input-dev_2.3.1-1 x11proto-kb-dev_1.0.7-0ubuntu1 x11proto-render-dev_2:0.11.1-2 x11proto-scrnsaver-dev_1.2.2-1 x11proto-xext-dev_7.3.0-1 xauth_1:1.0.9-1ubuntu2 xdg-utils_1.1.1-1ubuntu1 xfonts-base_1:1.0.4+nmu1 xfonts-encodings_1:1.0.4-2 xfonts-utils_1:7.7+3 xkb-data_2.16-1ubuntu1 xorg-sgml-doctools_1:1.11-1 xserver-common_2:1.18.3-1ubuntu3 xtrans-dev_1.3.5-1 xvfb_2:1.18.3-1ubuntu3 xz-utils_5.1.1alpha+20120614-2ubuntu2 zlib1g_1:1.2.8.dfsg-2ubuntu5 zlib1g-dev_1:1.2.8.dfsg-2ubuntu5 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: Signature made Tue May 3 11:24:15 2016 UTC using RSA key ID AB99A21A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./r-base_3.3.0-1.dsc dpkg-source: info: extracting r-base in r-base-3.3.0 dpkg-source: info: unpacking r-base_3.3.0.orig.tar.gz dpkg-source: info: applying r-base_3.3.0-1.diff.gz Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/«PKGBUILDDIR» SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«PKGBUILDDIR»' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ───────────────── dpkg-buildpackage: source package r-base dpkg-buildpackage: source version 3.3.0-1 dpkg-buildpackage: source distribution unstable dpkg-source --before-build r-base-3.3.0 dpkg-buildpackage: host architecture i386 fakeroot debian/rules clean *** clean *** dh_testdir dh_testroot rm -f configure-stamp \ build-stamp build-indep-stamp build-arch-stamp \ make-stamp make-arch-stamp make-indep-stamp \ install-indep-stamp install-arch-stamp \ check-stamp [ ! -f Makefile ] || /usr/bin/make distclean rm -f `find . -name "*~"` rm -rf debian/tmp debian/files* core debian/substvars rm -f doc/html/function.html doc/html/packages.html rm -f modules/*.so src/unix/Rscript dh_clean debian/rules build-arch *** configure *** #automake #autoconf dh_testdir R_TEXI2DVICMD=emulation \ R_PAPERSIZE=letter \ R_BROWSER=xdg-open \ R_GZIPCMD="/bin/gzip -n" \ PAGER=/usr/bin/pager \ PERL=/usr/bin/perl \ JAVA_HOME=/usr/lib/jvm/default-java \ R_UNZIPCMD=/usr/bin/unzip \ R_ZIPCMD=/usr/bin/zip \ R_PRINTCMD=/usr/bin/lpr \ LIBnn=lib \ AWK=/usr/bin/awk \ CC="gcc -std=gnu99" \ CXX=g++ \ F77=gfortran \ FC=gfortran \ CFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \ CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \ FFLAGS="-g -O2 -fstack-protector-strong" \ FCFLAGS="-g -O2 -fstack-protector-strong" \ CPPFLAGS= \ LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro" \ FLIBS= \ rsharedir=/usr/share/R/share \ rincludedir=/usr/share/R/include \ rdocdir=/usr/share/R/doc \ ./configure --prefix=/usr \ --with-cairo \ --with-jpeglib \ --with-readline \ --with-tcltk \ --with-system-bzlib \ --with-system-pcre \ --with-system-zlib \ --mandir=/usr/share/man \ --infodir=/usr/share/info \ --datadir=/usr/share/R/share \ --includedir=/usr/share/R/include \ --with-blas \ --with-lapack \ --enable-R-profiling \ --enable-R-shlib \ --enable-memory-profiling \ --without-recommended-packages \ --build i686-linux-gnu configure: WARNING: unrecognized options: --with-system-bzlib, --with-system-pcre, --with-system-zlib checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu loading site script './config.site' loading build-specific script './config.site' checking for pwd... /bin/pwd 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(cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for cos in -lm... yes checking for sin in -lm... yes checking for dlopen in -ldl... yes checking readline/history.h usability... yes checking readline/history.h presence... yes checking for readline/history.h... yes checking readline/readline.h usability... yes checking readline/readline.h presence... yes checking for readline/readline.h... yes checking for rl_callback_read_char in -lreadline... yes checking for history_truncate_file... yes checking whether rl_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 arpa/inet.h usability... yes checking arpa/inet.h presence... yes checking for arpa/inet.h... yes checking dl.h usability... no checking dl.h presence... no checking for dl.h... no checking for dlfcn.h... 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(cached) yes checking utime.h usability... yes checking utime.h presence... yes checking for utime.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... 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(cached) none needed checking for inline... inline checking size of int... 4 checking size of long... 4 checking size of long long... 8 checking size of double... 8 checking size of size_t... 4 checking size of long double... 12 checking whether we can compute C Make dependencies... yes, using $(CC) -MM checking whether gcc -std=gnu99 supports -c -o FILE.lo... yes checking for gcc -std=gnu99 option to support OpenMP... -fopenmp checking how to get verbose linking output from gfortran... -v checking for Fortran 77 libraries of gfortran... -L/usr/lib/gcc/i686-linux-gnu/5 -L/usr/lib/gcc/i686-linux-gnu/5/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/5/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/5/../../.. -lgfortran -lm -lquadmath checking how to get verbose linking output from gcc -std=gnu99... -v checking for C libraries of gcc -std=gnu99... -L/usr/lib/gcc/i686-linux-gnu/5 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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 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 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 __setfpucw... no checking for working calloc... yes checking for working isfinite... yes checking for working log1p... yes checking whether ftell works correctly on files opened for append... yes checking for working sigaction... yes checking whether mktime sets errno... no checking whether mktime works correctly outside 1902-2037... no checking complex.h usability... yes checking complex.h presence... yes checking for complex.h... yes checking for double complex... yes checking whether C99 double complex is supported... yes checking whether cabs exists and is declared... yes checking whether carg exists and is declared... yes checking whether cexp exists and is declared... yes checking whether clog exists and is declared... yes checking whether csqrt exists and is declared... yes checking whether cpow exists and is declared... yes checking whether ccos exists and is declared... yes checking whether csin exists and is declared... yes checking whether ctan exists and is declared... yes checking whether cacos exists and is declared... yes checking whether casin exists and is declared... yes checking whether catan exists and is declared... yes checking whether ccosh exists and is declared... yes checking whether csinh exists and is declared... yes checking whether ctanh exists and is declared... yes checking whether 'struct tm' includes tm_zone... yes checking whether 'struct tm' includes tm_gmtoff... yes checking for dgemm_... no checking for ATL_xerbla in -latlas... no checking for dgemm_ in -lblas... yes checking for dgemm_ in -ldgemm... no checking for dgemm_ in -lblas... 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(cached) yes checking whether the gfortran linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for Fortran flag to compile .f90 files... none checking for Fortran flag to compile .f95 files... none checking for gfortran option to support OpenMP... -fopenmp 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 ranlib... (cached) 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 gcc -std=gnu99... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for shared library run path origin... done checking whether imported symbols can be declared weak... yes checking for multithread API to use... none checking argz.h usability... yes checking argz.h presence... yes checking for argz.h... yes checking for inttypes.h... (cached) yes checking for limits.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... (cached) yes checking for getcwd... yes checking for getegid... yes checking for geteuid... yes checking for getgid... yes checking for getuid... yes checking for mempcpy... (cached) yes checking for munmap... yes checking for stpcpy... yes checking for strcasecmp... yes checking for strdup... (cached) yes checking for strtoul... yes checking for tsearch... yes checking for argz_count... yes checking for argz_stringify... yes checking for argz_next... yes checking for __fsetlocking... yes checking whether feof_unlocked is declared... yes checking whether fgets_unlocked is declared... yes checking for iconv... (cached) yes checking for iconv declaration... (cached) extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft); checking for NL_LOCALE_NAME macro... yes checking for bison... bison checking version of bison... 3.0.4, 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 using as R_SHELL for scripts ... /bin/bash configure: creating ./config.status config.status: creating Makeconf config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/html/Makefile config.status: creating doc/manual/Makefile config.status: creating etc/Makefile config.status: creating etc/Makeconf config.status: creating etc/Renviron config.status: creating etc/javaconf config.status: creating etc/ldpaths config.status: creating m4/Makefile config.status: creating po/Makefile config.status: creating share/Makefile config.status: creating src/Makefile config.status: creating src/appl/Makefile config.status: creating src/extra/Makefile config.status: creating src/extra/blas/Makefile config.status: creating src/extra/intl/Makefile config.status: creating src/extra/tre/Makefile config.status: creating src/extra/tzone/Makefile config.status: creating src/extra/xdr/Makefile config.status: creating src/include/Makefile config.status: creating src/include/Rmath.h0 config.status: creating src/include/R_ext/Makefile config.status: creating src/library/Recommended/Makefile config.status: creating src/library/Makefile config.status: creating src/library/base/DESCRIPTION config.status: creating src/library/base/Makefile config.status: creating src/library/compiler/DESCRIPTION config.status: creating src/library/compiler/Makefile config.status: creating src/library/datasets/DESCRIPTION config.status: creating src/library/datasets/Makefile config.status: creating src/library/graphics/DESCRIPTION config.status: creating src/library/graphics/Makefile config.status: creating src/library/graphics/src/Makefile config.status: creating src/library/grDevices/DESCRIPTION config.status: creating src/library/grDevices/Makefile config.status: creating src/library/grDevices/src/Makefile config.status: creating src/library/grDevices/src/cairo/Makefile config.status: creating src/library/grid/DESCRIPTION config.status: creating src/library/grid/Makefile config.status: creating src/library/grid/src/Makefile config.status: creating src/library/methods/DESCRIPTION config.status: creating src/library/methods/Makefile config.status: creating src/library/methods/src/Makefile config.status: creating src/library/parallel/DESCRIPTION config.status: creating src/library/parallel/Makefile config.status: creating src/library/parallel/src/Makefile config.status: creating src/library/profile/Makefile config.status: creating src/library/stats/DESCRIPTION config.status: creating src/library/stats/Makefile config.status: creating src/library/stats/src/Makefile config.status: creating src/library/stats4/DESCRIPTION config.status: creating src/library/stats4/Makefile config.status: creating src/library/splines/DESCRIPTION config.status: creating src/library/splines/Makefile config.status: creating src/library/splines/src/Makefile config.status: creating src/library/tcltk/DESCRIPTION config.status: creating src/library/tcltk/Makefile config.status: creating src/library/tcltk/src/Makefile config.status: creating src/library/tools/DESCRIPTION config.status: creating src/library/tools/Makefile config.status: creating src/library/tools/src/Makefile config.status: creating src/library/translations/DESCRIPTION config.status: creating src/library/translations/Makefile config.status: creating src/library/utils/DESCRIPTION config.status: creating src/library/utils/Makefile config.status: creating src/library/utils/src/Makefile config.status: creating src/main/Makefile config.status: creating src/modules/Makefile config.status: creating src/modules/X11/Makefile config.status: creating src/modules/internet/Makefile config.status: creating src/modules/lapack/Makefile config.status: creating src/nmath/Makefile config.status: creating src/nmath/standalone/Makefile config.status: creating src/scripts/Makefile config.status: creating src/scripts/R.sh config.status: creating src/scripts/Rcmd config.status: creating src/scripts/f77_f2c config.status: creating src/scripts/javareconf config.status: creating src/scripts/mkinstalldirs config.status: creating src/scripts/pager config.status: creating src/scripts/rtags config.status: creating src/unix/Makefile config.status: creating tests/Makefile config.status: creating tests/Embedding/Makefile config.status: creating tests/Examples/Makefile config.status: creating tools/Makefile config.status: creating src/include/config.h config.status: executing libtool commands config.status: executing stamp-h commands configure: WARNING: unrecognized options: --with-system-bzlib, --with-system-pcre, --with-system-zlib R is now configured for i686-pc-linux-gnu Source directory: . Installation directory: /usr C compiler: gcc -std=gnu99 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g Fortran 77 compiler: gfortran -g -O2 -fstack-protector-strong C++ compiler: g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g C++11 compiler: g++ -std=c++11 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g Fortran 90/95 compiler: gfortran -g -O2 -fstack-protector-strong Obj-C compiler: Interfaces supported: X11, tcltk External libraries: readline, BLAS(generic), LAPACK(generic), curl Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU Options enabled: shared R library, R profiling, memory profiling Capabilities skipped: Options not enabled: shared BLAS Recommended packages: no touch configure-stamp *** make-arch *** /usr/bin/make CFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \ CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \ FFLAGS="-g -O2 -fstack-protector-strong" \ FCFLAGS="-g -O2 -fstack-protector-strong" \ CC="gcc -std=gnu99" \ CXX=g++ \ F77=gfortran \ LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro" \ PKG_BUILT_STAMP="""" \ R_GZIPCMD="/bin/gzip -n" \ R make[1]: Entering directory '/«PKGBUILDDIR»' make[2]: Entering directory '/«PKGBUILDDIR»/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/«PKGBUILDDIR»/m4' make[2]: Entering directory '/«PKGBUILDDIR»/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/«PKGBUILDDIR»/tools' make[2]: Entering directory '/«PKGBUILDDIR»/doc' make[3]: Entering directory '/«PKGBUILDDIR»/doc/html' make[3]: Leaving directory '/«PKGBUILDDIR»/doc/html' make[3]: Entering directory '/«PKGBUILDDIR»/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/«PKGBUILDDIR»/doc/manual' make[2]: Leaving directory '/«PKGBUILDDIR»/doc' make[2]: Entering directory '/«PKGBUILDDIR»/etc' make[2]: Leaving directory '/«PKGBUILDDIR»/etc' make[2]: Entering directory '/«PKGBUILDDIR»/share' make[2]: Leaving directory '/«PKGBUILDDIR»/share' make[2]: Entering directory '/«PKGBUILDDIR»/src' make[3]: Entering directory '/«PKGBUILDDIR»/src/scripts' creating src/scripts/R.fe make[4]: Entering directory '/«PKGBUILDDIR»/src/scripts' mkdir -p -- ../../bin make[4]: Leaving directory '/«PKGBUILDDIR»/src/scripts' make[3]: Leaving directory '/«PKGBUILDDIR»/src/scripts' make[3]: Entering directory '/«PKGBUILDDIR»/src/include' mkdir -p -- ../../include make[4]: Entering directory '/«PKGBUILDDIR»/src/include/R_ext' mkdir -p -- ../../../include/R_ext make[4]: Leaving directory '/«PKGBUILDDIR»/src/include/R_ext' make[3]: Leaving directory '/«PKGBUILDDIR»/src/include' make[3]: Entering directory '/«PKGBUILDDIR»/src/extra' make[4]: Entering directory '/«PKGBUILDDIR»/src/extra/tre' make[5]: Entering directory '/«PKGBUILDDIR»/src/extra/tre' making regcomp.d from regcomp.c making regerror.d from regerror.c making regexec.d from regexec.c making tre-ast.d from tre-ast.c making tre-compile.d from tre-compile.c making tre-match-approx.d from tre-match-approx.c making tre-match-backtrack.d from tre-match-backtrack.c making tre-match-parallel.d from tre-match-parallel.c making tre-mem.d from tre-mem.c making tre-parse.d from tre-parse.c making tre-stack.d from tre-stack.c making xmalloc.d from xmalloc.c make[5]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre' make[5]: Entering directory '/«PKGBUILDDIR»/src/extra/tre' gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c regcomp.c -o regcomp.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c regerror.c -o regerror.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c regexec.c -o regexec.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-ast.c -o tre-ast.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-compile.c -o tre-compile.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-mem.c -o tre-mem.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-parse.c -o tre-parse.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-stack.c -o tre-stack.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c xmalloc.c -o xmalloc.o 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[5]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre' make[4]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre' make[3]: Leaving directory '/«PKGBUILDDIR»/src/extra' make[3]: Entering directory '/«PKGBUILDDIR»/src/appl' making integrate.d from integrate.c making interv.d from interv.c making maxcol.d from maxcol.c making optim.d from optim.c making pretty.d from pretty.c making uncmin.d from uncmin.c make[4]: Entering directory '/«PKGBUILDDIR»/src/appl' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c integrate.c -o integrate.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c interv.c -o interv.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c maxcol.c -o maxcol.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c optim.c -o optim.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pretty.c -o pretty.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c uncmin.c -o uncmin.o gfortran -fopenmp -fpic -g -O2 -fstack-protector-strong -c dchdc.f -o dchdc.o gfortran -fopenmp -fpic -g -O2 -fstack-protector-strong -c dpbfa.f -o dpbfa.o gfortran -fopenmp -fpic -g -O2 -fstack-protector-strong -c dpbsl.f -o dpbsl.o gfortran -fopenmp -fpic -g -O2 -fstack-protector-strong -c dpoco.f -o dpoco.o gfortran -fopenmp -fpic -g -O2 -fstack-protector-strong -c dpodi.f -o dpodi.o gfortran -fopenmp -fpic -g -O2 -fstack-protector-strong -c dpofa.f -o dpofa.o gfortran -fopenmp -fpic -g -O2 -fstack-protector-strong -c dposl.f -o dposl.o gfortran -fopenmp -fpic -g -O2 -fstack-protector-strong -c dqrdc.f -o dqrdc.o gfortran -fopenmp -fpic -g -O2 -fstack-protector-strong -c dqrdc2.f -o dqrdc2.o gfortran -fopenmp -fpic -g -O2 -fstack-protector-strong -c dqrls.f -o dqrls.o gfortran -fopenmp -fpic -g -O2 -fstack-protector-strong -c dqrsl.f -o dqrsl.o gfortran -fopenmp -fpic -g -O2 -fstack-protector-strong -c dqrutl.f -o dqrutl.o gfortran -fopenmp -fpic -g -O2 -fstack-protector-strong -c dsvdc.f -o dsvdc.o gfortran -fopenmp -fpic -g -O2 -fstack-protector-strong -c dtrco.f -o dtrco.o gfortran -fopenmp -fpic -g -O2 -fstack-protector-strong -c dtrsl.f -o dtrsl.o 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[4]: Leaving directory '/«PKGBUILDDIR»/src/appl' make[3]: Leaving directory '/«PKGBUILDDIR»/src/appl' make[3]: Entering directory '/«PKGBUILDDIR»/src/nmath' making mlutils.d from mlutils.c making d1mach.d from d1mach.c making i1mach.d from i1mach.c making fmax2.d from fmax2.c making fmin2.d from fmin2.c making fprec.d from fprec.c making fround.d from fround.c making ftrunc.d from ftrunc.c making sign.d from sign.c making fsign.d from fsign.c making imax2.d from imax2.c making imin2.d from imin2.c making chebyshev.d from chebyshev.c making log1p.d from log1p.c making expm1.d from expm1.c making lgammacor.d from lgammacor.c making gammalims.d from gammalims.c making stirlerr.d from stirlerr.c making bd0.d from bd0.c making gamma.d from gamma.c making lgamma.d from lgamma.c making gamma_cody.d from gamma_cody.c making beta.d from beta.c making lbeta.d from lbeta.c making polygamma.d from polygamma.c making cospi.d from cospi.c making bessel_i.d from bessel_i.c making bessel_j.d from bessel_j.c making bessel_k.d from bessel_k.c making bessel_y.d from bessel_y.c making choose.d from choose.c making snorm.d from snorm.c making sexp.d from sexp.c making dgamma.d from dgamma.c making pgamma.d from pgamma.c making qgamma.d from qgamma.c making rgamma.d from rgamma.c making dbeta.d from dbeta.c making pbeta.d from pbeta.c making qbeta.d from qbeta.c making rbeta.d from rbeta.c making dunif.d from dunif.c making punif.d from punif.c making qunif.d from qunif.c making runif.d from runif.c making dnorm.d from dnorm.c making pnorm.d from pnorm.c making qnorm.d from qnorm.c making rnorm.d from rnorm.c making dlnorm.d from dlnorm.c making plnorm.d from plnorm.c making qlnorm.d from qlnorm.c making rlnorm.d from rlnorm.c making df.d from df.c making pf.d from pf.c making qf.d from qf.c making rf.d from rf.c making dnf.d from dnf.c making dt.d from dt.c making pt.d from pt.c making qt.d from qt.c making rt.d from rt.c making dnt.d from dnt.c making dchisq.d from dchisq.c making pchisq.d from pchisq.c making qchisq.d from qchisq.c making rchisq.d from rchisq.c making rnchisq.d from rnchisq.c making dbinom.d from dbinom.c making pbinom.d from pbinom.c making qbinom.d from qbinom.c making rbinom.d from rbinom.c making rmultinom.d from rmultinom.c making dcauchy.d from dcauchy.c making pcauchy.d from pcauchy.c making qcauchy.d from qcauchy.c making rcauchy.d from rcauchy.c making dexp.d from dexp.c making pexp.d from pexp.c making qexp.d from qexp.c making rexp.d from rexp.c making dgeom.d from dgeom.c making pgeom.d from pgeom.c making qgeom.d from qgeom.c making rgeom.d from rgeom.c making dhyper.d from dhyper.c making phyper.d from phyper.c making qhyper.d from qhyper.c making rhyper.d from rhyper.c making dnbinom.d from dnbinom.c making pnbinom.d from pnbinom.c making qnbinom.d from qnbinom.c making rnbinom.d from rnbinom.c making dpois.d from dpois.c making ppois.d from ppois.c making qpois.d from qpois.c making rpois.d from rpois.c making dweibull.d from dweibull.c making pweibull.d from pweibull.c making qweibull.d from qweibull.c making rweibull.d from rweibull.c making dlogis.d from dlogis.c making plogis.d from plogis.c making qlogis.d from qlogis.c making rlogis.d from rlogis.c making dnchisq.d from dnchisq.c making pnchisq.d from pnchisq.c making qnchisq.d from qnchisq.c making dnbeta.d from dnbeta.c making pnbeta.d from pnbeta.c making qnbeta.d from qnbeta.c making pnf.d from pnf.c making pnt.d from pnt.c making qnf.d from qnf.c making qnt.d from qnt.c making ptukey.d from ptukey.c making qtukey.d from qtukey.c making toms708.d from toms708.c making wilcox.d from wilcox.c making signrank.d from signrank.c make[4]: Entering directory '/«PKGBUILDDIR»/src/nmath' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mlutils.c -o mlutils.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c d1mach.c -o d1mach.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c i1mach.c -o i1mach.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fmax2.c -o fmax2.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fmin2.c -o fmin2.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fprec.c -o fprec.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fround.c -o fround.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ftrunc.c -o ftrunc.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sign.c -o sign.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fsign.c -o fsign.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c imax2.c -o imax2.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c imin2.c -o imin2.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chebyshev.c -o chebyshev.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c log1p.c -o log1p.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c expm1.c -o expm1.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lgammacor.c -o lgammacor.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gammalims.c -o gammalims.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stirlerr.c -o stirlerr.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bd0.c -o bd0.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gamma.c -o gamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lgamma.c -o lgamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gamma_cody.c -o gamma_cody.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c beta.c -o beta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lbeta.c -o lbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c polygamma.c -o polygamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cospi.c -o cospi.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bessel_i.c -o bessel_i.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bessel_j.c -o bessel_j.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bessel_k.c -o bessel_k.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bessel_y.c -o bessel_y.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c choose.c -o choose.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c snorm.c -o snorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sexp.c -o sexp.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dgamma.c -o dgamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pgamma.c -o pgamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qgamma.c -o qgamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rgamma.c -o rgamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dbeta.c -o dbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pbeta.c -o pbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qbeta.c -o qbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rbeta.c -o rbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dunif.c -o dunif.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c punif.c -o punif.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qunif.c -o qunif.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c runif.c -o runif.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnorm.c -o dnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnorm.c -o pnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnorm.c -o qnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rnorm.c -o rnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dlnorm.c -o dlnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plnorm.c -o plnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qlnorm.c -o qlnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rlnorm.c -o rlnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c df.c -o df.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pf.c -o pf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qf.c -o qf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rf.c -o rf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnf.c -o dnf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dt.c -o dt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pt.c -o pt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qt.c -o qt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rt.c -o rt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnt.c -o dnt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dchisq.c -o dchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pchisq.c -o pchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qchisq.c -o qchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rchisq.c -o rchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rnchisq.c -o rnchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dbinom.c -o dbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pbinom.c -o pbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qbinom.c -o qbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rbinom.c -o rbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rmultinom.c -o rmultinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dcauchy.c -o dcauchy.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pcauchy.c -o pcauchy.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qcauchy.c -o qcauchy.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rcauchy.c -o rcauchy.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dexp.c -o dexp.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pexp.c -o pexp.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qexp.c -o qexp.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rexp.c -o rexp.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dgeom.c -o dgeom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pgeom.c -o pgeom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qgeom.c -o qgeom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rgeom.c -o rgeom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dhyper.c -o dhyper.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c phyper.c -o phyper.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qhyper.c -o qhyper.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rhyper.c -o rhyper.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnbinom.c -o dnbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnbinom.c -o pnbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnbinom.c -o qnbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rnbinom.c -o rnbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dpois.c -o dpois.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ppois.c -o ppois.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qpois.c -o qpois.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rpois.c -o rpois.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dweibull.c -o dweibull.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pweibull.c -o pweibull.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qweibull.c -o qweibull.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rweibull.c -o rweibull.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dlogis.c -o dlogis.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plogis.c -o plogis.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qlogis.c -o qlogis.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rlogis.c -o rlogis.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnchisq.c -o dnchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnchisq.c -o pnchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnchisq.c -o qnchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnbeta.c -o dnbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnbeta.c -o pnbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnbeta.c -o qnbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnf.c -o pnf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnt.c -o pnt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnf.c -o qnf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnt.c -o qnt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ptukey.c -o ptukey.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qtukey.c -o qtukey.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c toms708.c -o toms708.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c wilcox.c -o wilcox.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c signrank.c -o signrank.o 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 expm1.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[4]: Leaving directory '/«PKGBUILDDIR»/src/nmath' make[3]: Leaving directory '/«PKGBUILDDIR»/src/nmath' make[3]: Entering directory '/«PKGBUILDDIR»/src/unix' config.status: creating src/unix/Makefile making Rembedded.d from Rembedded.c making dynload.d from dynload.c making system.d from system.c making sys-unix.d from sys-unix.c making sys-std.d from sys-std.c making X11.d from X11.c make[4]: Entering directory '/«PKGBUILDDIR»/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rembedded.c -o Rembedded.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dynload.c -o dynload.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c system.c -o system.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sys-unix.c -o sys-unix.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sys-std.c -o sys-std.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c X11.c -o X11.o ar -cr libunix.a Rembedded.o dynload.o system.o sys-unix.o sys-std.o X11.o ranlib libunix.a make[4]: Leaving directory '/«PKGBUILDDIR»/src/unix' make[4]: Entering directory '/«PKGBUILDDIR»/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/«PKGBUILDDIR»"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/«PKGBUILDDIR»/src/unix' make[3]: Leaving directory '/«PKGBUILDDIR»/src/unix' make[3]: Entering directory '/«PKGBUILDDIR»/src/main' config.status: creating src/main/Makefile making CommandLineArgs.d from CommandLineArgs.c making Rdynload.d from Rdynload.c making Renviron.d from Renviron.c making RNG.d from RNG.c making agrep.d from agrep.c making apply.d from apply.c making arithmetic.d from arithmetic.c making array.d from array.c making attrib.d from attrib.c making bind.d from bind.c making builtin.d from builtin.c making character.d from character.c making coerce.d from coerce.c making colors.d from colors.c making complex.d from complex.c making connections.d from connections.c making context.d from context.c making cum.d from cum.c making dcf.d from dcf.c making datetime.d from datetime.c making debug.d from debug.c making deparse.d from deparse.c making devices.d from devices.c making dotcode.d from dotcode.c making dounzip.d from dounzip.c making dstruct.d from dstruct.c making duplicate.d from duplicate.c making edit.d from edit.c making engine.d from engine.c making envir.d from envir.c making errors.d from errors.c making eval.d from eval.c making format.d from format.c making gevents.d from gevents.c making gram.d from gram.c making gram-ex.d from gram-ex.c making graphics.d from graphics.c making grep.d from grep.c making identical.d from identical.c making inlined.d from inlined.c making inspect.d from inspect.c making internet.d from internet.c making iosupport.d from iosupport.c making lapack.d from lapack.c making list.d from list.c making localecharset.d from localecharset.c making logic.d from logic.c making main.d from main.c making mapply.d from mapply.c making match.d from match.c making memory.d from memory.c making names.d from names.c making objects.d from objects.c making options.d from options.c making paste.d from paste.c making platform.d from platform.c making plot.d from plot.c making plot3d.d from plot3d.c making plotmath.d from plotmath.c making print.d from print.c making printarray.d from printarray.c making printvector.d from printvector.c making printutils.d from printutils.c making qsort.d from qsort.c making radixsort.d from radixsort.c making random.d from random.c making raw.d from raw.c making registration.d from registration.c making relop.d from relop.c making rlocale.d from rlocale.c making saveload.d from saveload.c making scan.d from scan.c making seq.d from seq.c making serialize.d from serialize.c making sort.d from sort.c making source.d from source.c making split.d from split.c making sprintf.d from sprintf.c making startup.d from startup.c making subassign.d from subassign.c making subscript.d from subscript.c making subset.d from subset.c making summary.d from summary.c making sysutils.d from sysutils.c making times.d from times.c making unique.d from unique.c making util.d from util.c making version.d from version.c making g_alab_her.d from g_alab_her.c making g_cntrlify.d from g_cntrlify.c making g_fontdb.d from g_fontdb.c making g_her_glyph.d from g_her_glyph.c making Rmain.d from Rmain.c making alloca.d from alloca.c making mkdtemp.d from mkdtemp.c making strdup.d from strdup.c making strncasecmp.d from strncasecmp.c make[4]: Entering directory '/«PKGBUILDDIR»/src/main' gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c CommandLineArgs.c -o CommandLineArgs.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rdynload.c -o Rdynload.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Renviron.c -o Renviron.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RNG.c -o RNG.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c agrep.c -o agrep.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c apply.c -o apply.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c arithmetic.c -o arithmetic.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c array.c -o array.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c attrib.c -o attrib.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bind.c -o bind.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c builtin.c -o builtin.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c character.c -o character.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c coerce.c -o coerce.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c colors.c -o colors.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c complex.c -o complex.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c connections.c -o connections.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c context.c -o context.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cum.c -o cum.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dcf.c -o dcf.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c datetime.c -o datetime.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c debug.c -o debug.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c deparse.c -o deparse.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devices.c -o devices.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dotcode.c -o dotcode.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dounzip.c -o dounzip.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dstruct.c -o dstruct.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c duplicate.c -o duplicate.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c edit.c -o edit.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c engine.c -o engine.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c envir.c -o envir.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c errors.c -o errors.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c eval.c -o eval.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c format.c -o format.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gevents.c -o gevents.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gram.c -o gram.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gram-ex.c -o gram-ex.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c graphics.c -o graphics.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c grep.c -o grep.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c identical.c -o identical.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c inlined.c -o inlined.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c inspect.c -o inspect.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c internet.c -o internet.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c iosupport.c -o iosupport.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lapack.c -o lapack.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c list.c -o list.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c localecharset.c -o localecharset.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c logic.c -o logic.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c main.c -o main.o main.c: In function ‘dummy_ii’: main.c:1656:12: warning: function returns address of local variable [-Wreturn-local-addr] return (uintptr_t) ⅈ ^ gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mapply.c -o mapply.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match.c -o match.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c memory.c -o memory.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c names.c -o names.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c objects.c -o objects.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c options.c -o options.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c paste.c -o paste.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c platform.c -o platform.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plot.c -o plot.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plot3d.c -o plot3d.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plotmath.c -o plotmath.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c print.c -o print.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c printarray.c -o printarray.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c printvector.c -o printvector.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c printutils.c -o printutils.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qsort.c -o qsort.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c radixsort.c -o radixsort.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c random.c -o random.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c raw.c -o raw.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c registration.c -o registration.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c relop.c -o relop.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rlocale.c -o rlocale.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c saveload.c -o saveload.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c scan.c -o scan.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c seq.c -o seq.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c serialize.c -o serialize.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sort.c -o sort.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c source.c -o source.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c split.c -o split.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sprintf.c -o sprintf.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c startup.c -o startup.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c subassign.c -o subassign.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c subscript.c -o subscript.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c subset.c -o subset.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c summary.c -o summary.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sysutils.c -o sysutils.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c times.c -o times.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unique.c -o unique.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c util.c -o util.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c version.c -o version.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c g_alab_her.c -o g_alab_her.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c g_cntrlify.c -o g_cntrlify.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c g_fontdb.c -o g_fontdb.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c g_her_glyph.c -o g_her_glyph.o gfortran -fopenmp -fpic -g -O2 -fstack-protector-strong -c xxxpr.f -o xxxpr.o gcc -std=gnu99 -shared -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.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 -lblas -lgfortran -lm -lquadmath -lreadline -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n make[5]: Entering directory '/«PKGBUILDDIR»/src/main' mkdir -p -- /«PKGBUILDDIR»/bin/exec mkdir -p -- /«PKGBUILDDIR»/lib make[5]: Leaving directory '/«PKGBUILDDIR»/src/main' make[4]: Leaving directory '/«PKGBUILDDIR»/src/main' make[4]: Entering directory '/«PKGBUILDDIR»/src/main' gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rmain.c -o Rmain.o gcc -std=gnu99 -Wl,--export-dynamic -fopenmp -L../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o R.bin Rmain.o -lR make[5]: Entering directory '/«PKGBUILDDIR»/src/main' make[5]: Leaving directory '/«PKGBUILDDIR»/src/main' make[4]: Leaving directory '/«PKGBUILDDIR»/src/main' make[3]: Leaving directory '/«PKGBUILDDIR»/src/main' make[3]: Entering directory '/«PKGBUILDDIR»/src/modules' make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/internet' making Rhttpd.d from Rhttpd.c making Rsock.d from Rsock.c making internet.d from internet.c making libcurl.d from libcurl.c making nanoftp.d from nanoftp.c making nanohttp.d from nanohttp.c making sock.d from sock.c making sockconn.d from sockconn.c make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/internet' gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c Rsock.c -o Rsock.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c internet.c -o internet.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c libcurl.c -o libcurl.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c nanoftp.c -o nanoftp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c nanohttp.c -o nanohttp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c sock.c -o sock.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c sockconn.c -o sockconn.o gcc -std=gnu99 -shared -L../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o internet.so Rhttpd.o Rsock.o internet.o libcurl.o nanoftp.o nanohttp.o sock.o sockconn.o -L/usr/lib/i386-linux-gnu -lcurl -lR make[6]: Entering directory '/«PKGBUILDDIR»/src/modules/internet' mkdir -p -- /«PKGBUILDDIR»/modules make[6]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet' make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet' make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet' make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack' making Lapack.d from Lapack.c make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack' gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Lapack.c -o Lapack.o gcc -std=gnu99 -shared -L../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o lapack.so Lapack.o -lR -llapack -lblas -lgfortran -lm -lquadmath make[6]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack' make[6]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack' make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack' make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack' make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/X11' making devX11.d from devX11.c making rotated.d from rotated.c making rbitmap.d from rbitmap.c make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/X11' gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/i386-linux-gnu -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devX11.c -o devX11.o gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/i386-linux-gnu -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rotated.c -o rotated.o gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/i386-linux-gnu -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rbitmap.c -o rbitmap.o gcc -std=gnu99 -shared -L../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o R_X11.so devX11.o rotated.o rbitmap.o -ltiff -ljpeg -lpng16 -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt -lR -lm gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/i386-linux-gnu -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dataentry.c -o dataentry.o gcc -std=gnu99 -shared -L../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o R_de.so dataentry.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt -lR -lm make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11' make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/X11' make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11' make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11' make[3]: Leaving directory '/«PKGBUILDDIR»/src/modules' make[3]: Entering directory '/«PKGBUILDDIR»/src/library' mkdir -p -- ../../library make[4]: Entering directory '/«PKGBUILDDIR»/src/library/profile' building system startup profile mkdir -p -- ../../../library/base/R make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/profile' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/translations' building package 'translations' mkdir -p -- ../../../library/translations make[5]: Entering directory '/«PKGBUILDDIR»/src/library/translations' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/translations' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/translations' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base' building package 'base' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/base' mkdir -p -- ../../../library/base/demo make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/base' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tools' building package 'tools' mkdir -p -- ../../../library/tools make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools' mkdir -p -- ../../../library/tools/R make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/tools/src' making text.d from text.c making init.d from init.c making Rmd5.d from Rmd5.c making md5.d from md5.c making signals.d from signals.c making install.d from install.c making getfmts.d from getfmts.c making http.d from http.c making gramLatex.d from gramLatex.c making gramRd.d from gramRd.c gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c text.c -o text.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rmd5.c -o Rmd5.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c md5.c -o md5.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c signals.c -o signals.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c install.c -o install.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c getfmts.c -o getfmts.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c http.c -o http.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gramLatex.c -o gramLatex.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gramRd.c -o gramRd.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -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[7]: Entering directory '/«PKGBUILDDIR»/src/library/tools/src' mkdir -p -- ../../../../library/tools/libs make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/tools/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/tools/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/compiler' building package 'compiler' mkdir -p -- ../../../library/compiler make[5]: Entering directory '/«PKGBUILDDIR»/src/library/compiler' mkdir -p -- ../../../library/compiler/R make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/compiler' byte-compiling package 'compiler' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base' byte-compiling package 'base' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tools' byte-compiling package 'tools' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/utils' building package 'utils' mkdir -p -- ../../../library/utils mkdir -p -- ../../../library/utils/doc make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils' mkdir -p -- ../../../library/utils/R mkdir -p -- ../../../library/utils/Sweave mkdir -p -- ../../../library/utils/misc make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/utils/src' making init.d from init.c making io.d from io.c making size.d from size.c making sock.d from sock.c making stubs.d from stubs.c making utils.d from utils.c gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io.c -o io.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c size.c -o size.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sock.c -o sock.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stubs.c -o stubs.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o utils.so init.o io.o size.o sock.o stubs.o utils.o -L../../../../lib -lR make[7]: Entering directory '/«PKGBUILDDIR»/src/library/utils/src' mkdir -p -- ../../../../library/utils/libs make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/utils/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/utils/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils' byte-compiling package 'utils' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices' building package 'grDevices' mkdir -p -- ../../../library/grDevices make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices' mkdir -p -- ../../../library/grDevices/R mkdir -p -- ../../../library/grDevices/afm mkdir -p -- ../../../library/grDevices/enc mkdir -p -- ../../../library/grDevices/icc make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src' making axis_scales.d from axis_scales.c making chull.d from chull.c making devices.d from devices.c making init.d from init.c making stubs.d from stubs.c making colors.d from colors.c making devCairo.d from devCairo.c making devPicTeX.d from devPicTeX.c making devPS.d from devPS.c making devQuartz.d from devQuartz.c gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c axis_scales.c -o axis_scales.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chull.c -o chull.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devices.c -o devices.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stubs.c -o stubs.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c colors.c -o colors.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devCairo.c -o devCairo.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devPicTeX.c -o devPicTeX.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devPS.c -o devPS.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devQuartz.c -o devQuartz.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -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[7]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src' mkdir -p -- ../../../../library/grDevices/libs make[8]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' making cairoBM.d from cairoBM.c make[9]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[10]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' gcc -std=gnu99 -I. -I../../../../../src/include -I../../../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../../../src/modules/X11 -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cairoBM.c -o cairoBM.o gcc -std=gnu99 -shared -L../../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -ltiff -ljpeg -lpng16 -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -L../../../../../lib -lR -lm make[10]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[9]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[8]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices' byte-compiling package 'grDevices' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/graphics' building package 'graphics' mkdir -p -- ../../../library/graphics make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics' mkdir -p -- ../../../library/graphics/R make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/graphics/src' making init.d from init.c making base.d from base.c making graphics.d from graphics.c making par.d from par.c making plot.d from plot.c making plot3d.d from plot3d.c making stem.d from stem.c gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c base.c -o base.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c graphics.c -o graphics.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c par.c -o par.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plot.c -o plot.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plot3d.c -o plot3d.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stem.c -o stem.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR make[7]: Entering directory '/«PKGBUILDDIR»/src/library/graphics/src' mkdir -p -- ../../../../library/graphics/libs make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics' byte-compiling package 'graphics' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/stats' building package 'stats' mkdir -p -- ../../../library/stats make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats' mkdir -p -- ../../../library/stats/R make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/stats/src' making init.d from init.c making kmeans.d from kmeans.c making ansari.d from ansari.c making bandwidths.d from bandwidths.c making chisqsim.d from chisqsim.c making d2x2xk.d from d2x2xk.c making fexact.d from fexact.c making kendall.d from kendall.c making ks.d from ks.c making line.d from line.c making smooth.d from smooth.c making prho.d from prho.c making swilk.d from swilk.c making ksmooth.d from ksmooth.c making loessc.d from loessc.c making monoSpl.d from monoSpl.c making isoreg.d from isoreg.c making Srunmed.d from Srunmed.c making dblcen.d from dblcen.c making distance.d from distance.c making hclust-utils.d from hclust-utils.c making nls.d from nls.c making rWishart.d from rWishart.c making HoltWinters.d from HoltWinters.c making PPsum.d from PPsum.c making arima.d from arima.c making burg.d from burg.c making filter.d from filter.c making mAR.d from mAR.c making pacf.d from pacf.c making starma.d from starma.c making port.d from port.c making family.d from family.c making sbart.d from sbart.c making approx.d from approx.c making loglin.d from loglin.c making lowess.d from lowess.c making massdist.d from massdist.c making splines.d from splines.c making lm.d from lm.c making complete_cases.d from complete_cases.c making cov.d from cov.c making deriv.d from deriv.c making fft.d from fft.c making fourier.d from fourier.c making model.d from model.c making optim.d from optim.c making optimize.d from optimize.c making integrate.d from integrate.c making random.d from random.c making distn.d from distn.c making zeroin.d from zeroin.c making rcont.d from rcont.c making influence.d from influence.c gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c kmeans.c -o kmeans.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ansari.c -o ansari.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bandwidths.c -o bandwidths.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chisqsim.c -o chisqsim.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c d2x2xk.c -o d2x2xk.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fexact.c -o fexact.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c kendall.c -o kendall.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ks.c -o ks.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c line.c -o line.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c smooth.c -o smooth.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c prho.c -o prho.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c swilk.c -o swilk.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ksmooth.c -o ksmooth.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c loessc.c -o loessc.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c monoSpl.c -o monoSpl.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c isoreg.c -o isoreg.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Srunmed.c -o Srunmed.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dblcen.c -o dblcen.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c distance.c -o distance.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c hclust-utils.c -o hclust-utils.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nls.c -o nls.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rWishart.c -o rWishart.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c HoltWinters.c -o HoltWinters.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c PPsum.c -o PPsum.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c arima.c -o arima.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c burg.c -o burg.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c filter.c -o filter.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mAR.c -o mAR.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pacf.c -o pacf.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c starma.c -o starma.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c port.c -o port.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c family.c -o family.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sbart.c -o sbart.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c approx.c -o approx.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c loglin.c -o loglin.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lowess.c -o lowess.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c massdist.c -o massdist.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c splines.c -o splines.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lm.c -o lm.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c complete_cases.c -o complete_cases.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cov.c -o cov.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c deriv.c -o deriv.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fft.c -o fft.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fourier.c -o fourier.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c model.c -o model.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c optim.c -o optim.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c optimize.c -o optimize.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c integrate.c -o integrate.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c random.c -o random.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c distn.c -o distn.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c zeroin.c -o zeroin.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rcont.c -o rcont.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c influence.c -o influence.o gfortran -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -c bsplvd.f -o bsplvd.o gfortran -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -c bvalue.f -o bvalue.o gfortran -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -c bvalus.f -o bvalus.o gfortran -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -c loessf.f -o loessf.o gfortran -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -c ppr.f -o ppr.o gfortran -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -c qsbart.f -o qsbart.o gfortran -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -c sgram.f -o sgram.o gfortran -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -c sinerp.f -o sinerp.o gfortran -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -c sslvrg.f -o sslvrg.o gfortran -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -c stxwx.f -o stxwx.o gfortran -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -c hclust.f -o hclust.o gfortran -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -c kmns.f -o kmns.o gfortran -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -c eureka.f -o eureka.o gfortran -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -c stl.f -o stl.o gfortran -fpic -g -O2 -fstack-protector-strong -ffloat-store -c portsrc.f -o portsrc.o gfortran -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -c lminfl.f -o lminfl.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -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 -lblas -lgfortran -lm -lquadmath -L../../../../lib -lR make[7]: Entering directory '/«PKGBUILDDIR»/src/library/stats/src' mkdir -p -- ../../../../library/stats/libs make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/stats/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/stats/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats' byte-compiling package 'stats' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/stats' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/datasets' building package 'datasets' mkdir -p -- ../../../library/datasets make[5]: Entering directory '/«PKGBUILDDIR»/src/library/datasets' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/datasets' mkdir -p -- ../../../library/datasets/data make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/datasets' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/methods' building package 'methods' mkdir -p -- ../../../library/methods make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods' mkdir -p -- ../../../library/methods/R make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/methods/src' making do_substitute_direct.d from do_substitute_direct.c making init.d from init.c making methods_list_dispatch.d from methods_list_dispatch.c making slot.d from slot.c making class_support.d from class_support.c making tests.d from tests.c making utils.d from utils.c gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c do_substitute_direct.c -o do_substitute_direct.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c methods_list_dispatch.c -o methods_list_dispatch.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c slot.c -o slot.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c class_support.c -o class_support.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tests.c -o tests.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -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[7]: Entering directory '/«PKGBUILDDIR»/src/library/methods/src' mkdir -p -- ../../../../library/methods/libs make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/methods/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/methods/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods' byte-compiling 'methods' initializing class and method definitions ... done make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/methods' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/grid' building package 'grid' mkdir -p -- ../../../library/grid mkdir -p -- ../../../library/grid/doc make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid' mkdir -p -- ../../../library/grid/R make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/grid/src' making gpar.d from gpar.c making grid.d from grid.c making just.d from just.c making layout.d from layout.c making matrix.d from matrix.c making register.d from register.c making state.d from state.c making unit.d from unit.c making util.d from util.c making viewport.d from viewport.c gcc -std=gnu99 -I../../../../include -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gpar.c -o gpar.o gcc -std=gnu99 -I../../../../include -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c grid.c -o grid.o gcc -std=gnu99 -I../../../../include -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c just.c -o just.o gcc -std=gnu99 -I../../../../include -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c layout.c -o layout.o gcc -std=gnu99 -I../../../../include -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c matrix.c -o matrix.o gcc -std=gnu99 -I../../../../include -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c register.c -o register.o gcc -std=gnu99 -I../../../../include -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c state.c -o state.o gcc -std=gnu99 -I../../../../include -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unit.c -o unit.o gcc -std=gnu99 -I../../../../include -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c util.c -o util.o gcc -std=gnu99 -I../../../../include -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c viewport.c -o viewport.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -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[7]: Entering directory '/«PKGBUILDDIR»/src/library/grid/src' mkdir -p -- ../../../../library/grid/libs make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/grid/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/grid/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid' byte-compiling package 'grid' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/grid' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/splines' building package 'splines' mkdir -p -- ../../../library/splines make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines' mkdir -p -- ../../../library/splines/R make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/splines/src' making splines.d from splines.c gcc -std=gnu99 -I../../../../include -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c splines.c -o splines.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o splines.so splines.o -L../../../../lib -lR make[7]: Entering directory '/«PKGBUILDDIR»/src/library/splines/src' mkdir -p -- ../../../../library/splines/libs make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/splines/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/splines/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines' byte-compiling package 'splines' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/splines' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/stats4' building package 'stats4' mkdir -p -- ../../../library/stats4 make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats4' mkdir -p -- ../../../library/stats4/R make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats4' byte-compiling package 'stats4' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk' building package 'tcltk' mkdir -p -- ../../../library/tcltk/R make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk' mkdir -p -- ../../../library/tcltk/exec make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk/src' making init.d from init.c making tcltk.d from tcltk.c making tcltk_unix.d from tcltk_unix.c gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include/tcl8.6 -I/usr/include/tcl8.6 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include/tcl8.6 -I/usr/include/tcl8.6 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tcltk.c -o tcltk.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include/tcl8.6 -I/usr/include/tcl8.6 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tcltk_unix.c -o tcltk_unix.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib/i386-linux-gnu -ltcl8.6 -L/usr/lib/i386-linux-gnu -ltk8.6 -lX11 -lXss -lXext -lm -L../../../../lib -lR make[6]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk/src' mkdir -p -- ../../../../library/tcltk/libs make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk/src' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk' byte-compiling package 'tcltk' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/parallel' building package 'parallel' mkdir -p -- ../../../library/parallel mkdir -p -- ../../../library/parallel/doc make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel' mkdir -p -- ../../../library/parallel/R make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/parallel/src' making init.d from init.c making rngstream.d from rngstream.c making fork.d from fork.c gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rngstream.c -o rngstream.o gcc -std=gnu99 -I../../../../include -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fork.c -o fork.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR make[7]: Entering directory '/«PKGBUILDDIR»/src/library/parallel/src' mkdir -p -- ../../../../library/parallel/libs make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel' byte-compiling package 'parallel' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/«PKGBUILDDIR»/src/library' make[2]: Leaving directory '/«PKGBUILDDIR»/src' make[2]: Entering directory '/«PKGBUILDDIR»/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/«PKGBUILDDIR»/tests' you should 'make docs' now ... make[1]: Leaving directory '/«PKGBUILDDIR»' (cd src/nmath/standalone; \ /usr/bin/make CFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ FFLAGS="-g -O2 -fstack-protector-strong -D_REENTRANT" \ CC="gcc -std=gnu99" \ CXX=g++ \ F77=gfortran \ R_GZIPCMD="/bin/gzip -n" \ libRmath_la_LDFLAGS=-Wl,-soname,libRmath.so.1 \ shared static ) make[1]: Entering directory '/«PKGBUILDDIR»/src/nmath/standalone' (cd ../../include; /usr/bin/make Rmath.h) make[2]: Entering directory '/«PKGBUILDDIR»/src/include' make[2]: 'Rmath.h' is up to date. make[2]: Leaving directory '/«PKGBUILDDIR»/src/include' Copying source files make[2]: Entering directory '/«PKGBUILDDIR»/src/nmath/standalone' making mlutils.d from mlutils.c making d1mach.d from d1mach.c making i1mach.d from i1mach.c making fmax2.d from fmax2.c making fmin2.d from fmin2.c making fprec.d from fprec.c making fround.d from fround.c making ftrunc.d from ftrunc.c making sign.d from sign.c making fsign.d from fsign.c making imax2.d from imax2.c making imin2.d from imin2.c making chebyshev.d from chebyshev.c making log1p.d from log1p.c making expm1.d from expm1.c making lgammacor.d from lgammacor.c making gammalims.d from gammalims.c making stirlerr.d from stirlerr.c making bd0.d from bd0.c making gamma.d from gamma.c making lgamma.d from lgamma.c making gamma_cody.d from gamma_cody.c making beta.d from beta.c making lbeta.d from lbeta.c making polygamma.d from polygamma.c making cospi.d from cospi.c making bessel_i.d from bessel_i.c making bessel_j.d from bessel_j.c making bessel_k.d from bessel_k.c making bessel_y.d from bessel_y.c making choose.d from choose.c making snorm.d from snorm.c making sexp.d from sexp.c making dgamma.d from dgamma.c making pgamma.d from pgamma.c making qgamma.d from qgamma.c making rgamma.d from rgamma.c making dbeta.d from dbeta.c making pbeta.d from pbeta.c making qbeta.d from qbeta.c making rbeta.d from rbeta.c making dunif.d from dunif.c making punif.d from punif.c making qunif.d from qunif.c making runif.d from runif.c making dnorm.d from dnorm.c making pnorm.d from pnorm.c making qnorm.d from qnorm.c making rnorm.d from rnorm.c making dlnorm.d from dlnorm.c making plnorm.d from plnorm.c making qlnorm.d from qlnorm.c making rlnorm.d from rlnorm.c making df.d from df.c making pf.d from pf.c making qf.d from qf.c making rf.d from rf.c making dnf.d from dnf.c making dt.d from dt.c making pt.d from pt.c making qt.d from qt.c making rt.d from rt.c making dnt.d from dnt.c making dchisq.d from dchisq.c making pchisq.d from pchisq.c making qchisq.d from qchisq.c making rchisq.d from rchisq.c making rnchisq.d from rnchisq.c making dbinom.d from dbinom.c making pbinom.d from pbinom.c making qbinom.d from qbinom.c making rbinom.d from rbinom.c making rmultinom.d from rmultinom.c making dcauchy.d from dcauchy.c making pcauchy.d from pcauchy.c making qcauchy.d from qcauchy.c making rcauchy.d from rcauchy.c making dexp.d from dexp.c making pexp.d from pexp.c making qexp.d from qexp.c making rexp.d from rexp.c making dgeom.d from dgeom.c making pgeom.d from pgeom.c making qgeom.d from qgeom.c making rgeom.d from rgeom.c making dhyper.d from dhyper.c making phyper.d from phyper.c making qhyper.d from qhyper.c making rhyper.d from rhyper.c making dnbinom.d from dnbinom.c making pnbinom.d from pnbinom.c making qnbinom.d from qnbinom.c making rnbinom.d from rnbinom.c making dpois.d from dpois.c making ppois.d from ppois.c making qpois.d from qpois.c making rpois.d from rpois.c making dweibull.d from dweibull.c making pweibull.d from pweibull.c making qweibull.d from qweibull.c making rweibull.d from rweibull.c making dlogis.d from dlogis.c making plogis.d from plogis.c making qlogis.d from qlogis.c making rlogis.d from rlogis.c making dnchisq.d from dnchisq.c making pnchisq.d from pnchisq.c making qnchisq.d from qnchisq.c making dnbeta.d from dnbeta.c making pnbeta.d from pnbeta.c making qnbeta.d from qnbeta.c making pnf.d from pnf.c making pnt.d from pnt.c making qnf.d from qnf.c making qnt.d from qnt.c making ptukey.d from ptukey.c making qtukey.d from qtukey.c making toms708.d from toms708.c making wilcox.d from wilcox.c making signrank.d from signrank.c making std_unif.d from std_unif.c make[2]: Leaving directory '/«PKGBUILDDIR»/src/nmath/standalone' make[2]: Entering directory '/«PKGBUILDDIR»/src/nmath/standalone' gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c mlutils.c -o mlutils.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c d1mach.c -o d1mach.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c i1mach.c -o i1mach.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fmax2.c -o fmax2.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fmin2.c -o fmin2.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fprec.c -o fprec.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fround.c -o fround.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ftrunc.c -o ftrunc.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c sign.c -o sign.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fsign.c -o fsign.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c imax2.c -o imax2.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c imin2.c -o imin2.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c chebyshev.c -o chebyshev.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c log1p.c -o log1p.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c expm1.c -o expm1.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lgammacor.c -o lgammacor.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gammalims.c -o gammalims.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c stirlerr.c -o stirlerr.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bd0.c -o bd0.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gamma.c -o gamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lgamma.c -o lgamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gamma_cody.c -o gamma_cody.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c beta.c -o beta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lbeta.c -o lbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c polygamma.c -o polygamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c cospi.c -o cospi.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_i.c -o bessel_i.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_j.c -o bessel_j.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_k.c -o bessel_k.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_y.c -o bessel_y.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c choose.c -o choose.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c snorm.c -o snorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c sexp.c -o sexp.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dgamma.c -o dgamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pgamma.c -o pgamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qgamma.c -o qgamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rgamma.c -o rgamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dbeta.c -o dbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pbeta.c -o pbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbeta.c -o qbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rbeta.c -o rbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dunif.c -o dunif.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c punif.c -o punif.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qunif.c -o qunif.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c runif.c -o runif.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnorm.c -o dnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnorm.c -o pnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnorm.c -o qnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnorm.c -o rnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dlnorm.c -o dlnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c plnorm.c -o plnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qlnorm.c -o qlnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rlnorm.c -o rlnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c df.c -o df.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pf.c -o pf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qf.c -o qf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rf.c -o rf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnf.c -o dnf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dt.c -o dt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pt.c -o pt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qt.c -o qt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rt.c -o rt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnt.c -o dnt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dchisq.c -o dchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pchisq.c -o pchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qchisq.c -o qchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rchisq.c -o rchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnchisq.c -o rnchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dbinom.c -o dbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pbinom.c -o pbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbinom.c -o qbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rbinom.c -o rbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rmultinom.c -o rmultinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dcauchy.c -o dcauchy.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pcauchy.c -o pcauchy.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qcauchy.c -o qcauchy.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rcauchy.c -o rcauchy.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dexp.c -o dexp.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pexp.c -o pexp.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qexp.c -o qexp.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rexp.c -o rexp.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dgeom.c -o dgeom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pgeom.c -o pgeom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qgeom.c -o qgeom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rgeom.c -o rgeom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dhyper.c -o dhyper.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c phyper.c -o phyper.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qhyper.c -o qhyper.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rhyper.c -o rhyper.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnbinom.c -o dnbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnbinom.c -o pnbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnbinom.c -o qnbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnbinom.c -o rnbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dpois.c -o dpois.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ppois.c -o ppois.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qpois.c -o qpois.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rpois.c -o rpois.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dweibull.c -o dweibull.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pweibull.c -o pweibull.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qweibull.c -o qweibull.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rweibull.c -o rweibull.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dlogis.c -o dlogis.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c plogis.c -o plogis.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qlogis.c -o qlogis.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rlogis.c -o rlogis.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnchisq.c -o dnchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnchisq.c -o pnchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnchisq.c -o qnchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnbeta.c -o dnbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnbeta.c -o pnbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnbeta.c -o qnbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnf.c -o pnf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnt.c -o pnt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnf.c -o qnf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnt.c -o qnt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ptukey.c -o ptukey.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qtukey.c -o qtukey.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c toms708.c -o toms708.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c wilcox.c -o wilcox.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c signrank.c -o signrank.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c std_unif.c -o std_unif.lo gcc -std=gnu99 -shared -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -o libRmath.so -Wl,-soname,libRmath.so.1 mlutils.lo d1mach.lo i1mach.lo fmax2.lo fmin2.lo fprec.lo fround.lo ftrunc.lo sign.lo fsign.lo imax2.lo imin2.lo chebyshev.lo log1p.lo expm1.lo lgammacor.lo gammalims.lo stirlerr.lo bd0.lo gamma.lo lgamma.lo gamma_cody.lo beta.lo lbeta.lo polygamma.lo cospi.lo bessel_i.lo bessel_j.lo bessel_k.lo bessel_y.lo choose.lo snorm.lo sexp.lo dgamma.lo pgamma.lo qgamma.lo rgamma.lo dbeta.lo pbeta.lo qbeta.lo rbeta.lo dunif.lo punif.lo qunif.lo runif.lo dnorm.lo pnorm.lo qnorm.lo rnorm.lo dlnorm.lo plnorm.lo qlnorm.lo rlnorm.lo df.lo pf.lo qf.lo rf.lo dnf.lo dt.lo pt.lo qt.lo rt.lo dnt.lo dchisq.lo pchisq.lo qchisq.lo rchisq.lo rnchisq.lo dbinom.lo pbinom.lo qbinom.lo rbinom.lo rmultinom.lo dcauchy.lo pcauchy.lo qcauchy.lo rcauchy.lo dexp.lo pexp.lo qexp.lo rexp.lo dgeom.lo pgeom.lo qgeom.lo rgeom.lo dhyper.lo phyper.lo qhyper.lo rhyper.lo dnbinom.lo pnbinom.lo qnbinom.lo rnbinom.lo dpois.lo ppois.lo qpois.lo rpois.lo dweibull.lo pweibull.lo qweibull.lo rweibull.lo dlogis.lo plogis.lo qlogis.lo rlogis.lo dnchisq.lo pnchisq.lo qnchisq.lo dnbeta.lo pnbeta.lo qnbeta.lo pnf.lo pnt.lo qnf.lo qnt.lo ptukey.lo qtukey.lo toms708.lo wilcox.lo signrank.lo std_unif.lo -lm make[2]: Leaving directory '/«PKGBUILDDIR»/src/nmath/standalone' make[2]: Entering directory '/«PKGBUILDDIR»/src/nmath/standalone' gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c mlutils.c -o mlutils.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c d1mach.c -o d1mach.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c i1mach.c -o i1mach.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fmax2.c -o fmax2.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fmin2.c -o fmin2.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fprec.c -o fprec.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fround.c -o fround.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ftrunc.c -o ftrunc.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c sign.c -o sign.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fsign.c -o fsign.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c imax2.c -o imax2.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c imin2.c -o imin2.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c chebyshev.c -o chebyshev.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c log1p.c -o log1p.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c expm1.c -o expm1.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lgammacor.c -o lgammacor.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gammalims.c -o gammalims.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c stirlerr.c -o stirlerr.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bd0.c -o bd0.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gamma.c -o gamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lgamma.c -o lgamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gamma_cody.c -o gamma_cody.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c beta.c -o beta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lbeta.c -o lbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c polygamma.c -o polygamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c cospi.c -o cospi.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_i.c -o bessel_i.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_j.c -o bessel_j.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_k.c -o bessel_k.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_y.c -o bessel_y.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c choose.c -o choose.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c snorm.c -o snorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c sexp.c -o sexp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dgamma.c -o dgamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pgamma.c -o pgamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qgamma.c -o qgamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rgamma.c -o rgamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dbeta.c -o dbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pbeta.c -o pbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbeta.c -o qbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rbeta.c -o rbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dunif.c -o dunif.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c punif.c -o punif.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qunif.c -o qunif.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c runif.c -o runif.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnorm.c -o dnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnorm.c -o pnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnorm.c -o qnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnorm.c -o rnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dlnorm.c -o dlnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c plnorm.c -o plnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qlnorm.c -o qlnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rlnorm.c -o rlnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c df.c -o df.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pf.c -o pf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qf.c -o qf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rf.c -o rf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnf.c -o dnf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dt.c -o dt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pt.c -o pt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qt.c -o qt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rt.c -o rt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnt.c -o dnt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dchisq.c -o dchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pchisq.c -o pchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qchisq.c -o qchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rchisq.c -o rchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnchisq.c -o rnchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dbinom.c -o dbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pbinom.c -o pbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbinom.c -o qbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rbinom.c -o rbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rmultinom.c -o rmultinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dcauchy.c -o dcauchy.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pcauchy.c -o pcauchy.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qcauchy.c -o qcauchy.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rcauchy.c -o rcauchy.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dexp.c -o dexp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pexp.c -o pexp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qexp.c -o qexp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rexp.c -o rexp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dgeom.c -o dgeom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pgeom.c -o pgeom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qgeom.c -o qgeom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rgeom.c -o rgeom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dhyper.c -o dhyper.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c phyper.c -o phyper.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qhyper.c -o qhyper.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rhyper.c -o rhyper.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnbinom.c -o dnbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnbinom.c -o pnbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnbinom.c -o qnbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnbinom.c -o rnbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dpois.c -o dpois.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ppois.c -o ppois.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qpois.c -o qpois.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rpois.c -o rpois.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dweibull.c -o dweibull.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pweibull.c -o pweibull.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qweibull.c -o qweibull.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rweibull.c -o rweibull.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dlogis.c -o dlogis.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c plogis.c -o plogis.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qlogis.c -o qlogis.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rlogis.c -o rlogis.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnchisq.c -o dnchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnchisq.c -o pnchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnchisq.c -o qnchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnbeta.c -o dnbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnbeta.c -o pnbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnbeta.c -o qnbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnf.c -o pnf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnt.c -o pnt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnf.c -o qnf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnt.c -o qnt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ptukey.c -o ptukey.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qtukey.c -o qtukey.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c toms708.c -o toms708.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c wilcox.c -o wilcox.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c signrank.c -o signrank.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c std_unif.c -o std_unif.o ar -cr libRmath.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 expm1.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 std_unif.o ranlib libRmath.a make[2]: Leaving directory '/«PKGBUILDDIR»/src/nmath/standalone' make[1]: Leaving directory '/«PKGBUILDDIR»/src/nmath/standalone' R_GZIPCMD="/bin/gzip -n" \ /usr/bin/make docs R_CMD_BUILD_HELP_OPTS="--txt --example" make[1]: Entering directory '/«PKGBUILDDIR»' make[2]: Entering directory '/«PKGBUILDDIR»/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/«PKGBUILDDIR»/m4' make[2]: Entering directory '/«PKGBUILDDIR»/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/«PKGBUILDDIR»/tools' make[2]: Entering directory '/«PKGBUILDDIR»/doc' make[3]: Entering directory '/«PKGBUILDDIR»/doc/html' make[3]: Leaving directory '/«PKGBUILDDIR»/doc/html' make[3]: Entering directory '/«PKGBUILDDIR»/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/«PKGBUILDDIR»/doc/manual' make[2]: Leaving directory '/«PKGBUILDDIR»/doc' make[2]: Entering directory '/«PKGBUILDDIR»/etc' make[2]: Leaving directory '/«PKGBUILDDIR»/etc' make[2]: Entering directory '/«PKGBUILDDIR»/share' make[2]: Leaving directory '/«PKGBUILDDIR»/share' make[2]: Entering directory '/«PKGBUILDDIR»/src' make[3]: Entering directory '/«PKGBUILDDIR»/src/scripts' make[4]: Entering directory '/«PKGBUILDDIR»/src/scripts' make[4]: Leaving directory '/«PKGBUILDDIR»/src/scripts' make[3]: Leaving directory '/«PKGBUILDDIR»/src/scripts' make[3]: Entering directory '/«PKGBUILDDIR»/src/include' make[4]: Entering directory '/«PKGBUILDDIR»/src/include/R_ext' make[4]: Nothing to be done for 'R'. make[4]: Leaving directory '/«PKGBUILDDIR»/src/include/R_ext' make[3]: Leaving directory '/«PKGBUILDDIR»/src/include' make[3]: Entering directory '/«PKGBUILDDIR»/src/extra' make[4]: Entering directory '/«PKGBUILDDIR»/src/extra/tre' make[5]: Entering directory '/«PKGBUILDDIR»/src/extra/tre' make[5]: 'Makedeps' is up to date. make[5]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre' make[5]: Entering directory '/«PKGBUILDDIR»/src/extra/tre' make[5]: 'libtre.a' is up to date. make[5]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre' make[4]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre' make[3]: Leaving directory '/«PKGBUILDDIR»/src/extra' make[3]: Entering directory '/«PKGBUILDDIR»/src/appl' make[4]: Entering directory '/«PKGBUILDDIR»/src/appl' make[4]: 'libappl.a' is up to date. make[4]: Leaving directory '/«PKGBUILDDIR»/src/appl' make[3]: Leaving directory '/«PKGBUILDDIR»/src/appl' make[3]: Entering directory '/«PKGBUILDDIR»/src/nmath' make[4]: Entering directory '/«PKGBUILDDIR»/src/nmath' make[4]: 'libnmath.a' is up to date. make[4]: Leaving directory '/«PKGBUILDDIR»/src/nmath' make[3]: Leaving directory '/«PKGBUILDDIR»/src/nmath' make[3]: Entering directory '/«PKGBUILDDIR»/src/unix' make[4]: Entering directory '/«PKGBUILDDIR»/src/unix' make[4]: 'libunix.a' is up to date. make[4]: Leaving directory '/«PKGBUILDDIR»/src/unix' make[4]: Entering directory '/«PKGBUILDDIR»/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/«PKGBUILDDIR»"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/«PKGBUILDDIR»/src/unix' make[3]: Leaving directory '/«PKGBUILDDIR»/src/unix' make[3]: Entering directory '/«PKGBUILDDIR»/src/main' make[4]: Entering directory '/«PKGBUILDDIR»/src/main' make[5]: Entering directory '/«PKGBUILDDIR»/src/main' /«PKGBUILDDIR»/lib/libR.so is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/main' make[4]: Leaving directory '/«PKGBUILDDIR»/src/main' make[4]: Entering directory '/«PKGBUILDDIR»/src/main' make[5]: Entering directory '/«PKGBUILDDIR»/src/main' /«PKGBUILDDIR»/bin/exec/R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/main' make[4]: Leaving directory '/«PKGBUILDDIR»/src/main' make[3]: Leaving directory '/«PKGBUILDDIR»/src/main' make[3]: Entering directory '/«PKGBUILDDIR»/src/modules' make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/internet' make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/internet' make[5]: 'internet.so' is up to date. make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet' make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet' make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack' make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack' make[5]: 'lapack.so' is up to date. make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack' make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack' make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/X11' make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/X11' make[5]: 'R_X11.so' is up to date. make[5]: 'R_de.so' is up to date. make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11' make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/X11' /«PKGBUILDDIR»/modules/R_X11.so is unchanged /«PKGBUILDDIR»/modules/R_de.so is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11' make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11' make[3]: Leaving directory '/«PKGBUILDDIR»/src/modules' make[3]: Entering directory '/«PKGBUILDDIR»/src/library' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/profile' building system startup profile make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/profile' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/translations' building package 'translations' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/translations' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/translations' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/translations' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base' building package 'base' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/base' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/base' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tools' building package 'tools' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/tools/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/tools/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/tools/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/compiler' building package 'compiler' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/compiler' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/compiler' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tools' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/utils' building package 'utils' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils' all.R is unchanged make[5]: Nothing to be done for 'iconvlist'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/utils/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/utils/src' ../../../../library/utils/libs/utils.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/utils/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/utils/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices' building package 'grDevices' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[8]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[9]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[10]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[9]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[8]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/graphics' building package 'graphics' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/graphics/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/stats' building package 'stats' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/stats/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/stats/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/stats/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/stats' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/datasets' building package 'datasets' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/datasets' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/datasets' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/datasets' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/methods' building package 'methods' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/methods/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/methods/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/methods/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/methods' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/grid' building package 'grid' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/grid/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/grid/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/grid/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/grid' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/splines' building package 'splines' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/splines/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/splines/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/splines/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/splines' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/stats4' building package 'stats4' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk/src' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk/src' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/parallel' building package 'parallel' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/parallel/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/«PKGBUILDDIR»/src/library' make[2]: Leaving directory '/«PKGBUILDDIR»/src' make[2]: Entering directory '/«PKGBUILDDIR»/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/«PKGBUILDDIR»/tests' you should 'make docs' now ... make[2]: Entering directory '/«PKGBUILDDIR»/doc' creating NEWS creating NEWS.pdf make[3]: Entering directory '/«PKGBUILDDIR»/doc/manual' creating doc/manual/R-FAQ.html creating doc/manual/version.texi creating doc/manual/R-admin.html creating doc/manual/R-data.html creating doc/manual/R-exts.html creating doc/manual/R-intro.html creating doc/manual/R-ints.html creating doc/manual/R-lang.html make[4]: Entering directory '/«PKGBUILDDIR»/doc/html' make[4]: Leaving directory '/«PKGBUILDDIR»/doc/html' make[3]: Leaving directory '/«PKGBUILDDIR»/doc/manual' make[2]: Leaving directory '/«PKGBUILDDIR»/doc' make[2]: Entering directory '/«PKGBUILDDIR»/src/library' make[3]: Entering directory '/«PKGBUILDDIR»/src/library' installing parsed Rd make[4]: Entering directory '/«PKGBUILDDIR»/src/library' base stats utils methods graphics grDevices datasets grid tools tcltk splines stats4 compiler parallel make[4]: Leaving directory '/«PKGBUILDDIR»/src/library' make[3]: Leaving directory '/«PKGBUILDDIR»/src/library' make[3]: Entering directory '/«PKGBUILDDIR»/src/library' building/updating package metadata ... make[3]: Leaving directory '/«PKGBUILDDIR»/src/library' make[3]: Entering directory '/«PKGBUILDDIR»/src/library' writing package indices make[4]: Entering directory '/«PKGBUILDDIR»/src/library' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library' make[3]: Leaving directory '/«PKGBUILDDIR»/src/library' make[2]: Leaving directory '/«PKGBUILDDIR»/src/library' make[1]: Leaving directory '/«PKGBUILDDIR»' /usr/bin/make javaconf make[1]: Entering directory '/«PKGBUILDDIR»' make[2]: Entering directory '/«PKGBUILDDIR»/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/«PKGBUILDDIR»/m4' make[2]: Entering directory '/«PKGBUILDDIR»/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/«PKGBUILDDIR»/tools' make[2]: Entering directory '/«PKGBUILDDIR»/doc' make[3]: Entering directory '/«PKGBUILDDIR»/doc/html' make[3]: Leaving directory '/«PKGBUILDDIR»/doc/html' make[3]: Entering directory '/«PKGBUILDDIR»/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/«PKGBUILDDIR»/doc/manual' make[2]: Leaving directory '/«PKGBUILDDIR»/doc' make[2]: Entering directory '/«PKGBUILDDIR»/etc' make[2]: Leaving directory '/«PKGBUILDDIR»/etc' make[2]: Entering directory '/«PKGBUILDDIR»/share' make[2]: Leaving directory '/«PKGBUILDDIR»/share' make[2]: Entering directory '/«PKGBUILDDIR»/src' make[3]: Entering directory '/«PKGBUILDDIR»/src/scripts' make[4]: Entering directory '/«PKGBUILDDIR»/src/scripts' make[4]: Leaving directory '/«PKGBUILDDIR»/src/scripts' make[3]: Leaving directory '/«PKGBUILDDIR»/src/scripts' make[3]: Entering directory '/«PKGBUILDDIR»/src/include' make[4]: Entering directory '/«PKGBUILDDIR»/src/include/R_ext' make[4]: Nothing to be done for 'R'. make[4]: Leaving directory '/«PKGBUILDDIR»/src/include/R_ext' make[3]: Leaving directory '/«PKGBUILDDIR»/src/include' make[3]: Entering directory '/«PKGBUILDDIR»/src/extra' make[4]: Entering directory '/«PKGBUILDDIR»/src/extra/tre' make[5]: Entering directory '/«PKGBUILDDIR»/src/extra/tre' make[5]: 'Makedeps' is up to date. make[5]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre' make[5]: Entering directory '/«PKGBUILDDIR»/src/extra/tre' make[5]: 'libtre.a' is up to date. make[5]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre' make[4]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre' make[3]: Leaving directory '/«PKGBUILDDIR»/src/extra' make[3]: Entering directory '/«PKGBUILDDIR»/src/appl' make[4]: Entering directory '/«PKGBUILDDIR»/src/appl' make[4]: 'libappl.a' is up to date. make[4]: Leaving directory '/«PKGBUILDDIR»/src/appl' make[3]: Leaving directory '/«PKGBUILDDIR»/src/appl' make[3]: Entering directory '/«PKGBUILDDIR»/src/nmath' make[4]: Entering directory '/«PKGBUILDDIR»/src/nmath' make[4]: 'libnmath.a' is up to date. make[4]: Leaving directory '/«PKGBUILDDIR»/src/nmath' make[3]: Leaving directory '/«PKGBUILDDIR»/src/nmath' make[3]: Entering directory '/«PKGBUILDDIR»/src/unix' make[4]: Entering directory '/«PKGBUILDDIR»/src/unix' make[4]: 'libunix.a' is up to date. make[4]: Leaving directory '/«PKGBUILDDIR»/src/unix' make[4]: Entering directory '/«PKGBUILDDIR»/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/«PKGBUILDDIR»"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/«PKGBUILDDIR»/src/unix' make[3]: Leaving directory '/«PKGBUILDDIR»/src/unix' make[3]: Entering directory '/«PKGBUILDDIR»/src/main' make[4]: Entering directory '/«PKGBUILDDIR»/src/main' make[5]: Entering directory '/«PKGBUILDDIR»/src/main' /«PKGBUILDDIR»/lib/libR.so is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/main' make[4]: Leaving directory '/«PKGBUILDDIR»/src/main' make[4]: Entering directory '/«PKGBUILDDIR»/src/main' make[5]: Entering directory '/«PKGBUILDDIR»/src/main' /«PKGBUILDDIR»/bin/exec/R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/main' make[4]: Leaving directory '/«PKGBUILDDIR»/src/main' make[3]: Leaving directory '/«PKGBUILDDIR»/src/main' make[3]: Entering directory '/«PKGBUILDDIR»/src/modules' make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/internet' make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/internet' make[5]: 'internet.so' is up to date. make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet' make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet' make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack' make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack' make[5]: 'lapack.so' is up to date. make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack' make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack' make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/X11' make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/X11' make[5]: 'R_X11.so' is up to date. make[5]: 'R_de.so' is up to date. make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11' make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/X11' /«PKGBUILDDIR»/modules/R_X11.so is unchanged /«PKGBUILDDIR»/modules/R_de.so is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11' make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11' make[3]: Leaving directory '/«PKGBUILDDIR»/src/modules' make[3]: Entering directory '/«PKGBUILDDIR»/src/library' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/profile' building system startup profile make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/profile' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/translations' building package 'translations' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/translations' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/translations' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/translations' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base' building package 'base' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/base' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/base' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tools' building package 'tools' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/tools/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/tools/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/tools/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/compiler' building package 'compiler' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/compiler' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/compiler' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tools' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/utils' building package 'utils' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils' all.R is unchanged make[5]: Nothing to be done for 'iconvlist'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/utils/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/utils/src' ../../../../library/utils/libs/utils.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/utils/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/utils/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices' building package 'grDevices' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[8]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[9]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[10]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[9]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[8]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/graphics' building package 'graphics' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/graphics/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/stats' building package 'stats' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/stats/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/stats/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/stats/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/stats' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/datasets' building package 'datasets' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/datasets' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/datasets' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/datasets' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/methods' building package 'methods' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/methods/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/methods/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/methods/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/methods' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/grid' building package 'grid' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/grid/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/grid/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/grid/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/grid' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/splines' building package 'splines' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/splines/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/splines/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/splines/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/splines' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/stats4' building package 'stats4' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk/src' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk/src' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/parallel' building package 'parallel' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/parallel/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/«PKGBUILDDIR»/src/library' make[2]: Leaving directory '/«PKGBUILDDIR»/src' make[2]: Entering directory '/«PKGBUILDDIR»/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/«PKGBUILDDIR»/tests' make[2]: Entering directory '/«PKGBUILDDIR»' configuring Java ... Java interpreter : /usr/lib/jvm/default-java/jre/bin/java Java version : 1.8.0_91 Java home path : /usr/lib/jvm/default-java Java compiler : /usr/lib/jvm/default-java/bin/javac Java headers gen.: /usr/lib/jvm/default-java/bin/javah Java archive tool: /usr/lib/jvm/default-java/bin/jar trying to compile and link a JNI program detected JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux detected JNI linker flags : -L$(JAVA_HOME)/jre/lib/i386/server -ljvm make[3]: Entering directory '/tmp/Rjavareconf.ibbW9O' gcc -std=gnu99 -I/«PKGBUILDDIR»/include -DNDEBUG -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.o gcc -std=gnu99 -shared -L/«PKGBUILDDIR»/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/default-java/jre/lib/i386/server -ljvm -L/«PKGBUILDDIR»/lib -lR make[3]: Leaving directory '/tmp/Rjavareconf.ibbW9O' JAVA_HOME : /usr/lib/jvm/default-java Java library path: $(JAVA_HOME)/jre/lib/i386/server JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux JNI linker flags : -L$(JAVA_HOME)/jre/lib/i386/server -ljvm Updating Java configuration in /«PKGBUILDDIR» Done. make[2]: Leaving directory '/«PKGBUILDDIR»' make[1]: Leaving directory '/«PKGBUILDDIR»' touch make-arch-stamp *** make-indep *** /usr/bin/make -k docs make[1]: Entering directory '/«PKGBUILDDIR»' make[2]: Entering directory '/«PKGBUILDDIR»/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/«PKGBUILDDIR»/m4' make[2]: Entering directory '/«PKGBUILDDIR»/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/«PKGBUILDDIR»/tools' make[2]: Entering directory '/«PKGBUILDDIR»/doc' make[3]: Entering directory '/«PKGBUILDDIR»/doc/html' make[3]: Leaving directory '/«PKGBUILDDIR»/doc/html' make[3]: Entering directory '/«PKGBUILDDIR»/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/«PKGBUILDDIR»/doc/manual' make[2]: Leaving directory '/«PKGBUILDDIR»/doc' make[2]: Entering directory '/«PKGBUILDDIR»/etc' make[2]: Leaving directory '/«PKGBUILDDIR»/etc' make[2]: Entering directory '/«PKGBUILDDIR»/share' make[2]: Leaving directory '/«PKGBUILDDIR»/share' make[2]: Entering directory '/«PKGBUILDDIR»/src' make[3]: Entering directory '/«PKGBUILDDIR»/src/scripts' make[4]: Entering directory '/«PKGBUILDDIR»/src/scripts' make[4]: Leaving directory '/«PKGBUILDDIR»/src/scripts' make[3]: Leaving directory '/«PKGBUILDDIR»/src/scripts' make[3]: Entering directory '/«PKGBUILDDIR»/src/include' make[4]: Entering directory '/«PKGBUILDDIR»/src/include/R_ext' make[4]: Nothing to be done for 'R'. make[4]: Leaving directory '/«PKGBUILDDIR»/src/include/R_ext' make[3]: Leaving directory '/«PKGBUILDDIR»/src/include' make[3]: Entering directory '/«PKGBUILDDIR»/src/extra' make[4]: Entering directory '/«PKGBUILDDIR»/src/extra/tre' make[5]: Entering directory '/«PKGBUILDDIR»/src/extra/tre' make[5]: 'Makedeps' is up to date. make[5]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre' make[5]: Entering directory '/«PKGBUILDDIR»/src/extra/tre' make[5]: 'libtre.a' is up to date. make[5]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre' make[4]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre' make[3]: Leaving directory '/«PKGBUILDDIR»/src/extra' make[3]: Entering directory '/«PKGBUILDDIR»/src/appl' make[4]: Entering directory '/«PKGBUILDDIR»/src/appl' make[4]: 'libappl.a' is up to date. make[4]: Leaving directory '/«PKGBUILDDIR»/src/appl' make[3]: Leaving directory '/«PKGBUILDDIR»/src/appl' make[3]: Entering directory '/«PKGBUILDDIR»/src/nmath' make[4]: Entering directory '/«PKGBUILDDIR»/src/nmath' make[4]: 'libnmath.a' is up to date. make[4]: Leaving directory '/«PKGBUILDDIR»/src/nmath' make[3]: Leaving directory '/«PKGBUILDDIR»/src/nmath' make[3]: Entering directory '/«PKGBUILDDIR»/src/unix' make[4]: Entering directory '/«PKGBUILDDIR»/src/unix' make[4]: 'libunix.a' is up to date. make[4]: Leaving directory '/«PKGBUILDDIR»/src/unix' make[4]: Entering directory '/«PKGBUILDDIR»/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/«PKGBUILDDIR»"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/«PKGBUILDDIR»/src/unix' make[3]: Leaving directory '/«PKGBUILDDIR»/src/unix' make[3]: Entering directory '/«PKGBUILDDIR»/src/main' make[4]: Entering directory '/«PKGBUILDDIR»/src/main' make[5]: Entering directory '/«PKGBUILDDIR»/src/main' /«PKGBUILDDIR»/lib/libR.so is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/main' make[4]: Leaving directory '/«PKGBUILDDIR»/src/main' make[4]: Entering directory '/«PKGBUILDDIR»/src/main' make[5]: Entering directory '/«PKGBUILDDIR»/src/main' /«PKGBUILDDIR»/bin/exec/R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/main' make[4]: Leaving directory '/«PKGBUILDDIR»/src/main' make[3]: Leaving directory '/«PKGBUILDDIR»/src/main' make[3]: Entering directory '/«PKGBUILDDIR»/src/modules' make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/internet' make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/internet' make[5]: 'internet.so' is up to date. make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet' make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet' make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack' make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack' make[5]: 'lapack.so' is up to date. make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack' make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack' make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/X11' make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/X11' make[5]: 'R_X11.so' is up to date. make[5]: 'R_de.so' is up to date. make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11' make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/X11' /«PKGBUILDDIR»/modules/R_X11.so is unchanged /«PKGBUILDDIR»/modules/R_de.so is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11' make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11' make[3]: Leaving directory '/«PKGBUILDDIR»/src/modules' make[3]: Entering directory '/«PKGBUILDDIR»/src/library' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/profile' building system startup profile make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/profile' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/translations' building package 'translations' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/translations' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/translations' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/translations' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base' building package 'base' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/base' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/base' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tools' building package 'tools' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/tools/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/tools/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/tools/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/compiler' building package 'compiler' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/compiler' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/compiler' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tools' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/utils' building package 'utils' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils' all.R is unchanged make[5]: Nothing to be done for 'iconvlist'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/utils/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/utils/src' ../../../../library/utils/libs/utils.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/utils/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/utils/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices' building package 'grDevices' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[8]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[9]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[10]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[9]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[8]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/graphics' building package 'graphics' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/graphics/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/stats' building package 'stats' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/stats/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/stats/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/stats/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/stats' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/datasets' building package 'datasets' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/datasets' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/datasets' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/datasets' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/methods' building package 'methods' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/methods/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/methods/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/methods/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/methods' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/grid' building package 'grid' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/grid/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/grid/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/grid/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/grid' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/splines' building package 'splines' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/splines/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/splines/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/splines/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/splines' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/stats4' building package 'stats4' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4' make[4]: Entering directory 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R-FAQ.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-admin.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-data.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-exts.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-intro.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-ints.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-lang.texi make[3]: Leaving directory '/«PKGBUILDDIR»/doc/manual' make[2]: Leaving directory '/«PKGBUILDDIR»/doc' make[1]: Leaving directory '/«PKGBUILDDIR»' (cd doc/manual && \ /usr/bin/make refman.pdf R-admin.pdf R-data.pdf R-exts.pdf \ R-FAQ.pdf R-intro.pdf R-ints.pdf R-lang.pdf) make[1]: Entering directory '/«PKGBUILDDIR»/doc/manual' creating doc/manual/version.tex collecting LaTeX docs for package 'base' ... Converting parsed Rd's to LaTeX .......................................... collecting LaTeX docs for package 'tools' ... Converting parsed Rd's to LaTeX ...... collecting LaTeX docs for package 'utils' ... Converting parsed Rd's to LaTeX ............. collecting LaTeX docs for package 'grDevices' ... Converting parsed Rd's to LaTeX ...... collecting LaTeX docs for package 'graphics' ... Converting parsed Rd's to LaTeX ....... collecting LaTeX docs for package 'stats' ... Converting parsed Rd's to LaTeX .............................. collecting LaTeX docs for package 'datasets' ... Converting parsed Rd's to LaTeX ........ collecting LaTeX docs for package 'methods' ... Converting parsed Rd's to LaTeX ....... collecting LaTeX docs for package 'grid' ... Converting parsed Rd's to LaTeX ......... collecting LaTeX docs for package 'splines' ... Converting parsed Rd's to LaTeX . collecting LaTeX docs for package 'stats4' ... Converting parsed Rd's to LaTeX . collecting LaTeX docs for package 'tcltk' ... Converting parsed Rd's to LaTeX . collecting LaTeX docs for package 'compiler' ... Converting parsed Rd's to LaTeX collecting LaTeX docs for package 'parallel' ... Converting parsed Rd's to LaTeX . PDF/LaTeX documentation: reference index ... This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2016/02/01> Babel <3.9q> and hyphenation patterns for 3 language(s) loaded. 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(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./version.tex) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [1] [2] (./base-pkg.tex Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) Underfull \hbox (badness 4595) in paragraph at lines 40--43 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [1] [2] Underfull \hbox (badness 1960) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is 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 [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 296--300 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 381--384 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 524--530 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/n/10 insertions\T1/ptm/m/n/10 ', [9] [10] [11] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 2671) in paragraph at lines 1135--1138 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] [22] Underfull \hbox (badness 4072) in paragraph at lines 1369--1375 []\T1/zi4/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/zi4/m/n/10 x mod y \T1/ptm/m /n/10 and \T1/zi4/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I t is guar-an-teed that [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.88089pt too wide) in paragraph at lines 1894--1894 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2079--2081 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3580--3582 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] Underfull \hbox (badness 2521) in paragraph at lines 4782--4784 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] Overfull \hbox (7.0809pt too wide) in paragraph at lines 5909--5909 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [93] [94] [95] Underfull \hbox (badness 2096) in paragraph at lines 6090--6103 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [96] [97] [98] Overfull \hbox (58.35893pt too wide) in paragraph at lines 6293--6295 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [99] [100] Underfull \hbox (badness 10000) in paragraph at lines 6434--6437 []\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is [101] [102] Underfull \hbox (badness 1442) in paragraph at lines 6599--6605 []\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/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6599--6605 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6599--6605 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). 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[114] Underfull \hbox (badness 4595) in paragraph at lines 7355--7358 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [115] Underfull \hbox (badness 3000) in paragraph at lines 7391--7393 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7416--7419 [][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [116] [117] [118] [119] Underfull \hbox (badness 10000) in paragraph at lines 7671--7682 []\T1/zi4/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 [120] [121] Underfull \hbox (badness 4479) in paragraph at lines 7743--7752 [][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), Underfull \hbox (badness 2469) in paragraph at lines 7743--7752 [][]\T1/zi4/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods, [][]\T1/zi4/m/n/10 Math.data.frame[][][] \T1/ptm/m/n/10 etc, about \T1/ptm/m/i t/10 Group \T1/ptm/m/n/10 meth-ods for [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] Underfull \hbox (badness 1394) in paragraph at lines 9355--9360 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [146] [147] [148] [149] [150] Underfull \hbox (badness 1052) in paragraph at lines 9698--9703 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 9698--9703 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [151] [152] Underfull \hbox (badness 1735) in paragraph at lines 9836--9840 \T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ zi4/m/n/10 https : / / en . wikipedia . [153] [154] [155] [156] [157] [158] Underfull \hbox (badness 2150) in paragraph at lines 10240--10243 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse [159] Underfull \hbox (badness 6396) in paragraph at lines 10254--10262 []\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 2409) in paragraph at lines 10295--10302 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] Underfull \hbox (badness 4569) in paragraph at lines 11341--11345 []\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 11341--11345 \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 [176] [177] [178] [179] [180] [181] [182] [183] Underfull \hbox (badness 2698) in paragraph at lines 11917--11926 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 11917--11926 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] Underfull \hbox (badness 6236) in paragraph at lines 12561--12564 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [194] [195] [196] [197] [198] [199] Underfull \hbox (badness 2253) in paragraph at lines 12939--12941 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [200] Underfull \hbox (badness 1565) in paragraph at lines 13010--13014 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and [201] Underfull \hbox (badness 10000) in paragraph at lines 13054--13056 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with [202] [203] Underfull \hbox (badness 1466) in paragraph at lines 13195--13198 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ zi4/m/n/10 file.copy \T1/ptm/m/n/10 and [204] [205] Underfull \hbox (badness 10000) in paragraph at lines 13303--13307 [][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13314--13317 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [206] [207] [208] [209] Underfull \hbox (badness 3965) in paragraph at lines 13577--13581 []\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, [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] Underfull \hbox (badness 4429) in paragraph at lines 14338--14341 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [222] Underfull \hbox (badness 10000) in paragraph at lines 14430--14432 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14436--14440 []\T1/zi4/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 [223] Underfull \hbox (badness 10000) in paragraph at lines 14478--14482 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 14478--14482 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [224] Underfull \vbox (badness 3803) has occurred while \output is active [225] [226] [227] [228] [229] [230] [231] [232] Underfull \hbox (badness 2452) in paragraph at lines 15058--15062 []\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 15058--15062 \T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_ WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and [233] [234] [235] Underfull \hbox (badness 1092) in paragraph at lines 15231--15236 [][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [236] [237] [238] [239] Underfull \hbox (badness 6741) in paragraph at lines 15479--15483 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [240] [241] [242] [243] Underfull \hbox (badness 1867) in paragraph at lines 15785--15792 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [244] [245] [246] [247] Underfull \vbox (badness 10000) has occurred while \output is active [248] [249] Underfull \hbox (badness 3679) in paragraph at lines 16166--16168 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [250] [251] [252] [253] [254] [255] [256] [257] Underfull \hbox (badness 1478) in paragraph at lines 16711--16714 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [258] [259] [260] [261] Underfull \hbox (badness 10000) in paragraph at lines 16964--16966 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [262] [263] [264] [265] [266] [267] [268] [269] [270] Underfull \hbox (badness 1442) in paragraph at lines 17527--17529 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [271] Underfull \hbox (badness 2452) in paragraph at lines 17619--17635 [][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [272] [273] [274] [275] [276] [277] [278] Underfull \hbox (badness 1248) in paragraph at lines 18033--18036 []\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/ m/n/10 , [279] [280] [281] [282] Underfull \hbox (badness 4739) in paragraph at lines 18291--18293 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] Underfull \hbox (badness 1360) in paragraph at lines 19249--19254 \T1/zi4/m/n/10 "none"\T1/ptm/m/n/10 . It is in-tended for the ver-sion of OpenS SL used, but not all Underfull \hbox (badness 10000) in paragraph at lines 19272--19278 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / Underfull \hbox (badness 1127) in paragraph at lines 19272--19278 \T1/zi4/m/n/10 ssl-[]compared . html$[][] \T1/ptm/m/n/10 for more de-tails on S SL ver-sions. Nor-mally \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 used with \T1/phv /m/n/10 R [299] Underfull \hbox (badness 10000) in paragraph at lines 19345--19349 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 19345--19349 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [300] [301] Underfull \hbox (badness 1509) in paragraph at lines 19480--19487 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1354) in paragraph at lines 19480--19487 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19496--19501 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313] Underfull \hbox (badness 1264) in paragraph at lines 20227--20232 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] Underfull \hbox (badness 10000) in paragraph at lines 20981--20983 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] Underfull \hbox (badness 1077) in paragraph at lines 21979--21985 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [341] [342] [343] Underfull \hbox (badness 1484) in paragraph at lines 22140--22148 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [344] [345] [346] [347] Underfull \hbox (badness 2790) in paragraph at lines 22411--22414 []\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 22411--22414 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [348] [349] [350] [351] Underfull \hbox (badness 1194) in paragraph at lines 22692--22695 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 . It calls [352] [353] [354] [355] Underfull \hbox (badness 10000) in paragraph at lines 22898--22904 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 5862) in paragraph at lines 22898--22904 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 22908--22911 []\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 22908--22911 \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 [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] [367] [368] [369] Underfull \hbox (badness 10000) in paragraph at lines 23839--23841 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [370] [371] [372] [373] Underfull \hbox (badness 1199) in paragraph at lines 24066--24072 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24066--24072 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [374] [375] [376] [377] [378] [379] [380] [381] Underfull \hbox (badness 1038) in paragraph at lines 24645--24653 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 1881) in paragraph at lines 24654--24657 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 24673--24675 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [382] Underfull \hbox (badness 10000) in paragraph at lines 24745--24755 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 24756--24762 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able Underfull \hbox (badness 1968) in paragraph at lines 24769--24774 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 24779--24781 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [383] [384] Underfull \vbox (badness 10000) has occurred while \output is active [385] Underfull \hbox (badness 10000) in paragraph at lines 25034--25040 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/zi4/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25034--25040 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 25034--25040 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by [386] Underfull \hbox (badness 10000) in paragraph at lines 25047--25050 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 25071--25073 []\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 25103--25108 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 25109--25120 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 25121--25124 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and [387] Underfull \hbox (badness 4084) in paragraph at lines 25131--25143 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN OS X build), Underfull \hbox (badness 10000) in paragraph at lines 25131--25143 \T1/zi4/m/n/10 "mac.binary."\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.maveric ks" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for C RAN Underfull \hbox (badness 7397) in paragraph at lines 25131--25143 \T1/ptm/m/n/10 OS X builds). Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m /n/10 . (\T1/zi4/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 25145--25152 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 25145--25152 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 25145--25152 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1082) in paragraph at lines 25145--25152 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [388] [389] [390] [391] [392] Underfull \hbox (badness 10000) in paragraph at lines 25491--25495 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 25491--25495 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [393] [394] [395] [396] [397] Underfull \hbox (badness 1735) in paragraph at lines 25809--25813 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [398] [399] [400] [401] [402] [403] [404] [405] [406] Underfull \hbox (badness 2726) in paragraph at lines 26369--26372 []\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] [418] [419] Underfull \hbox (badness 1052) in paragraph at lines 27186--27191 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [420] [421] [422] [423] [424] Underfull \vbox (badness 10000) has occurred while \output is active [425] [426] [427] [428] [429] [430] [431] Underfull \hbox (badness 1533) in paragraph at lines 27995--27998 []\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 [432] [433] [434] Underfull \hbox (badness 1163) in paragraph at lines 28157--28168 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] Underfull \hbox (badness 10000) in paragraph at lines 29676--29680 []\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 29676--29680 \T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. Underfull \hbox (badness 6188) in paragraph at lines 29698--29700 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [459] [460] [461] [462] [463] [464] [465] [466] [467] Underfull \hbox (badness 1655) in paragraph at lines 30246--30248 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm /m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for [468] [469] [470] [471] [472] [473] [474] [475] [476] [477] [478] Underfull \hbox (badness 10000) in paragraph at lines 30914--30918 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [479] [480] [481] Underfull \hbox (badness 2302) in paragraph at lines 31154--31161 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 31154--31161 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 2980) in paragraph at lines 31154--31161 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 31154--31161 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [482] [483] [484] Underfull \hbox (badness 2261) in paragraph at lines 31310--31315 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if Underfull \hbox (badness 10000) in paragraph at lines 31337--31343 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [485] Underfull \hbox (badness 10000) in paragraph at lines 31413--31418 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [486] [487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] Underfull \hbox (badness 1072) in paragraph at lines 34333--34337 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 34338--34342 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 34366--34372 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 34366--34372 \T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 34366--34372 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in Underfull \hbox (badness 3343) in paragraph at lines 34379--34386 \T1/ptm/m/n/10 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 34379--34386 \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 Underfull \hbox (badness 1917) in paragraph at lines 34379--34386 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [532] [533] [534] [535] [536] Underfull \hbox (badness 10000) in paragraph at lines 34670--34676 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1152) in paragraph at lines 34670--34676 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] Underfull \hbox (badness 3333) in paragraph at lines 36500--36505 []\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] Underfull \hbox (badness 1472) in paragraph at lines 37120--37123 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [576] [577] [578] [579] [580] [581] [582] [583] [584] [585] [586] Underfull \hbox (badness 2671) in paragraph at lines 37785--37788 []\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/zi4/m/n/10 ...\T1/pt m/m/n/10 . If set to \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies [587] [588] [589] [590] [591] [592] Underfull \hbox (badness 10000) in paragraph at lines 38200--38203 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [593] [594] Underfull \hbox (badness 10000) in paragraph at lines 38318--38322 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [595] Underfull \hbox (badness 10000) in paragraph at lines 38380--38384 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614] [615] Underfull \hbox (badness 1990) in paragraph at lines 39706--39714 []\T1/zi4/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 4846) in paragraph at lines 39706--39714 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [616] [617] [618] [619] Underfull \hbox (badness 1515) in paragraph at lines 39978--39983 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0 [620] [621] [622] [623] Underfull \hbox (badness 1917) in paragraph at lines 40208--40215 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [624] [625] [626] [627] [628] [629] [630] [631] [632] [633] Underfull \hbox (badness 3668) in paragraph at lines 40869--40871 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [634] [635] Underfull \hbox (badness 2401) in paragraph at lines 40974--40978 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [636] [637] Underfull \hbox (badness 2111) in paragraph at lines 41143--41148 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. [638] Underfull \hbox (badness 6542) in paragraph at lines 41159--41164 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [639] [640] [641] [642] [643] [644] [645] Underfull \hbox (badness 10000) in paragraph at lines 41604--41609 []\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu nc-tion than [][]\T1/zi4/m/n/10 rank[][][] Underfull \hbox (badness 10000) in paragraph at lines 41604--41609 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to [646] Underfull \hbox (badness 5417) in paragraph at lines 41696--41700 []\T1/zi4/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 [647] Underfull \hbox (badness 10000) in paragraph at lines 41757--41761 []\T1/zi4/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 [648] [649]) (./compiler-pkg.tex [650] Chapter 2. [651] [652] [653] [654]) (./datasets-pkg.tex Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple te list, use [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] Underfull \vbox (badness 1515) has occurred while \output is active [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] Underfull \hbox (badness 6658) in paragraph at lines 3940--3942 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h ttp : / / www . ltrr . arizona . edu / ~hallman / [722] Underfull \vbox (badness 10000) has occurred while \output is active [723] [724] [725] [726] Underfull \vbox (badness 10000) has occurred while \output is active [727] Underfull \vbox (badness 10000) has occurred while \output is active [728] [729] [730] [731] [732] [733] [734] [735]) (./grDevices-pkg.tex [736] Chapter 4. [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] Underfull \hbox (badness 5175) in paragraph at lines 1071--1073 []\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 [754] [755] [756] [757] Underfull \hbox (badness 1852) in paragraph at lines 1268--1271 []\T1/zi4/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 [758] [759] [760] Underfull \hbox (badness 1490) in paragraph at lines 1474--1479 \T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and [761] Underfull \hbox (badness 2698) in paragraph at lines 1528--1531 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture, oth-er-wise a ma-trix of color names (for [762] Underfull \hbox (badness 10000) in paragraph at lines 1597--1601 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [763] [764] [765] [766] Underfull \hbox (badness 1325) in paragraph at lines 1880--1890 \T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/ 10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1 /ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 , [767] [768] Underfull \hbox (badness 10000) in paragraph at lines 1985--1987 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [769] [770] [771] Underfull \hbox (badness 6758) in paragraph at lines 2146--2149 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [772] [773] [774] [775] [776] [777] [778] [779] [780] Underfull \hbox (badness 10000) in paragraph at lines 2712--2713 [781] [782] [783] [784] [785] [786] [787] Underfull \hbox (badness 1152) in paragraph at lines 3150--3152 []\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/zi4/m/n/10 nr, nc \T1/ptm/m /n/10 giv-ing the num-ber of rows and columns, ful-fill-ing [788] [789] [790] [791] [792] Underfull \hbox (badness 2856) in paragraph at lines 3470--3473 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3484--3486 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [793] [794] Underfull \hbox (badness 1173) in paragraph at lines 3600--3610 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 paper \T1/ptm/m/n/10 ar-gu-ment sets the `\ T1/zi4/m/n/10 /MediaBox\T1/ptm/m/n/10 ' en-try in the file, which de-faults to \T1/zi4/m/n/10 width \T1/ptm/m/n/10 by [795] [796] [797] [798] [799] [800] [801] [802] [803] [804] [805] Underfull \hbox (badness 1067) in paragraph at lines 4307--4314 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [806] [807] Underfull \hbox (badness 3364) in paragraph at lines 4468--4470 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$ \T1/zi4/m/n/10 https : / / partners . adobe . com / public / [808] Underfull \hbox (badness 1789) in paragraph at lines 4545--4547 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [809] Underfull \hbox (badness 1377) in paragraph at lines 4595--4600 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [810] Underfull \hbox (badness 2671) in paragraph at lines 4622--4630 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4671--4678 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4679--4688 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4679--4688 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4689--4691 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [811] [812] Underfull \hbox (badness 1057) in paragraph at lines 4800--4805 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/zi4/m/n/10 "rgb"\T1/ptm/m/n/10 ) (which is RGB+gray) and [813] Underfull \hbox (badness 7344) in paragraph at lines 4860--4862 []\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 [814] [815] Underfull \hbox (badness 2035) in paragraph at lines 4984--4993 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 10000) in paragraph at lines 4984--4993 \T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 4984--4993 \T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [816] Underfull \hbox (badness 10000) in paragraph at lines 5053--5060 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5053--5060 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [817] [818] [819] Underfull \hbox (badness 1546) in paragraph at lines 5195--5203 []\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/ n/10 , [820] Underfull \hbox (badness 1648) in paragraph at lines 5272--5276 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [821] [822] [823] [824] [825] [826] [827] Underfull \hbox (badness 10000) in paragraph at lines 5724--5727 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [828] [829] [830] [831] [832] [833] Underfull \hbox (badness 1189) in paragraph at lines 6121--6123 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [834] [835] Underfull \hbox (badness 10000) in paragraph at lines 6219--6221 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [836] [837] [838] [839] Underfull \hbox (badness 3780) in paragraph at lines 6510--6516 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [840] [841] [842] Underfull \hbox (badness 2680) in paragraph at lines 6706--6708 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [843] [844] [845]) (./graphics-pkg.tex [846] Chapter 5. [847] [848] [849] [850] [851] [852] [853] [854] [855] [856] [857] Underfull \hbox (badness 10000) in paragraph at lines 683--690 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [858] [859] [860] [861] Underfull \vbox (badness 3803) has occurred while \output is active [862] [863] [864] [865] [866] Underfull \hbox (badness 4634) in paragraph at lines 1246--1249 [][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [867] [868] [869] [870] [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] [883] Underfull \hbox (badness 1009) in paragraph at lines 2280--2287 \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 [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] Underfull \vbox (badness 10000) has occurred while \output is active [906] Underfull \vbox (badness 10000) has occurred while \output is active [907] [908] [909] [910] Underfull \hbox (badness 1867) in paragraph at lines 3912--3916 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [911] [912] [913] [914] [915] [916] [917] Underfull \hbox (badness 1924) in paragraph at lines 4359--4364 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain [918] Underfull \hbox (badness 2529) in paragraph at lines 4390--4393 []\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 [919] [920] [921] [922] [923] Underfull \hbox (badness 10000) in paragraph at lines 4740--4746 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4740--4746 \T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that [924] Underfull \hbox (badness 10000) in paragraph at lines 4871--4874 [925] </«PKGBUILDDIR»/library/graphics/help/figures/mai.pdf, id=15 314, 289.08pt x 289.08pt> <use /«PKGBUILDDIR»/library/graphics/help/figures/mai.pdf> [926 </«PKGBUILDDIR»/library/graphics/help/figures/mai.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 4932--4934 </«PKGBUILDDIR»/library/graphics/help/figures/oma.pdf, id=15 327, 259.97125pt x 332.24126pt> <use /«PKGBUILDDIR»/library/graphics/help/figures/oma.pdf> [927 </«PKGBUILDDIR»/library/graphics/help/figures/oma.pdf>] [928] Underfull \hbox (badness 10000) in paragraph at lines 5122--5124 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [929] [930] [931] [932] [933] Underfull \vbox (badness 10000) has occurred while \output is active [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] </«PKGBUILDDIR»/library/graphics/help/figures/pch.pdf, id=15 774, 361.35pt x 50.1875pt> <use /«PKGBUILDDIR»/library/graphics/help/figures/pch.pdf> Overfull \hbox (31.57222pt too wide) in paragraph at lines 6592--6593 [][] [953 </«PKGBUILDDIR»/library/graphics/help/figures/pch.pdf>] [954] Underfull \vbox (badness 10000) has occurred while \output is active [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] Underfull \hbox (badness 1048) in paragraph at lines 7301--7306 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [965] Underfull \hbox (badness 1038) in paragraph at lines 7417--7420 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [966] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] Underfull \hbox (badness 10000) in paragraph at lines 8653--8655 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8655--8657 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [988]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored <to be read again> \relax l.8735 \HeaderA{units}{Graphical Units}{units} [989] [990] [991] [992]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [993] [994] [995] [996] [997] [998] Underfull \hbox (badness 2680) in paragraph at lines 390--393 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] Underfull \hbox (badness 4279) in paragraph at lines 970--979 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] Underfull \vbox (badness 3803) has occurred while \output is active [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] Underfull \hbox (badness 1067) in paragraph at lines 4340--4343 []\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 [1066] [1067] [1068] [1069] Underfull \hbox (badness 7256) in paragraph at lines 4583--4585 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] Underfull \hbox (badness 10000) in paragraph at lines 5860--5866 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] Underfull \hbox (badness 7649) in paragraph at lines 6334--6337 []\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 [1100] [1101] [1102] [1103]) (./methods-pkg.tex [1104] Chapter 7. [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] Underfull \hbox (badness 2237) in paragraph at lines 1454--1456 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1125] [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] Underfull \hbox (badness 10000) in paragraph at lines 2050--2055 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 2050--2055 \T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] Underfull \hbox (badness 10000) in paragraph at lines 2655--2658 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1142] [1143] Underfull \hbox (badness 1132) in paragraph at lines 2795--2799 []\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in [1144] Underfull \hbox (badness 1033) in paragraph at lines 2827--2832 \T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1145] [1146] [1147] [1148] [1149] [1150] [1151] Underfull \hbox (badness 1102) in paragraph at lines 3339--3341 []\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1152] [1153] [1154] [1155] [1156] Underfull \hbox (badness 10000) in paragraph at lines 3667--3672 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Underfull \hbox (badness 10000) in paragraph at lines 3675--3684 []\T1/ptm/m/n/10 The [1157] [1158] [1159] [1160] [1161] [1162] Underfull \vbox (badness 10000) has occurred while \output is active [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] Underfull \hbox (badness 1436) in paragraph at lines 4580--4583 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4609--4615 []\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4609--4615 \T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1171] [1172] [1173] [1174] [1175] [1176] Underfull \vbox (badness 2452) has occurred while \output is active [1177] [1178] Underfull \vbox (badness 10000) has occurred while \output is active [1179] [1180] Underfull \hbox (badness 1092) in paragraph at lines 5281--5288 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 5281--5288 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and Underfull \hbox (badness 4036) in paragraph at lines 5329--5332 []\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1181] [1182] [1183] [1184] [1185] Underfull \hbox (badness 1087) in paragraph at lines 5649--5654 []\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 [1186] [1187] [1188] [1189] Underfull \hbox (badness 2221) in paragraph at lines 5878--5883 []\T1/ptm/m/n/10 Two op-tional method names are in-ter-preted spe-cially, \T1/z i4/m/n/10 initialize \T1/ptm/m/n/10 and [1190] [1191] [1192] [1193] [1194] Underfull \hbox (badness 1675) in paragraph at lines 6345--6351 \T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1195] [1196] [1197] [1198] Underfull \vbox (badness 10000) has occurred while \output is active [1199] [1200]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4} ) has been already used, duplicate ignored <to be read again> \relax l.6828 \aliasA{S4}{S3Part}{S4} [1201] [1202] [1203] [1204]pdfTeX warning (ext4) : destination with the same identifier (name{Rfn.Complex}) has been already use d, duplicate ignored <to be read again> \relax l.7096 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored <to be read again> \relax l.7098 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red <to be read again> \relax l.7099 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored <to be read again> \relax l.7101 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed <to be read again> \relax l.7102 \aliasA{Summary}{S4groupGeneric}{Summary} [1205] Underfull \hbox (badness 2050) in paragraph at lines 7163--7167 []\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 [1206] [1207] [1208] Underfull \hbox (badness 1286) in paragraph at lines 7348--7350 []\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] Underfull \hbox (badness 1852) in paragraph at lines 9765--9769 []\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., [1243] [1244] [1245] [1246]) (./parallel-pkg.tex Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 15--17 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4 /m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] Underfull \hbox (badness 3386) in paragraph at lines 1254--1257 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1267] [1268]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 <bates@stat.wisc.edu> \T1/ptm/ m/n/10 and William N. Ven-ables [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283]) (./stats-pkg.tex [1284] Chapter 10. [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] Underfull \hbox (badness 1412) in paragraph at lines 846--848 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] Underfull \hbox (badness 2503) in paragraph at lines 1327--1330 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1306] [1307] [1308] Underfull \hbox (badness 10000) in paragraph at lines 1506--1510 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] Underfull \hbox (badness 3965) in paragraph at lines 2166--2168 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1320] [1321] [1322] [1323] [1324] Underfull \hbox (badness 3965) in paragraph at lines 2508--2510 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] Underfull \hbox (badness 2503) in paragraph at lines 3325--3328 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] Underfull \hbox (badness 3989) in paragraph at lines 4553--4560 []\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 = [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] Underfull \hbox (badness 2556) in paragraph at lines 5164--5167 []\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/ ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p tm/m/n/10 . For Underfull \hbox (badness 2932) in paragraph at lines 5181--5183 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is given by [1368] [1369] [1370] [1371] Underfull \hbox (badness 1142) in paragraph at lines 5422--5434 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1372] [1373] Underfull \hbox (badness 2503) in paragraph at lines 5561--5565 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1374] Underfull \hbox (badness 1168) in paragraph at lines 5622--5627 []\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and [1375] [1376] [1377] [1378] [1379] [1380] [1381] Underfull \hbox (badness 8132) in paragraph at lines 6064--6069 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1382] [1383] [1384] [1385] [1386] Underfull \hbox (badness 7081) in paragraph at lines 6342--6345 []\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6346--6348 []\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1387] [1388] [1389] [1390] [1391] Underfull \vbox (badness 3803) has occurred while \output is active [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] Underfull \hbox (badness 10000) in paragraph at lines 7159--7162 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1400] [1401] Underfull \hbox (badness 10000) in paragraph at lines 7296--7299 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/zi4/m/n/10 ht tps : / / cran . r-[]project . org / web / views / [1402] [1403] [1404] [1405] Underfull \vbox (badness 3803) has occurred while \output is active [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] Underfull \hbox (badness 2626) in paragraph at lines 8794--8797 []\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1427] Underfull \hbox (badness 2503) in paragraph at lines 8894--8898 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1428] [1429] [1430] [1431] [1432] Overfull \hbox (6.88992pt too wide) in paragraph at lines 9228--9230 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] Underfull \hbox (badness 4518) in paragraph at lines 10155--10160 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1448] [1449] [1450] [1451] Underfull \hbox (badness 2142) in paragraph at lines 10497--10500 []\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 ^^@ [1452] Underfull \hbox (badness 1253) in paragraph at lines 10516--10519 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1453] Underfull \hbox (badness 1708) in paragraph at lines 10578--10582 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1454] [1455] [1456] [1457] [1458] [1459] Underfull \hbox (badness 1694) in paragraph at lines 10974--10977 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1867) in paragraph at lines 10993--11002 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 10000) in paragraph at lines 11300--11303 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1465] [1466] [1467]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored <to be read again> \relax l.11454 \aliasA{hat}{influence.measures}{hat} [1468] [1469] Underfull \hbox (badness 1484) in paragraph at lines 11577--11579 []\T1/ptm/m/n/10 The func-tion \T1/zi4/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 [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] Underfull \hbox (badness 4441) in paragraph at lines 12135--12137 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12142--12144 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1479] [1480] [1481] [1482] [1483] [1484] Underfull \hbox (badness 2894) in paragraph at lines 12476--12480 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1485] [1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494] [1495] [1496] Underfull \hbox (badness 4518) in paragraph at lines 13171--13176 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] Underfull \hbox (badness 4518) in paragraph at lines 13818--13823 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1506] [1507] [1508] Underfull \hbox (badness 10000) in paragraph at lines 13956--13960 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 13963--13965 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] [1523] [1524] [1525] Underfull \hbox (badness 2503) in paragraph at lines 15025--15029 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] Underfull \hbox (badness 1418) in paragraph at lines 15534--15540 []\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1 /ptm/m/n/10 and [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] Underfull \hbox (badness 2359) in paragraph at lines 17158--17160 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1560] [1561] Underfull \vbox (badness 10000) has occurred while \output is active [1562] Underfull \vbox (badness 10000) has occurred while \output is active [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] Underfull \hbox (badness 1377) in paragraph at lines 18069--18074 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) in paragraph at lines 18074--18077 []\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 1184) in paragraph at lines 18087--18091 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18095--18099 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1576] [1577] [1578] Underfull \vbox (badness 10000) has occurred while \output is active [1579] [1580] [1581] [1582] [1583] [1584] [1585] Underfull \hbox (badness 1337) in paragraph at lines 18711--18714 []\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 [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] Underfull \hbox (badness 5563) in paragraph at lines 19441--19443 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19444--19447 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1599] [1600] [1601] [1602] [1603] [1604] Underfull \hbox (badness 2503) in paragraph at lines 19811--19814 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1605] Underfull \hbox (badness 10000) in paragraph at lines 19838--19840 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] Underfull \hbox (badness 10000) in paragraph at lines 20863--20869 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] Underfull \hbox (badness 1337) in paragraph at lines 22198--22204 []\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 [1645] [1646] [1647] [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] Underfull \hbox (badness 10000) in paragraph at lines 22991--22994 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] Underfull \hbox (badness 10000) in paragraph at lines 23568--23571 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1667] Underfull \hbox (badness 3690) in paragraph at lines 23619--23623 [][][]\T1/zi4/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 [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] Underfull \hbox (badness 3439) in paragraph at lines 24089--24095 [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1 0 , [1676] [1677] [1678] Underfull \hbox (badness 1867) in paragraph at lines 24286--24288 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to [1679] Underfull \hbox (badness 10000) in paragraph at lines 24299--24301 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and [1680] [1681] [1682] [1683] [1684] [1685] [1686] Underfull \hbox (badness 10000) in paragraph at lines 24757--24762 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1687] [1688] [1689] Underfull \vbox (badness 3803) has occurred while \output is active [1690] [1691] [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] Underfull \vbox (badness 10000) has occurred while \output is active [1702] Underfull \hbox (badness 3514) in paragraph at lines 25775--25780 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1703] Underfull \hbox (badness 3514) in paragraph at lines 25837--25842 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1704] Underfull \hbox (badness 3514) in paragraph at lines 25894--25899 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1705] Underfull \hbox (badness 3514) in paragraph at lines 25955--25961 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1706] [1707] [1708] [1709] Underfull \hbox (badness 3514) in paragraph at lines 26168--26173 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1710] Underfull \hbox (badness 3514) in paragraph at lines 26224--26229 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1711] Underfull \hbox (badness 3514) in paragraph at lines 26281--26286 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1712] Underfull \hbox (badness 3514) in paragraph at lines 26336--26341 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1713] Underfull \hbox (badness 6691) in paragraph at lines 26405--26410 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] [1722] Underfull \hbox (badness 10000) in paragraph at lines 26929--26932 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 26929--26932 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732] Underfull \hbox (badness 5431) in paragraph at lines 27535--27537 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1733] [1734] [1735] Underfull \hbox (badness 5431) in paragraph at lines 27745--27748 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1736] [1737] [1738] [1739] [1740] [1741] Underfull \hbox (badness 1337) in paragraph at lines 28057--28061 []\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 [1742] [1743] Underfull \hbox (badness 10000) in paragraph at lines 28174--28177 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1744] [1745] Underfull \hbox (badness 1616) in paragraph at lines 28357--28360 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1746] [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] [1763] [1764] Underfull \hbox (badness 10000) in paragraph at lines 29483--29487 []\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect [1765] [1766] [1767] Underfull \vbox (badness 10000) has occurred while \output is active [1768] [1769] [1770] Underfull \hbox (badness 1337) in paragraph at lines 29847--29851 []\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 [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] Underfull \hbox (badness 1337) in paragraph at lines 30331--30335 []\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 [1779] Underfull \hbox (badness 5161) in paragraph at lines 30424--30426 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1780] [1781] [1782] [1783] [1784] [1785] Underfull \hbox (badness 10000) in paragraph at lines 30788--30793 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1786] [1787] [1788]) (./stats4-pkg.tex Chapter 11. [1789] [1790] [1791] [1792] [1793] [1794]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored <to be read again> \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1795] [1796] [1797] [1798]) (./tcltk-pkg.tex Chapter 12. [1799] [1800] [1801] [1802] [1803] [1804] [1805] Underfull \vbox (badness 10000) has occurred while \output is active [1806] Underfull \vbox (badness 10000) has occurred while \output is active [1807] Underfull \hbox (badness 1546) in paragraph at lines 664--671 []\T1/zi4/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 [1808] [1809] [1810] [1811] [1812] [1813] [1814] [1815] [1816] [1817] [1818] Underfull \hbox (badness 3375) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the OS X GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh ose [1819]) (./tools-pkg.tex [1820] Chapter 13. [1821] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1822] Underfull \hbox (badness 3039) in paragraph at lines 164--167 []\T1/zi4/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 [1823] [1824] Underfull \hbox (badness 1308) 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 types Underfull \hbox (badness 4967) in paragraph at lines 285--298 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1825] [1826] Underfull \hbox (badness 3039) in paragraph at lines 389--391 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] [1835] [1836] [1837] Underfull \hbox (badness 1635) in paragraph at lines 1050--1052 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1838] Underfull \hbox (badness 4441) in paragraph at lines 1126--1136 \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- [1839] Underfull \hbox (badness 1014) in paragraph at lines 1148--1150 []\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 1154--1156 []\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 1185--1188 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1185--1188 \T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1840] [1841] [1842] Underfull \hbox (badness 10000) in paragraph at lines 1348--1350 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1843] [1844] [1845] Underfull \hbox (badness 7981) in paragraph at lines 1518--1523 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 1082) in paragraph at lines 1525--1527 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1846] [1847] [1848] [1849]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored <to be read again> \relax l.1722 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1850] Underfull \hbox (badness 1137) in paragraph at lines 1807--1809 []\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 Underfull \hbox (badness 5726) in paragraph at lines 1836--1841 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/n/10 De pendsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 1836--1841 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1851] [1852] [1853] [1854] [1855] [1856] Overfull \hbox (17.88089pt too wide) in paragraph at lines 2173--2173 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1857] [1858] [1859] [1860] Underfull \hbox (badness 7981) in paragraph at lines 2376--2382 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1861] [1862] [1863] [1864] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2660. [1865] [1866] [1867] [1868] Underfull \hbox (badness 1424) in paragraph at lines 2942--2944 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1869] [1870] [1871] [1872] [1873] [1874] [1875] [1876] [1877] [1878] [1879] [1880] Underfull \hbox (badness 10000) in paragraph at lines 3638--3640 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1881] [1882] Underfull \hbox (badness 10000) in paragraph at lines 3777--3780 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1883] [1884] [1885] [1886] Underfull \hbox (badness 1838) in paragraph at lines 4037--4043 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4037--4043 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1887] [1888] Underfull \hbox (badness 5726) in paragraph at lines 4117--4122 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4117--4122 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1889] [1890] Underfull \hbox (badness 1688) in paragraph at lines 4260--4272 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/zi4/m/sl/10 PACKAGES\T1/ptm/m/n/10 ' and [1891] [1892] [1893] [1894]) (./utils-pkg.tex Chapter 14. [1895] Underfull \hbox (badness 2556) 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/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1896] [1897] Underfull \hbox (badness 1454) in paragraph at lines 197--200 []\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive , \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 by de- Underfull \hbox (badness 1540) in paragraph at lines 213--216 []\T1/zi4/m/sl/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for the same task as \T1/zi4/m/sl/10 apropos\T1/ptm/m/n/10 . How-ever, by de-fault [1898] [1899] [1900] [1901] [1902] [1903] Underfull \hbox (badness 10000) in paragraph at lines 543--549 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 543--549 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1904] Underfull \hbox (badness 5847) in paragraph at lines 657--663 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 657--663 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1905] Underfull \hbox (badness 3861) in paragraph at lines 725--730 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1906] [1907] [1908] [1909] [1910] Underfull \vbox (badness 10000) has occurred while \output is active [1911] [1912] [1913] [1914] [1915] Underfull \hbox (badness 1371) in paragraph at lines 1321--1323 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1916] [1917] [1918] [1919] [1920] [1921] [1922] Underfull \hbox (badness 2057) in paragraph at lines 1807--1809 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1923] [1924] Underfull \hbox (badness 10000) in paragraph at lines 1901--1903 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1925] Underfull \hbox (badness 5189) in paragraph at lines 1991--1993 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1926] [1927] [1928] [1929] Underfull \hbox (badness 1661) in paragraph at lines 2209--2216 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1990) in paragraph at lines 2226--2229 []\T1/ptm/m/n/10 a [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1930] [1931] [1932] [1933] [1934] [1935] Underfull \hbox (badness 10000) in paragraph at lines 2635--2639 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing [1936] Overfull \hbox (64.10922pt too wide) in paragraph at lines 2640--2643 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1937] [1938] [1939] [1940] [1941] [1942] [1943] [1944] Underfull \hbox (badness 1412) in paragraph at lines 3220--3225 []\T1/ptm/m/n/10 The \T1/zi4/m/sl/10 "libcurl" \T1/ptm/m/n/10 and \T1/zi4/m/sl/ 10 "wget" \T1/ptm/m/n/10 meth-ods fol-low `\T1/zi4/m/sl/10 http://\T1/ptm/m/n/1 0 ' and `\T1/zi4/m/sl/10 https://\T1/ptm/m/n/10 ' redi-rec-tions: the [1945] Underfull \hbox (badness 1430) in paragraph at lines 3246--3254 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 1231) in paragraph at lines 3289--3295 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1946] [1947] [1948] [1949] [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] [1958] [1959]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored <to be read again> \relax l.4109 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored <to be read again> \relax l.4109 ...mat Unordered and Ordered Lists}{format} [1960] [1961] [1962] [1963] [1964] [1965] [1966] [1967] [1968] [1969] [1970] [1971] [1972] [1973] [1974] Underfull \hbox (badness 1371) in paragraph at lines 5062--5064 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1975] Underfull \hbox (badness 1502) in paragraph at lines 5151--5156 []\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 5151--5156 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1976] [1977] [1978] Underfull \hbox (badness 10000) in paragraph at lines 5324--5333 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [1979] Underfull \hbox (badness 2150) in paragraph at lines 5387--5390 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [1980] [1981] Underfull \hbox (badness 3118) in paragraph at lines 5524--5526 []\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 [1982] Underfull \hbox (badness 2409) in paragraph at lines 5557--5561 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [1983] Underfull \hbox (badness 1325) in paragraph at lines 5665--5669 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [1984] Underfull \hbox (badness 10000) in paragraph at lines 5748--5751 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 5748--5751 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [1985] Underfull \hbox (badness 3219) in paragraph at lines 5821--5828 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 5821--5828 \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 5821--5828 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [1986] Underfull \hbox (badness 10000) in paragraph at lines 5901--5906 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] Underfull \hbox (badness 10000) in paragraph at lines 7203--7205 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7208--7213 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2008] [2009] [2010] [2011] [2012] [2013] [2014] [2015] [2016] Underfull \hbox (badness 1789) in paragraph at lines 7758--7760 []\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 [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] Underfull \hbox (badness 1097) in paragraph at lines 8583--8586 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2030] Underfull \hbox (badness 3000) in paragraph at lines 8719--8724 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] Underfull \hbox (badness 2134) in paragraph at lines 9302--9307 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2040] [2041] [2042] [2043] [2044] [2045] [2046] Underfull \hbox (badness 5077) in paragraph at lines 9727--9731 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 9727--9731 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 9739--9743 []\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia , The Free En-cy-clo-pe-dia. Underfull \hbox (badness 3428) in paragraph at lines 9739--9743 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2047] [2048] [2049] [2050] [2051] [2052] Underfull \hbox (badness 10000) in paragraph at lines 10093--10095 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][] []\T1/ptm/m/n/10 s are nicely viewed via [2053] [2054] [2055] Underfull \hbox (badness 2150) in paragraph at lines 10269--10271 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2056] [2057] [2058] Underfull \hbox (badness 10000) in paragraph at lines 10447--10451 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 10478--10484 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2059] [2060] Underfull \hbox (badness 2096) in paragraph at lines 10596--10599 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 10600--10603 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether JPEG fig-ures should be gen-er-ated. Ig-nored if [2061] Underfull \hbox (badness 1009) in paragraph at lines 10666--10677 []\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 [2062] [2063] [2064] [2065] [2066] Underfull \hbox (badness 3780) in paragraph at lines 10965--10969 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 10981--10984 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2067] [2068] [2069] [2070] [2071] [2072] Underfull \hbox (badness 5970) in paragraph at lines 11350--11353 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2073] [2074] [2075] Underfull \hbox (badness 10000) in paragraph at lines 11529--11531 []\T1/ptm/m/n/10 Options other than \T1/zi4/m/sl/10 memory = "none" \T1/ptm/m/n /10 ap-ply only to files pro-duced by [2076] [2077] [2078] [2079] [2080] [2081] Underfull \hbox (badness 10000) in paragraph at lines 11930--11933 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 11930--11933 \T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2082] [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] Underfull \hbox (badness 10000) in paragraph at lines 12460--12462 []\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 1052) in paragraph at lines 12463--12465 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. 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Transcript written on refman.log. This is makeindex, version 2.15 [TeX Live 2015] (kpathsea + Thai support). Scanning input file refman.idx.................done (13047 entries accepted, 33 rejected). Sorting entries.......................................................................................................................................done (197084 comparisons). Generating output file refman.ind................done (12956 lines written, 50 warnings). Output written in refman.ind. Transcript written in refman.ilg. This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2016/02/01> Babel <3.9q> and hyphenation patterns for 3 language(s) loaded. 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Underfull \hbox (badness 4595) in paragraph at lines 40--43 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [1] [2] Underfull \hbox (badness 1960) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is 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 [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 296--300 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 381--384 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? 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I t is guar-an-teed that [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.88089pt too wide) in paragraph at lines 1894--1894 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2079--2081 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3580--3582 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] Underfull \hbox (badness 2521) in paragraph at lines 4782--4784 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] Overfull \hbox (7.0809pt too wide) in paragraph at lines 5909--5909 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [93] [94] [95] Underfull \hbox (badness 2096) in paragraph at lines 6090--6103 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [96] [97] [98] Overfull \hbox (58.35893pt too wide) in paragraph at lines 6293--6295 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [99] [100] Underfull \hbox (badness 10000) in paragraph at lines 6434--6437 []\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is [101] [102] Underfull \hbox (badness 1442) in paragraph at lines 6599--6605 []\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/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6599--6605 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6599--6605 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [103] Underfull \hbox (badness 3568) in paragraph at lines 6660--6667 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [104] [105] Underfull \vbox (badness 10000) has occurred while \output is active [106] [107] [108] [109] [110] [111] [112] [113] Underfull \hbox (badness 2096) in paragraph at lines 7298--7302 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [114] Underfull \hbox (badness 4595) in paragraph at lines 7355--7358 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [115] Underfull \hbox (badness 3000) in paragraph at lines 7391--7393 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7416--7419 [][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [116] [117] [118] [119] Underfull \hbox (badness 10000) in paragraph at lines 7671--7682 []\T1/zi4/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 [120] [121] Underfull \hbox (badness 4479) in paragraph at lines 7743--7752 [][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), Underfull \hbox (badness 2469) in paragraph at lines 7743--7752 [][]\T1/zi4/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods, [][]\T1/zi4/m/n/10 Math.data.frame[][][] \T1/ptm/m/n/10 etc, about \T1/ptm/m/i t/10 Group \T1/ptm/m/n/10 meth-ods for [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] Underfull \hbox (badness 1394) in paragraph at lines 9355--9360 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [146] [147] [148] [149] [150] Underfull \hbox (badness 1052) in paragraph at lines 9698--9703 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 9698--9703 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [151] [152] Underfull \hbox (badness 1735) in paragraph at lines 9836--9840 \T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ zi4/m/n/10 https : / / en . wikipedia . [153] [154] [155] [156] [157] [158] Underfull \hbox (badness 2150) in paragraph at lines 10240--10243 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse [159] Underfull \hbox (badness 6396) in paragraph at lines 10254--10262 []\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 2409) in paragraph at lines 10295--10302 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] Underfull \hbox (badness 4569) in paragraph at lines 11341--11345 []\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 11341--11345 \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 [176] [177] [178] [179] [180] [181] [182] [183] Underfull \hbox (badness 2698) in paragraph at lines 11917--11926 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 11917--11926 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] Underfull \hbox (badness 6236) in paragraph at lines 12561--12564 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [194] [195] [196] [197] [198] [199] Underfull \hbox (badness 2253) in paragraph at lines 12939--12941 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [200] Underfull \hbox (badness 1565) in paragraph at lines 13010--13014 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and [201] Underfull \hbox (badness 10000) in paragraph at lines 13054--13056 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with [202] [203] Underfull \hbox (badness 1466) in paragraph at lines 13195--13198 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ zi4/m/n/10 file.copy \T1/ptm/m/n/10 and [204] [205] Underfull \hbox (badness 10000) in paragraph at lines 13303--13307 [][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13314--13317 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [206] [207] [208] [209] Underfull \hbox (badness 3965) in paragraph at lines 13577--13581 []\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, [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] Underfull \hbox (badness 4429) in paragraph at lines 14338--14341 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [222] Underfull \hbox (badness 10000) in paragraph at lines 14430--14432 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14436--14440 []\T1/zi4/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 [223] Underfull \hbox (badness 10000) in paragraph at lines 14478--14482 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 14478--14482 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [224] Underfull \vbox (badness 3803) has occurred while \output is active [225] [226] [227] [228] [229] [230] [231] [232] Underfull \hbox (badness 2452) in paragraph at lines 15058--15062 []\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 15058--15062 \T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_ WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and [233] [234] [235] Underfull \hbox (badness 1092) in paragraph at lines 15231--15236 [][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [236] [237] [238] [239] Underfull \hbox (badness 6741) in paragraph at lines 15479--15483 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [240] [241] [242] [243] Underfull \hbox (badness 1867) in paragraph at lines 15785--15792 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [244] [245] [246] [247] Underfull \vbox (badness 10000) has occurred while \output is active [248] [249] Underfull \hbox (badness 3679) in paragraph at lines 16166--16168 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [250] [251] [252] [253] [254] [255] [256] [257] Underfull \hbox (badness 1478) in paragraph at lines 16711--16714 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [258] [259] [260] [261] Underfull \hbox (badness 10000) in paragraph at lines 16964--16966 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [262] [263] [264] [265] [266] [267] [268] [269] [270] Underfull \hbox (badness 1442) in paragraph at lines 17527--17529 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [271] Underfull \hbox (badness 2452) in paragraph at lines 17619--17635 [][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [272] [273] [274] [275] [276] [277] [278] Underfull \hbox (badness 1248) in paragraph at lines 18033--18036 []\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/ m/n/10 , [279] [280] [281] [282] Underfull \hbox (badness 4739) in paragraph at lines 18291--18293 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] Underfull \hbox (badness 1360) in paragraph at lines 19249--19254 \T1/zi4/m/n/10 "none"\T1/ptm/m/n/10 . It is in-tended for the ver-sion of OpenS SL used, but not all Underfull \hbox (badness 10000) in paragraph at lines 19272--19278 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / Underfull \hbox (badness 1127) in paragraph at lines 19272--19278 \T1/zi4/m/n/10 ssl-[]compared . html$[][] \T1/ptm/m/n/10 for more de-tails on S SL ver-sions. Nor-mally \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 used with \T1/phv /m/n/10 R [299] Underfull \hbox (badness 10000) in paragraph at lines 19345--19349 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 19345--19349 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [300] [301] Underfull \hbox (badness 1509) in paragraph at lines 19480--19487 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1354) in paragraph at lines 19480--19487 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19496--19501 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313] Underfull \hbox (badness 1264) in paragraph at lines 20227--20232 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] Underfull \hbox (badness 10000) in paragraph at lines 20981--20983 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] Underfull \hbox (badness 1077) in paragraph at lines 21979--21985 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [341] [342] [343] Underfull \hbox (badness 1484) in paragraph at lines 22140--22148 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [344] [345] [346] [347] Underfull \hbox (badness 2790) in paragraph at lines 22411--22414 []\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 22411--22414 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [348] [349] [350] [351] Underfull \hbox (badness 1194) in paragraph at lines 22692--22695 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 . It calls [352] [353] [354] [355] Underfull \hbox (badness 10000) in paragraph at lines 22898--22904 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 5862) in paragraph at lines 22898--22904 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 22908--22911 []\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 22908--22911 \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 [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] [367] [368] [369] Underfull \hbox (badness 10000) in paragraph at lines 23839--23841 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [370] [371] [372] [373] Underfull \hbox (badness 1199) in paragraph at lines 24066--24072 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24066--24072 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [374] [375] [376] [377] [378] [379] [380] [381] Underfull \hbox (badness 1038) in paragraph at lines 24645--24653 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 1881) in paragraph at lines 24654--24657 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 24673--24675 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [382] Underfull \hbox (badness 10000) in paragraph at lines 24745--24755 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 24756--24762 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able Underfull \hbox (badness 1968) in paragraph at lines 24769--24774 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 24779--24781 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [383] [384] Underfull \vbox (badness 10000) has occurred while \output is active [385] Underfull \hbox (badness 10000) in paragraph at lines 25034--25040 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/zi4/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25034--25040 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 25034--25040 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by [386] Underfull \hbox (badness 10000) in paragraph at lines 25047--25050 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 25071--25073 []\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 25103--25108 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 25109--25120 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 25121--25124 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and [387] Underfull \hbox (badness 4084) in paragraph at lines 25131--25143 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN OS X build), Underfull \hbox (badness 10000) in paragraph at lines 25131--25143 \T1/zi4/m/n/10 "mac.binary."\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.maveric ks" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for C RAN Underfull \hbox (badness 7397) in paragraph at lines 25131--25143 \T1/ptm/m/n/10 OS X builds). Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m /n/10 . (\T1/zi4/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 25145--25152 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 25145--25152 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 25145--25152 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1082) in paragraph at lines 25145--25152 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [388] [389] [390] [391] [392] Underfull \hbox (badness 10000) in paragraph at lines 25491--25495 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 25491--25495 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [393] [394] [395] [396] [397] Underfull \hbox (badness 1735) in paragraph at lines 25809--25813 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [398] [399] [400] [401] [402] [403] [404] [405] [406] Underfull \hbox (badness 2726) in paragraph at lines 26369--26372 []\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] [418] [419] Underfull \hbox (badness 1052) in paragraph at lines 27186--27191 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [420] [421] [422] [423] [424] Underfull \vbox (badness 10000) has occurred while \output is active [425] [426] [427] [428] [429] [430] [431] Underfull \hbox (badness 1533) in paragraph at lines 27995--27998 []\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 [432] [433] [434] Underfull \hbox (badness 1163) in paragraph at lines 28157--28168 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] Underfull \hbox (badness 10000) in paragraph at lines 29676--29680 []\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 29676--29680 \T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. Underfull \hbox (badness 6188) in paragraph at lines 29698--29700 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [459] [460] [461] [462] [463] [464] [465] [466] [467] Underfull \hbox (badness 1655) in paragraph at lines 30246--30248 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm /m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for [468] [469] [470] [471] [472] [473] [474] [475] [476] [477] [478] Underfull \hbox (badness 10000) in paragraph at lines 30914--30918 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [479] [480] [481] Underfull \hbox (badness 2302) in paragraph at lines 31154--31161 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 31154--31161 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 2980) in paragraph at lines 31154--31161 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 31154--31161 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [482] [483] [484] Underfull \hbox (badness 2261) in paragraph at lines 31310--31315 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if Underfull \hbox (badness 10000) in paragraph at lines 31337--31343 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [485] Underfull \hbox (badness 10000) in paragraph at lines 31413--31418 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [486] [487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] Underfull \hbox (badness 1072) in paragraph at lines 34333--34337 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 34338--34342 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 34366--34372 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 34366--34372 \T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 34366--34372 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in Underfull \hbox (badness 3343) in paragraph at lines 34379--34386 \T1/ptm/m/n/10 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 34379--34386 \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 Underfull \hbox (badness 1917) in paragraph at lines 34379--34386 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [532] [533] [534] [535] [536] Underfull \hbox (badness 10000) in paragraph at lines 34670--34676 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1152) in paragraph at lines 34670--34676 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] Underfull \hbox (badness 3333) in paragraph at lines 36500--36505 []\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] Underfull \hbox (badness 1472) in paragraph at lines 37120--37123 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [576] [577] [578] [579] [580] [581] [582] [583] [584] [585] [586] Underfull \hbox (badness 2671) in paragraph at lines 37785--37788 []\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/zi4/m/n/10 ...\T1/pt m/m/n/10 . If set to \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies [587] [588] [589] [590] [591] [592] Underfull \hbox (badness 10000) in paragraph at lines 38200--38203 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [593] [594] Underfull \hbox (badness 10000) in paragraph at lines 38318--38322 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [595] Underfull \hbox (badness 10000) in paragraph at lines 38380--38384 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614] [615] Underfull \hbox (badness 1990) in paragraph at lines 39706--39714 []\T1/zi4/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 4846) in paragraph at lines 39706--39714 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [616] [617] [618] [619] Underfull \hbox (badness 1515) in paragraph at lines 39978--39983 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0 [620] [621] [622] [623] Underfull \hbox (badness 1917) in paragraph at lines 40208--40215 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [624] [625] [626] [627] [628] [629] [630] [631] [632] [633] Underfull \hbox (badness 3668) in paragraph at lines 40869--40871 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [634] [635] Underfull \hbox (badness 2401) in paragraph at lines 40974--40978 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [636] [637] Underfull \hbox (badness 2111) in paragraph at lines 41143--41148 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. [638] Underfull \hbox (badness 6542) in paragraph at lines 41159--41164 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [639] [640] [641] [642] [643] [644] [645] Underfull \hbox (badness 10000) in paragraph at lines 41604--41609 []\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu nc-tion than [][]\T1/zi4/m/n/10 rank[][][] Underfull \hbox (badness 10000) in paragraph at lines 41604--41609 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to [646] Underfull \hbox (badness 5417) in paragraph at lines 41696--41700 []\T1/zi4/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 [647] Underfull \hbox (badness 10000) in paragraph at lines 41757--41761 []\T1/zi4/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 [648] [649]) (./compiler-pkg.tex [650] Chapter 2. [651] [652] [653] [654]) (./datasets-pkg.tex Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple te list, use [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] Underfull \vbox (badness 1515) has occurred while \output is active [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] Underfull \hbox (badness 6658) in paragraph at lines 3940--3942 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h ttp : / / www . ltrr . arizona . edu / ~hallman / [722] Underfull \vbox (badness 10000) has occurred while \output is active [723] [724] [725] [726] Underfull \vbox (badness 10000) has occurred while \output is active [727] Underfull \vbox (badness 10000) has occurred while \output is active [728] [729] [730] [731] [732] [733] [734] [735]) (./grDevices-pkg.tex [736] Chapter 4. [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] Underfull \hbox (badness 5175) in paragraph at lines 1071--1073 []\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 [754] [755] [756] [757] Underfull \hbox (badness 1852) in paragraph at lines 1268--1271 []\T1/zi4/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 [758] [759] [760] Underfull \hbox (badness 1490) in paragraph at lines 1474--1479 \T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and [761] Underfull \hbox (badness 2698) in paragraph at lines 1528--1531 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture, oth-er-wise a ma-trix of color names (for [762] Underfull \hbox (badness 10000) in paragraph at lines 1597--1601 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [763] [764] [765] [766] Underfull \hbox (badness 1325) in paragraph at lines 1880--1890 \T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/ 10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1 /ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 , [767] [768] Underfull \hbox (badness 10000) in paragraph at lines 1985--1987 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [769] [770] [771] Underfull \hbox (badness 6758) in paragraph at lines 2146--2149 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [772] [773] [774] [775] [776] [777] [778] [779] [780] Underfull \hbox (badness 10000) in paragraph at lines 2712--2713 [781] [782] [783] [784] [785] [786] [787] Underfull \hbox (badness 1152) in paragraph at lines 3150--3152 []\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/zi4/m/n/10 nr, nc \T1/ptm/m /n/10 giv-ing the num-ber of rows and columns, ful-fill-ing [788] [789] [790] [791] [792] Underfull \hbox (badness 2856) in paragraph at lines 3470--3473 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3484--3486 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [793] [794] Underfull \hbox (badness 1173) in paragraph at lines 3600--3610 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 paper \T1/ptm/m/n/10 ar-gu-ment sets the `\ T1/zi4/m/n/10 /MediaBox\T1/ptm/m/n/10 ' en-try in the file, which de-faults to \T1/zi4/m/n/10 width \T1/ptm/m/n/10 by [795] [796] [797] [798] [799] [800] [801] [802] [803] [804] [805] Underfull \hbox (badness 1067) in paragraph at lines 4307--4314 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [806] [807] Underfull \hbox (badness 3364) in paragraph at lines 4468--4470 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$ \T1/zi4/m/n/10 https : / / partners . adobe . com / public / [808] Underfull \hbox (badness 1789) in paragraph at lines 4545--4547 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [809] Underfull \hbox (badness 1377) in paragraph at lines 4595--4600 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [810] Underfull \hbox (badness 2671) in paragraph at lines 4622--4630 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4671--4678 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4679--4688 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4679--4688 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4689--4691 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [811] [812] Underfull \hbox (badness 1057) in paragraph at lines 4800--4805 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/zi4/m/n/10 "rgb"\T1/ptm/m/n/10 ) (which is RGB+gray) and [813] Underfull \hbox (badness 7344) in paragraph at lines 4860--4862 []\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 [814] [815] Underfull \hbox (badness 2035) in paragraph at lines 4984--4993 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 10000) in paragraph at lines 4984--4993 \T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 4984--4993 \T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [816] Underfull \hbox (badness 10000) in paragraph at lines 5053--5060 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5053--5060 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [817] [818] [819] Underfull \hbox (badness 1546) in paragraph at lines 5195--5203 []\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/ n/10 , [820] Underfull \hbox (badness 1648) in paragraph at lines 5272--5276 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [821] [822] [823] [824] [825] [826] [827] Underfull \hbox (badness 10000) in paragraph at lines 5724--5727 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [828] [829] [830] [831] [832] [833] Underfull \hbox (badness 1189) in paragraph at lines 6121--6123 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [834] [835] Underfull \hbox (badness 10000) in paragraph at lines 6219--6221 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [836] [837] [838] [839] Underfull \hbox (badness 3780) in paragraph at lines 6510--6516 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [840] [841] [842] Underfull \hbox (badness 2680) in paragraph at lines 6706--6708 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [843] [844] [845]) (./graphics-pkg.tex [846] Chapter 5. [847] [848] [849] [850] [851] [852] [853] [854] [855] [856] [857] Underfull \hbox (badness 10000) in paragraph at lines 683--690 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [858] [859] [860] [861] Underfull \vbox (badness 3803) has occurred while \output is active [862] [863] [864] [865] [866] Underfull \hbox (badness 4634) in paragraph at lines 1246--1249 [][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [867] [868] [869] [870] [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] [883] Underfull \hbox (badness 1009) in paragraph at lines 2280--2287 \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 [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] Underfull \vbox (badness 10000) has occurred while \output is active [906] Underfull \vbox (badness 10000) has occurred while \output is active [907] [908] [909] [910] Underfull \hbox (badness 1867) in paragraph at lines 3912--3916 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [911] [912] [913] [914] [915] [916] [917] Underfull \hbox (badness 1924) in paragraph at lines 4359--4364 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain [918] Underfull \hbox (badness 2529) in paragraph at lines 4390--4393 []\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 [919] [920] [921] [922] [923] Underfull \hbox (badness 10000) in paragraph at lines 4740--4746 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4740--4746 \T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that [924] Underfull \hbox (badness 10000) in paragraph at lines 4871--4874 [925] </«PKGBUILDDIR»/library/graphics/help/figures/mai.pdf, id=22 376, 289.08pt x 289.08pt> <use /«PKGBUILDDIR»/library/graphics/help/figures/mai.pdf> [926 </«PKGBUILDDIR»/library/graphics/help/figures/mai.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 4932--4934 </«PKGBUILDDIR»/library/graphics/help/figures/oma.pdf, id=22 389, 259.97125pt x 332.24126pt> <use /«PKGBUILDDIR»/library/graphics/help/figures/oma.pdf> [927 </«PKGBUILDDIR»/library/graphics/help/figures/oma.pdf>] [928] Underfull \hbox (badness 10000) in paragraph at lines 5122--5124 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [929] [930] [931] [932] [933] Underfull \vbox (badness 10000) has occurred while \output is active [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] </«PKGBUILDDIR»/library/graphics/help/figures/pch.pdf, id=22 807, 361.35pt x 50.1875pt> <use /«PKGBUILDDIR»/library/graphics/help/figures/pch.pdf> Overfull \hbox (31.57222pt too wide) in paragraph at lines 6592--6593 [][] [953 </«PKGBUILDDIR»/library/graphics/help/figures/pch.pdf>] [954] Underfull \vbox (badness 10000) has occurred while \output is active [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] Underfull \hbox (badness 1048) in paragraph at lines 7301--7306 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [965] Underfull \hbox (badness 1038) in paragraph at lines 7417--7420 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [966] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] Underfull \hbox (badness 10000) in paragraph at lines 8653--8655 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8655--8657 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [988]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored <to be read again> \relax l.8735 \HeaderA{units}{Graphical Units}{units} [989] [990] [991] [992]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [993] [994] [995] [996] [997] [998] Underfull \hbox (badness 2680) in paragraph at lines 390--393 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] Underfull \hbox (badness 4279) in paragraph at lines 970--979 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] Underfull \vbox (badness 3803) has occurred while \output is active [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] Underfull \hbox (badness 1067) in paragraph at lines 4340--4343 []\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 [1066] [1067] [1068] [1069] Underfull \hbox (badness 7256) in paragraph at lines 4583--4585 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] Underfull \hbox (badness 10000) in paragraph at lines 5860--5866 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] Underfull \hbox (badness 7649) in paragraph at lines 6334--6337 []\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 [1100] [1101] [1102] [1103]) (./methods-pkg.tex [1104] Chapter 7. [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] Underfull \hbox (badness 2237) in paragraph at lines 1454--1456 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1125] [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] Underfull \hbox (badness 10000) in paragraph at lines 2050--2055 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 2050--2055 \T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] Underfull \hbox (badness 10000) in paragraph at lines 2655--2658 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1142] [1143] Underfull \hbox (badness 1132) in paragraph at lines 2795--2799 []\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in [1144] Underfull \hbox (badness 1033) in paragraph at lines 2827--2832 \T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1145] [1146] [1147] [1148] [1149] [1150] [1151] Underfull \hbox (badness 1102) in paragraph at lines 3339--3341 []\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1152] [1153] [1154] [1155] [1156] Underfull \hbox (badness 10000) in paragraph at lines 3667--3672 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Underfull \hbox (badness 10000) in paragraph at lines 3675--3684 []\T1/ptm/m/n/10 The [1157] [1158] [1159] [1160] [1161] [1162] Underfull \vbox (badness 10000) has occurred while \output is active [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] Underfull \hbox (badness 1436) in paragraph at lines 4580--4583 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4609--4615 []\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4609--4615 \T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1171] [1172] [1173] [1174] [1175] [1176] Underfull \vbox (badness 2452) has occurred while \output is active [1177] [1178] Underfull \vbox (badness 10000) has occurred while \output is active [1179] [1180] Underfull \hbox (badness 1092) in paragraph at lines 5281--5288 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 5281--5288 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and Underfull \hbox (badness 4036) in paragraph at lines 5329--5332 []\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1181] [1182] [1183] [1184] [1185] Underfull \hbox (badness 1087) in paragraph at lines 5649--5654 []\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 [1186] [1187] [1188] [1189] Underfull \hbox (badness 2221) in paragraph at lines 5878--5883 []\T1/ptm/m/n/10 Two op-tional method names are in-ter-preted spe-cially, \T1/z i4/m/n/10 initialize \T1/ptm/m/n/10 and [1190] [1191] [1192] [1193] [1194] Underfull \hbox (badness 1675) in paragraph at lines 6345--6351 \T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1195] [1196] [1197] [1198] Underfull \vbox (badness 10000) has occurred while \output is active [1199] [1200]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4} ) has been already used, duplicate ignored <to be read again> \relax l.6828 \aliasA{S4}{S3Part}{S4} [1201] [1202] [1203] [1204]pdfTeX warning (ext4) : destination with the same identifier (name{Rfn.Complex}) has been already use d, duplicate ignored <to be read again> \relax l.7096 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored <to be read again> \relax l.7098 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red <to be read again> \relax l.7099 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored <to be read again> \relax l.7101 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed <to be read again> \relax l.7102 \aliasA{Summary}{S4groupGeneric}{Summary} [1205] Underfull \hbox (badness 2050) in paragraph at lines 7163--7167 []\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 [1206] [1207] [1208] Underfull \hbox (badness 1286) in paragraph at lines 7348--7350 []\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] Underfull \hbox (badness 1852) in paragraph at lines 9765--9769 []\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., [1243] [1244] [1245] [1246]) (./parallel-pkg.tex Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 15--17 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4 /m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] Underfull \hbox (badness 3386) in paragraph at lines 1254--1257 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1267] [1268]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 <bates@stat.wisc.edu> \T1/ptm/ m/n/10 and William N. Ven-ables [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283]) (./stats-pkg.tex [1284] Chapter 10. [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] Underfull \hbox (badness 1412) in paragraph at lines 846--848 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] Underfull \hbox (badness 2503) in paragraph at lines 1327--1330 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1306] [1307] [1308] Underfull \hbox (badness 10000) in paragraph at lines 1506--1510 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] Underfull \hbox (badness 3965) in paragraph at lines 2166--2168 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1320] [1321] [1322] [1323] [1324] Underfull \hbox (badness 3965) in paragraph at lines 2508--2510 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] Underfull \hbox (badness 2503) in paragraph at lines 3325--3328 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] Underfull \hbox (badness 3989) in paragraph at lines 4553--4560 []\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 = [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] Underfull \hbox (badness 2556) in paragraph at lines 5164--5167 []\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/ ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p tm/m/n/10 . For Underfull \hbox (badness 2932) in paragraph at lines 5181--5183 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is given by [1368] [1369] [1370] [1371] Underfull \hbox (badness 1142) in paragraph at lines 5422--5434 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1372] [1373] Underfull \hbox (badness 2503) in paragraph at lines 5561--5565 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1374] Underfull \hbox (badness 1168) in paragraph at lines 5622--5627 []\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and [1375] [1376] [1377] [1378] [1379] [1380] [1381] Underfull \hbox (badness 8132) in paragraph at lines 6064--6069 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1382] [1383] [1384] [1385] [1386] Underfull \hbox (badness 7081) in paragraph at lines 6342--6345 []\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6346--6348 []\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1387] [1388] [1389] [1390] [1391] Underfull \vbox (badness 3803) has occurred while \output is active [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] Underfull \hbox (badness 10000) in paragraph at lines 7159--7162 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1400] [1401] Underfull \hbox (badness 10000) in paragraph at lines 7296--7299 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/zi4/m/n/10 ht tps : / / cran . r-[]project . org / web / views / [1402] [1403] [1404] [1405] Underfull \vbox (badness 3803) has occurred while \output is active [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] Underfull \hbox (badness 2626) in paragraph at lines 8794--8797 []\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1427] Underfull \hbox (badness 2503) in paragraph at lines 8894--8898 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1428] [1429] [1430] [1431] [1432] Overfull \hbox (6.88992pt too wide) in paragraph at lines 9228--9230 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] Underfull \hbox (badness 4518) in paragraph at lines 10155--10160 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1448] [1449] [1450] [1451] Underfull \hbox (badness 2142) in paragraph at lines 10497--10500 []\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 ^^@ [1452] Underfull \hbox (badness 1253) in paragraph at lines 10516--10519 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1453] Underfull \hbox (badness 1708) in paragraph at lines 10578--10582 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1454] [1455] [1456] [1457] [1458] [1459] Underfull \hbox (badness 1694) in paragraph at lines 10974--10977 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1867) in paragraph at lines 10993--11002 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 10000) in paragraph at lines 11300--11303 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1465] [1466] [1467]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored <to be read again> \relax l.11454 \aliasA{hat}{influence.measures}{hat} [1468] [1469] Underfull \hbox (badness 1484) in paragraph at lines 11577--11579 []\T1/ptm/m/n/10 The func-tion \T1/zi4/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 [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] Underfull \hbox (badness 4441) in paragraph at lines 12135--12137 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12142--12144 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1479] [1480] [1481] [1482] [1483] [1484] Underfull \hbox (badness 2894) in paragraph at lines 12476--12480 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1485] [1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494] [1495] [1496] Underfull \hbox (badness 4518) in paragraph at lines 13171--13176 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] Underfull \hbox (badness 4518) in paragraph at lines 13818--13823 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1506] [1507] [1508] Underfull \hbox (badness 10000) in paragraph at lines 13956--13960 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 13963--13965 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] [1523] [1524] [1525] Underfull \hbox (badness 2503) in paragraph at lines 15025--15029 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] Underfull \hbox (badness 1418) in paragraph at lines 15534--15540 []\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1 /ptm/m/n/10 and [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] Underfull \hbox (badness 2359) in paragraph at lines 17158--17160 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1560] [1561] Underfull \vbox (badness 10000) has occurred while \output is active [1562] Underfull \vbox (badness 10000) has occurred while \output is active [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] Underfull \hbox (badness 1377) in paragraph at lines 18069--18074 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) in paragraph at lines 18074--18077 []\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 1184) in paragraph at lines 18087--18091 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18095--18099 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1576] [1577] [1578] Underfull \vbox (badness 10000) has occurred while \output is active [1579] [1580] [1581] [1582] [1583] [1584] [1585] Underfull \hbox (badness 1337) in paragraph at lines 18711--18714 []\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 [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] Underfull \hbox (badness 5563) in paragraph at lines 19441--19443 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19444--19447 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1599] [1600] [1601] [1602] [1603] [1604] Underfull \hbox (badness 2503) in paragraph at lines 19811--19814 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1605] Underfull \hbox (badness 10000) in paragraph at lines 19838--19840 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] Underfull \hbox (badness 10000) in paragraph at lines 20863--20869 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] Underfull \hbox (badness 1337) in paragraph at lines 22198--22204 []\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 [1645] [1646] [1647] [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] Underfull \hbox (badness 10000) in paragraph at lines 22991--22994 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] Underfull \hbox (badness 10000) in paragraph at lines 23568--23571 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1667] Underfull \hbox (badness 3690) in paragraph at lines 23619--23623 [][][]\T1/zi4/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 [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] Underfull \hbox (badness 3439) in paragraph at lines 24089--24095 [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1 0 , [1676] [1677] [1678] Underfull \hbox (badness 1867) in paragraph at lines 24286--24288 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to [1679] Underfull \hbox (badness 10000) in paragraph at lines 24299--24301 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and [1680] [1681] [1682] [1683] [1684] [1685] [1686] Underfull \hbox (badness 10000) in paragraph at lines 24757--24762 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1687] [1688] [1689] Underfull \vbox (badness 3803) has occurred while \output is active [1690] [1691] [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] Underfull \vbox (badness 10000) has occurred while \output is active [1702] Underfull \hbox (badness 3514) in paragraph at lines 25775--25780 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1703] Underfull \hbox (badness 3514) in paragraph at lines 25837--25842 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1704] Underfull \hbox (badness 3514) in paragraph at lines 25894--25899 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1705] Underfull \hbox (badness 3514) in paragraph at lines 25955--25961 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1706] [1707] [1708] [1709] Underfull \hbox (badness 3514) in paragraph at lines 26168--26173 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1710] Underfull \hbox (badness 3514) in paragraph at lines 26224--26229 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1711] Underfull \hbox (badness 3514) in paragraph at lines 26281--26286 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1712] Underfull \hbox (badness 3514) in paragraph at lines 26336--26341 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1713] Underfull \hbox (badness 6691) in paragraph at lines 26405--26410 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] [1722] Underfull \hbox (badness 10000) in paragraph at lines 26929--26932 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 26929--26932 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732] Underfull \hbox (badness 5431) in paragraph at lines 27535--27537 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1733] [1734] [1735] Underfull \hbox (badness 5431) in paragraph at lines 27745--27748 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1736] [1737] [1738] [1739] [1740] [1741] Underfull \hbox (badness 1337) in paragraph at lines 28057--28061 []\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 [1742] [1743] Underfull \hbox (badness 10000) in paragraph at lines 28174--28177 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1744] [1745] Underfull \hbox (badness 1616) in paragraph at lines 28357--28360 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1746] [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] [1763] [1764] Underfull \hbox (badness 10000) in paragraph at lines 29483--29487 []\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect [1765] [1766] [1767] Underfull \vbox (badness 10000) has occurred while \output is active [1768] [1769] [1770] Underfull \hbox (badness 1337) in paragraph at lines 29847--29851 []\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 [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] Underfull \hbox (badness 1337) in paragraph at lines 30331--30335 []\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 [1779] Underfull \hbox (badness 5161) in paragraph at lines 30424--30426 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1780] [1781] [1782] [1783] [1784] [1785] Underfull \hbox (badness 10000) in paragraph at lines 30788--30793 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1786] [1787] [1788]) (./stats4-pkg.tex Chapter 11. [1789] [1790] [1791] [1792] [1793] [1794]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored <to be read again> \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1795] [1796] [1797] [1798]) (./tcltk-pkg.tex Chapter 12. [1799] [1800] [1801] [1802] [1803] [1804] [1805] Underfull \vbox (badness 10000) has occurred while \output is active [1806] Underfull \vbox (badness 10000) has occurred while \output is active [1807] Underfull \hbox (badness 1546) in paragraph at lines 664--671 []\T1/zi4/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 [1808] [1809] [1810] [1811] [1812] [1813] [1814] [1815] [1816] [1817] [1818] Underfull \hbox (badness 3375) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the OS X GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh ose [1819]) (./tools-pkg.tex [1820] Chapter 13. [1821] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1822] Underfull \hbox (badness 3039) in paragraph at lines 164--167 []\T1/zi4/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 [1823] [1824] Underfull \hbox (badness 1308) 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 types Underfull \hbox (badness 4967) in paragraph at lines 285--298 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1825] [1826] Underfull \hbox (badness 3039) in paragraph at lines 389--391 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] [1835] [1836] [1837] Underfull \hbox (badness 1635) in paragraph at lines 1050--1052 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1838] Underfull \hbox (badness 4441) in paragraph at lines 1126--1136 \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- [1839] Underfull \hbox (badness 1014) in paragraph at lines 1148--1150 []\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 1154--1156 []\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 1185--1188 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1185--1188 \T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1840] [1841] [1842] Underfull \hbox (badness 10000) in paragraph at lines 1348--1350 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1843] [1844] [1845] Underfull \hbox (badness 7981) in paragraph at lines 1518--1523 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 1082) in paragraph at lines 1525--1527 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1846] [1847] [1848] [1849]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored <to be read again> \relax l.1722 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1850] Underfull \hbox (badness 1137) in paragraph at lines 1807--1809 []\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 Underfull \hbox (badness 5726) in paragraph at lines 1836--1841 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/n/10 De pendsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 1836--1841 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1851] [1852] [1853] [1854] [1855] [1856] Overfull \hbox (17.88089pt too wide) in paragraph at lines 2173--2173 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1857] [1858] [1859] [1860] Underfull \hbox (badness 7981) in paragraph at lines 2376--2382 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1861] [1862] [1863] [1864] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2660. [1865] [1866] [1867] [1868] Underfull \hbox (badness 1424) in paragraph at lines 2942--2944 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1869] [1870] [1871] [1872] [1873] [1874] [1875] [1876] [1877] [1878] [1879] [1880] Underfull \hbox (badness 10000) in paragraph at lines 3638--3640 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1881] [1882] Underfull \hbox (badness 10000) in paragraph at lines 3777--3780 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1883] [1884] [1885] [1886] Underfull \hbox (badness 1838) in paragraph at lines 4037--4043 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4037--4043 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1887] [1888] Underfull \hbox (badness 5726) in paragraph at lines 4117--4122 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4117--4122 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1889] [1890] Underfull \hbox (badness 1688) in paragraph at lines 4260--4272 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/zi4/m/sl/10 PACKAGES\T1/ptm/m/n/10 ' and [1891] [1892] [1893] [1894]) (./utils-pkg.tex Chapter 14. [1895] Underfull \hbox (badness 2556) 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/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1896] [1897] Underfull \hbox (badness 1454) in paragraph at lines 197--200 []\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive , \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 by de- Underfull \hbox (badness 1540) in paragraph at lines 213--216 []\T1/zi4/m/sl/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for the same task as \T1/zi4/m/sl/10 apropos\T1/ptm/m/n/10 . How-ever, by de-fault [1898] [1899] [1900] [1901] [1902] [1903] Underfull \hbox (badness 10000) in paragraph at lines 543--549 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 543--549 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1904] Underfull \hbox (badness 5847) in paragraph at lines 657--663 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 657--663 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1905] Underfull \hbox (badness 3861) in paragraph at lines 725--730 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1906] [1907] [1908] [1909] [1910] Underfull \vbox (badness 10000) has occurred while \output is active [1911] [1912] [1913] [1914] [1915] Underfull \hbox (badness 1371) in paragraph at lines 1321--1323 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1916] [1917] [1918] [1919] [1920] [1921] [1922] Underfull \hbox (badness 2057) in paragraph at lines 1807--1809 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1923] [1924] Underfull \hbox (badness 10000) in paragraph at lines 1901--1903 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1925] Underfull \hbox (badness 5189) in paragraph at lines 1991--1993 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1926] [1927] [1928] [1929] Underfull \hbox (badness 1661) in paragraph at lines 2209--2216 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1990) in paragraph at lines 2226--2229 []\T1/ptm/m/n/10 a [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1930] [1931] [1932] [1933] [1934] [1935] Underfull \hbox (badness 10000) in paragraph at lines 2635--2639 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing [1936] Overfull \hbox (64.10922pt too wide) in paragraph at lines 2640--2643 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1937] [1938] [1939] [1940] [1941] [1942] [1943] [1944] Underfull \hbox (badness 1412) in paragraph at lines 3220--3225 []\T1/ptm/m/n/10 The \T1/zi4/m/sl/10 "libcurl" \T1/ptm/m/n/10 and \T1/zi4/m/sl/ 10 "wget" \T1/ptm/m/n/10 meth-ods fol-low `\T1/zi4/m/sl/10 http://\T1/ptm/m/n/1 0 ' and `\T1/zi4/m/sl/10 https://\T1/ptm/m/n/10 ' redi-rec-tions: the [1945] Underfull \hbox (badness 1430) in paragraph at lines 3246--3254 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 1231) in paragraph at lines 3289--3295 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1946] [1947] [1948] [1949] [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] [1958] [1959]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored <to be read again> \relax l.4109 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored <to be read again> \relax l.4109 ...mat Unordered and Ordered Lists}{format} [1960] [1961] [1962] [1963] [1964] [1965] [1966] [1967] [1968] [1969] [1970] [1971] [1972] [1973] [1974] Underfull \hbox (badness 1371) in paragraph at lines 5062--5064 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1975] Underfull \hbox (badness 1502) in paragraph at lines 5151--5156 []\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 5151--5156 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1976] [1977] [1978] Underfull \hbox (badness 10000) in paragraph at lines 5324--5333 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [1979] Underfull \hbox (badness 2150) in paragraph at lines 5387--5390 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [1980] [1981] Underfull \hbox (badness 3118) in paragraph at lines 5524--5526 []\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 [1982] Underfull \hbox (badness 2409) in paragraph at lines 5557--5561 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [1983] Underfull \hbox (badness 1325) in paragraph at lines 5665--5669 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [1984] Underfull \hbox (badness 10000) in paragraph at lines 5748--5751 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 5748--5751 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [1985] Underfull \hbox (badness 3219) in paragraph at lines 5821--5828 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 5821--5828 \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 5821--5828 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [1986] Underfull \hbox (badness 10000) in paragraph at lines 5901--5906 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] Underfull \hbox (badness 10000) in paragraph at lines 7203--7205 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7208--7213 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2008] [2009] [2010] [2011] [2012] [2013] [2014] [2015] [2016] Underfull \hbox (badness 1789) in paragraph at lines 7758--7760 []\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 [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] Underfull \hbox (badness 1097) in paragraph at lines 8583--8586 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2030] Underfull \hbox (badness 3000) in paragraph at lines 8719--8724 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] Underfull \hbox (badness 2134) in paragraph at lines 9302--9307 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2040] [2041] [2042] [2043] [2044] [2045] [2046] Underfull \hbox (badness 5077) in paragraph at lines 9727--9731 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 9727--9731 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 9739--9743 []\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia , The Free En-cy-clo-pe-dia. Underfull \hbox (badness 3428) in paragraph at lines 9739--9743 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2047] [2048] [2049] [2050] [2051] [2052] Underfull \hbox (badness 10000) in paragraph at lines 10093--10095 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][] []\T1/ptm/m/n/10 s are nicely viewed via [2053] [2054] [2055] Underfull \hbox (badness 2150) in paragraph at lines 10269--10271 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2056] [2057] [2058] Underfull \hbox (badness 10000) in paragraph at lines 10447--10451 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 10478--10484 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2059] [2060] Underfull \hbox (badness 2096) in paragraph at lines 10596--10599 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. 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Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 524--530 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/n/10 insertions\T1/ptm/m/n/10 ', [9] [10] [11] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 2671) in paragraph at lines 1135--1138 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] [22] Underfull \hbox (badness 4072) in paragraph at lines 1369--1375 []\T1/zi4/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/zi4/m/n/10 x mod y \T1/ptm/m /n/10 and \T1/zi4/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I t is guar-an-teed that [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.88089pt too wide) in paragraph at lines 1894--1894 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2079--2081 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3580--3582 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] Underfull \hbox (badness 2521) in paragraph at lines 4782--4784 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] Overfull \hbox (7.0809pt too wide) in paragraph at lines 5909--5909 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [93] [94] [95] Underfull \hbox (badness 2096) in paragraph at lines 6090--6103 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [96] [97] [98] Overfull \hbox (58.35893pt too wide) in paragraph at lines 6293--6295 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [99] [100] Underfull \hbox (badness 10000) in paragraph at lines 6434--6437 []\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is [101] [102] Underfull \hbox (badness 1442) in paragraph at lines 6599--6605 []\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/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6599--6605 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6599--6605 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [103] Underfull \hbox (badness 3568) in paragraph at lines 6660--6667 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [104] [105] Underfull \vbox (badness 10000) has occurred while \output is active [106] [107] [108] [109] [110] [111] [112] [113] Underfull \hbox (badness 2096) in paragraph at lines 7298--7302 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [114] Underfull \hbox (badness 4595) in paragraph at lines 7355--7358 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [115] Underfull \hbox (badness 3000) in paragraph at lines 7391--7393 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7416--7419 [][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [116] [117] [118] [119] Underfull \hbox (badness 10000) in paragraph at lines 7671--7682 []\T1/zi4/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 [120] [121] Underfull \hbox (badness 4479) in paragraph at lines 7743--7752 [][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), Underfull \hbox (badness 2469) in paragraph at lines 7743--7752 [][]\T1/zi4/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods, [][]\T1/zi4/m/n/10 Math.data.frame[][][] \T1/ptm/m/n/10 etc, about \T1/ptm/m/i t/10 Group \T1/ptm/m/n/10 meth-ods for [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] Underfull \hbox (badness 1394) in paragraph at lines 9355--9360 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [146] [147] [148] [149] [150] Underfull \hbox (badness 1052) in paragraph at lines 9698--9703 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 9698--9703 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [151] [152] Underfull \hbox (badness 1735) in paragraph at lines 9836--9840 \T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ zi4/m/n/10 https : / / en . wikipedia . [153] [154] [155] [156] [157] [158] Underfull \hbox (badness 2150) in paragraph at lines 10240--10243 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse [159] Underfull \hbox (badness 6396) in paragraph at lines 10254--10262 []\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 2409) in paragraph at lines 10295--10302 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] Underfull \hbox (badness 4569) in paragraph at lines 11341--11345 []\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 11341--11345 \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 [176] [177] [178] [179] [180] [181] [182] [183] Underfull \hbox (badness 2698) in paragraph at lines 11917--11926 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 11917--11926 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] Underfull \hbox (badness 6236) in paragraph at lines 12561--12564 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [194] [195] [196] [197] [198] [199] Underfull \hbox (badness 2253) in paragraph at lines 12939--12941 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [200] Underfull \hbox (badness 1565) in paragraph at lines 13010--13014 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and [201] Underfull \hbox (badness 10000) in paragraph at lines 13054--13056 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with [202] [203] Underfull \hbox (badness 1466) in paragraph at lines 13195--13198 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ zi4/m/n/10 file.copy \T1/ptm/m/n/10 and [204] [205] Underfull \hbox (badness 10000) in paragraph at lines 13303--13307 [][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13314--13317 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [206] [207] [208] [209] Underfull \hbox (badness 3965) in paragraph at lines 13577--13581 []\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, [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] Underfull \hbox (badness 4429) in paragraph at lines 14338--14341 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [222] Underfull \hbox (badness 10000) in paragraph at lines 14430--14432 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14436--14440 []\T1/zi4/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 [223] Underfull \hbox (badness 10000) in paragraph at lines 14478--14482 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 14478--14482 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [224] Underfull \vbox (badness 3803) has occurred while \output is active [225] [226] [227] [228] [229] [230] [231] [232] Underfull \hbox (badness 2452) in paragraph at lines 15058--15062 []\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 15058--15062 \T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_ WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and [233] [234] [235] Underfull \hbox (badness 1092) in paragraph at lines 15231--15236 [][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [236] [237] [238] [239] Underfull \hbox (badness 6741) in paragraph at lines 15479--15483 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [240] [241] [242] [243] Underfull \hbox (badness 1867) in paragraph at lines 15785--15792 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [244] [245] [246] [247] Underfull \vbox (badness 10000) has occurred while \output is active [248] [249] Underfull \hbox (badness 3679) in paragraph at lines 16166--16168 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [250] [251] [252] [253] [254] [255] [256] [257] Underfull \hbox (badness 1478) in paragraph at lines 16711--16714 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [258] [259] [260] [261] Underfull \hbox (badness 10000) in paragraph at lines 16964--16966 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [262] [263] [264] [265] [266] [267] [268] [269] [270] Underfull \hbox (badness 1442) in paragraph at lines 17527--17529 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [271] Underfull \hbox (badness 2452) in paragraph at lines 17619--17635 [][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [272] [273] [274] [275] [276] [277] [278] Underfull \hbox (badness 1248) in paragraph at lines 18033--18036 []\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/ m/n/10 , [279] [280] [281] [282] Underfull \hbox (badness 4739) in paragraph at lines 18291--18293 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] Underfull \hbox (badness 1360) in paragraph at lines 19249--19254 \T1/zi4/m/n/10 "none"\T1/ptm/m/n/10 . It is in-tended for the ver-sion of OpenS SL used, but not all Underfull \hbox (badness 10000) in paragraph at lines 19272--19278 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / Underfull \hbox (badness 1127) in paragraph at lines 19272--19278 \T1/zi4/m/n/10 ssl-[]compared . html$[][] \T1/ptm/m/n/10 for more de-tails on S SL ver-sions. Nor-mally \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 used with \T1/phv /m/n/10 R [299] Underfull \hbox (badness 10000) in paragraph at lines 19345--19349 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 19345--19349 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [300] [301] Underfull \hbox (badness 1509) in paragraph at lines 19480--19487 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1354) in paragraph at lines 19480--19487 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19496--19501 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313] Underfull \hbox (badness 1264) in paragraph at lines 20227--20232 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] Underfull \hbox (badness 10000) in paragraph at lines 20981--20983 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] Underfull \hbox (badness 1077) in paragraph at lines 21979--21985 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [341] [342] [343] Underfull \hbox (badness 1484) in paragraph at lines 22140--22148 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [344] [345] [346] [347] Underfull \hbox (badness 2790) in paragraph at lines 22411--22414 []\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 22411--22414 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [348] [349] [350] [351] Underfull \hbox (badness 1194) in paragraph at lines 22692--22695 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 . It calls [352] [353] [354] [355] Underfull \hbox (badness 10000) in paragraph at lines 22898--22904 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 5862) in paragraph at lines 22898--22904 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 22908--22911 []\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 22908--22911 \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 [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] [367] [368] [369] Underfull \hbox (badness 10000) in paragraph at lines 23839--23841 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [370] [371] [372] [373] Underfull \hbox (badness 1199) in paragraph at lines 24066--24072 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24066--24072 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [374] [375] [376] [377] [378] [379] [380] [381] Underfull \hbox (badness 1038) in paragraph at lines 24645--24653 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 1881) in paragraph at lines 24654--24657 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 24673--24675 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [382] Underfull \hbox (badness 10000) in paragraph at lines 24745--24755 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 24756--24762 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able Underfull \hbox (badness 1968) in paragraph at lines 24769--24774 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 24779--24781 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [383] [384] Underfull \vbox (badness 10000) has occurred while \output is active [385] Underfull \hbox (badness 10000) in paragraph at lines 25034--25040 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/zi4/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25034--25040 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 25034--25040 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by [386] Underfull \hbox (badness 10000) in paragraph at lines 25047--25050 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 25071--25073 []\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 25103--25108 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 25109--25120 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 25121--25124 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and [387] Underfull \hbox (badness 4084) in paragraph at lines 25131--25143 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN OS X build), Underfull \hbox (badness 10000) in paragraph at lines 25131--25143 \T1/zi4/m/n/10 "mac.binary."\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.maveric ks" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for C RAN Underfull \hbox (badness 7397) in paragraph at lines 25131--25143 \T1/ptm/m/n/10 OS X builds). Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m /n/10 . (\T1/zi4/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 25145--25152 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 25145--25152 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 25145--25152 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1082) in paragraph at lines 25145--25152 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [388] [389] [390] [391] [392] Underfull \hbox (badness 10000) in paragraph at lines 25491--25495 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 25491--25495 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [393] [394] [395] [396] [397] Underfull \hbox (badness 1735) in paragraph at lines 25809--25813 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [398] [399] [400] [401] [402] [403] [404] [405] [406] Underfull \hbox (badness 2726) in paragraph at lines 26369--26372 []\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] [418] [419] Underfull \hbox (badness 1052) in paragraph at lines 27186--27191 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [420] [421] [422] [423] [424] Underfull \vbox (badness 10000) has occurred while \output is active [425] [426] [427] [428] [429] [430] [431] Underfull \hbox (badness 1533) in paragraph at lines 27995--27998 []\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 [432] [433] [434] Underfull \hbox (badness 1163) in paragraph at lines 28157--28168 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] Underfull \hbox (badness 10000) in paragraph at lines 29676--29680 []\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 29676--29680 \T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. Underfull \hbox (badness 6188) in paragraph at lines 29698--29700 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [459] [460] [461] [462] [463] [464] [465] [466] [467] Underfull \hbox (badness 1655) in paragraph at lines 30246--30248 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm /m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for [468] [469] [470] [471] [472] [473] [474] [475] [476] [477] [478] Underfull \hbox (badness 10000) in paragraph at lines 30914--30918 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [479] [480] [481] Underfull \hbox (badness 2302) in paragraph at lines 31154--31161 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 31154--31161 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 2980) in paragraph at lines 31154--31161 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 31154--31161 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [482] [483] [484] Underfull \hbox (badness 2261) in paragraph at lines 31310--31315 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if Underfull \hbox (badness 10000) in paragraph at lines 31337--31343 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [485] Underfull \hbox (badness 10000) in paragraph at lines 31413--31418 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [486] [487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] Underfull \hbox (badness 1072) in paragraph at lines 34333--34337 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 34338--34342 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 34366--34372 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 34366--34372 \T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 34366--34372 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in Underfull \hbox (badness 3343) in paragraph at lines 34379--34386 \T1/ptm/m/n/10 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 34379--34386 \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 Underfull \hbox (badness 1917) in paragraph at lines 34379--34386 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [532] [533] [534] [535] [536] Underfull \hbox (badness 10000) in paragraph at lines 34670--34676 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1152) in paragraph at lines 34670--34676 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] Underfull \hbox (badness 3333) in paragraph at lines 36500--36505 []\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] Underfull \hbox (badness 1472) in paragraph at lines 37120--37123 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [576] [577] [578] [579] [580] [581] [582] [583] [584] [585] [586] Underfull \hbox (badness 2671) in paragraph at lines 37785--37788 []\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/zi4/m/n/10 ...\T1/pt m/m/n/10 . If set to \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies [587] [588] [589] [590] [591] [592] Underfull \hbox (badness 10000) in paragraph at lines 38200--38203 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [593] [594] Underfull \hbox (badness 10000) in paragraph at lines 38318--38322 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [595] Underfull \hbox (badness 10000) in paragraph at lines 38380--38384 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614] [615] Underfull \hbox (badness 1990) in paragraph at lines 39706--39714 []\T1/zi4/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 4846) in paragraph at lines 39706--39714 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [616] [617] [618] [619] Underfull \hbox (badness 1515) in paragraph at lines 39978--39983 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0 [620] [621] [622] [623] Underfull \hbox (badness 1917) in paragraph at lines 40208--40215 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [624] [625] [626] [627] [628] [629] [630] [631] [632] [633] Underfull \hbox (badness 3668) in paragraph at lines 40869--40871 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [634] [635] Underfull \hbox (badness 2401) in paragraph at lines 40974--40978 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [636] [637] Underfull \hbox (badness 2111) in paragraph at lines 41143--41148 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. [638] Underfull \hbox (badness 6542) in paragraph at lines 41159--41164 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [639] [640] [641] [642] [643] [644] [645] Underfull \hbox (badness 10000) in paragraph at lines 41604--41609 []\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu nc-tion than [][]\T1/zi4/m/n/10 rank[][][] Underfull \hbox (badness 10000) in paragraph at lines 41604--41609 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to [646] Underfull \hbox (badness 5417) in paragraph at lines 41696--41700 []\T1/zi4/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 [647] Underfull \hbox (badness 10000) in paragraph at lines 41757--41761 []\T1/zi4/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 [648] [649]) (./compiler-pkg.tex [650] Chapter 2. [651] [652] [653] [654]) (./datasets-pkg.tex Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple te list, use [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] Underfull \vbox (badness 1515) has occurred while \output is active [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] Underfull \hbox (badness 6658) in paragraph at lines 3940--3942 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h ttp : / / www . ltrr . arizona . edu / ~hallman / [722] Underfull \vbox (badness 10000) has occurred while \output is active [723] [724] [725] [726] Underfull \vbox (badness 10000) has occurred while \output is active [727] Underfull \vbox (badness 10000) has occurred while \output is active [728] [729] [730] [731] [732] [733] [734] [735]) (./grDevices-pkg.tex [736] Chapter 4. [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] Underfull \hbox (badness 5175) in paragraph at lines 1071--1073 []\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 [754] [755] [756] [757] Underfull \hbox (badness 1852) in paragraph at lines 1268--1271 []\T1/zi4/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 [758] [759] [760] Underfull \hbox (badness 1490) in paragraph at lines 1474--1479 \T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and [761] Underfull \hbox (badness 2698) in paragraph at lines 1528--1531 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture, oth-er-wise a ma-trix of color names (for [762] Underfull \hbox (badness 10000) in paragraph at lines 1597--1601 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [763] [764] [765] [766] Underfull \hbox (badness 1325) in paragraph at lines 1880--1890 \T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/ 10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1 /ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 , [767] [768] Underfull \hbox (badness 10000) in paragraph at lines 1985--1987 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [769] [770] [771] Underfull \hbox (badness 6758) in paragraph at lines 2146--2149 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [772] [773] [774] [775] [776] [777] [778] [779] [780] Underfull \hbox (badness 10000) in paragraph at lines 2712--2713 [781] [782] [783] [784] [785] [786] [787] Underfull \hbox (badness 1152) in paragraph at lines 3150--3152 []\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/zi4/m/n/10 nr, nc \T1/ptm/m /n/10 giv-ing the num-ber of rows and columns, ful-fill-ing [788] [789] [790] [791] [792] Underfull \hbox (badness 2856) in paragraph at lines 3470--3473 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3484--3486 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [793] [794] Underfull \hbox (badness 1173) in paragraph at lines 3600--3610 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 paper \T1/ptm/m/n/10 ar-gu-ment sets the `\ T1/zi4/m/n/10 /MediaBox\T1/ptm/m/n/10 ' en-try in the file, which de-faults to \T1/zi4/m/n/10 width \T1/ptm/m/n/10 by [795] [796] [797] [798] [799] [800] [801] [802] [803] [804] [805] Underfull \hbox (badness 1067) in paragraph at lines 4307--4314 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [806] [807] Underfull \hbox (badness 3364) in paragraph at lines 4468--4470 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$ \T1/zi4/m/n/10 https : / / partners . adobe . com / public / [808] Underfull \hbox (badness 1789) in paragraph at lines 4545--4547 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [809] Underfull \hbox (badness 1377) in paragraph at lines 4595--4600 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [810] Underfull \hbox (badness 2671) in paragraph at lines 4622--4630 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4671--4678 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4679--4688 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4679--4688 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4689--4691 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [811] [812] Underfull \hbox (badness 1057) in paragraph at lines 4800--4805 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/zi4/m/n/10 "rgb"\T1/ptm/m/n/10 ) (which is RGB+gray) and [813] Underfull \hbox (badness 7344) in paragraph at lines 4860--4862 []\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 [814] [815] Underfull \hbox (badness 2035) in paragraph at lines 4984--4993 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 10000) in paragraph at lines 4984--4993 \T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 4984--4993 \T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [816] Underfull \hbox (badness 10000) in paragraph at lines 5053--5060 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5053--5060 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [817] [818] [819] Underfull \hbox (badness 1546) in paragraph at lines 5195--5203 []\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/ n/10 , [820] Underfull \hbox (badness 1648) in paragraph at lines 5272--5276 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [821] [822] [823] [824] [825] [826] [827] Underfull \hbox (badness 10000) in paragraph at lines 5724--5727 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [828] [829] [830] [831] [832] [833] Underfull \hbox (badness 1189) in paragraph at lines 6121--6123 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [834] [835] Underfull \hbox (badness 10000) in paragraph at lines 6219--6221 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [836] [837] [838] [839] Underfull \hbox (badness 3780) in paragraph at lines 6510--6516 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [840] [841] [842] Underfull \hbox (badness 2680) in paragraph at lines 6706--6708 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [843] [844] [845]) (./graphics-pkg.tex [846] Chapter 5. [847] [848] [849] [850] [851] [852] [853] [854] [855] [856] [857] Underfull \hbox (badness 10000) in paragraph at lines 683--690 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [858] [859] [860] [861] Underfull \vbox (badness 3803) has occurred while \output is active [862] [863] [864] [865] [866] Underfull \hbox (badness 4634) in paragraph at lines 1246--1249 [][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [867] [868] [869] [870] [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] [883] Underfull \hbox (badness 1009) in paragraph at lines 2280--2287 \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 [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] Underfull \vbox (badness 10000) has occurred while \output is active [906] Underfull \vbox (badness 10000) has occurred while \output is active [907] [908] [909] [910] Underfull \hbox (badness 1867) in paragraph at lines 3912--3916 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [911] [912] [913] [914] [915] [916] [917] Underfull \hbox (badness 1924) in paragraph at lines 4359--4364 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain [918] Underfull \hbox (badness 2529) in paragraph at lines 4390--4393 []\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 [919] [920] [921] [922] [923] Underfull \hbox (badness 10000) in paragraph at lines 4740--4746 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4740--4746 \T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that [924] Underfull \hbox (badness 10000) in paragraph at lines 4871--4874 [925] </«PKGBUILDDIR»/library/graphics/help/figures/mai.pdf, id=22 382, 289.08pt x 289.08pt> <use /«PKGBUILDDIR»/library/graphics/help/figures/mai.pdf> [926 </«PKGBUILDDIR»/library/graphics/help/figures/mai.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 4932--4934 </«PKGBUILDDIR»/library/graphics/help/figures/oma.pdf, id=22 395, 259.97125pt x 332.24126pt> <use /«PKGBUILDDIR»/library/graphics/help/figures/oma.pdf> [927 </«PKGBUILDDIR»/library/graphics/help/figures/oma.pdf>] [928] Underfull \hbox (badness 10000) in paragraph at lines 5122--5124 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [929] [930] [931] [932] [933] Underfull \vbox (badness 10000) has occurred while \output is active [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] </«PKGBUILDDIR»/library/graphics/help/figures/pch.pdf, id=22 813, 361.35pt x 50.1875pt> <use /«PKGBUILDDIR»/library/graphics/help/figures/pch.pdf> Overfull \hbox (31.57222pt too wide) in paragraph at lines 6592--6593 [][] [953 </«PKGBUILDDIR»/library/graphics/help/figures/pch.pdf>] [954] Underfull \vbox (badness 10000) has occurred while \output is active [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] Underfull \hbox (badness 1048) in paragraph at lines 7301--7306 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [965] Underfull \hbox (badness 1038) in paragraph at lines 7417--7420 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [966] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] Underfull \hbox (badness 10000) in paragraph at lines 8653--8655 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8655--8657 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [988]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored <to be read again> \relax l.8735 \HeaderA{units}{Graphical Units}{units} [989] [990] [991] [992]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [993] [994] [995] [996] [997] [998] Underfull \hbox (badness 2680) in paragraph at lines 390--393 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] Underfull \hbox (badness 4279) in paragraph at lines 970--979 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] Underfull \vbox (badness 3803) has occurred while \output is active [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] Underfull \hbox (badness 1067) in paragraph at lines 4340--4343 []\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 [1066] [1067] [1068] [1069] Underfull \hbox (badness 7256) in paragraph at lines 4583--4585 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] Underfull \hbox (badness 10000) in paragraph at lines 5860--5866 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] Underfull \hbox (badness 7649) in paragraph at lines 6334--6337 []\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 [1100] [1101] [1102] [1103]) (./methods-pkg.tex [1104] Chapter 7. [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] Underfull \hbox (badness 2237) in paragraph at lines 1454--1456 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1125] [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] Underfull \hbox (badness 10000) in paragraph at lines 2050--2055 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 2050--2055 \T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] Underfull \hbox (badness 10000) in paragraph at lines 2655--2658 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1142] [1143] Underfull \hbox (badness 1132) in paragraph at lines 2795--2799 []\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in [1144] Underfull \hbox (badness 1033) in paragraph at lines 2827--2832 \T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1145] [1146] [1147] [1148] [1149] [1150] [1151] Underfull \hbox (badness 1102) in paragraph at lines 3339--3341 []\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1152] [1153] [1154] [1155] [1156] Underfull \hbox (badness 10000) in paragraph at lines 3667--3672 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Underfull \hbox (badness 10000) in paragraph at lines 3675--3684 []\T1/ptm/m/n/10 The [1157] [1158] [1159] [1160] [1161] [1162] Underfull \vbox (badness 10000) has occurred while \output is active [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] Underfull \hbox (badness 1436) in paragraph at lines 4580--4583 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4609--4615 []\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4609--4615 \T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1171] [1172] [1173] [1174] [1175] [1176] Underfull \vbox (badness 2452) has occurred while \output is active [1177] [1178] Underfull \vbox (badness 10000) has occurred while \output is active [1179] [1180] Underfull \hbox (badness 1092) in paragraph at lines 5281--5288 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 5281--5288 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and Underfull \hbox (badness 4036) in paragraph at lines 5329--5332 []\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1181] [1182] [1183] [1184] [1185] Underfull \hbox (badness 1087) in paragraph at lines 5649--5654 []\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 [1186] [1187] [1188] [1189] Underfull \hbox (badness 2221) in paragraph at lines 5878--5883 []\T1/ptm/m/n/10 Two op-tional method names are in-ter-preted spe-cially, \T1/z i4/m/n/10 initialize \T1/ptm/m/n/10 and [1190] [1191] [1192] [1193] [1194] Underfull \hbox (badness 1675) in paragraph at lines 6345--6351 \T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1195] [1196] [1197] [1198] Underfull \vbox (badness 10000) has occurred while \output is active [1199] [1200]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4} ) has been already used, duplicate ignored <to be read again> \relax l.6828 \aliasA{S4}{S3Part}{S4} [1201] [1202] [1203] [1204]pdfTeX warning (ext4) : destination with the same identifier (name{Rfn.Complex}) has been already use d, duplicate ignored <to be read again> \relax l.7096 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored <to be read again> \relax l.7098 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red <to be read again> \relax l.7099 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored <to be read again> \relax l.7101 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed <to be read again> \relax l.7102 \aliasA{Summary}{S4groupGeneric}{Summary} [1205] Underfull \hbox (badness 2050) in paragraph at lines 7163--7167 []\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 [1206] [1207] [1208] Underfull \hbox (badness 1286) in paragraph at lines 7348--7350 []\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] Underfull \hbox (badness 1852) in paragraph at lines 9765--9769 []\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., [1243] [1244] [1245] [1246]) (./parallel-pkg.tex Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 15--17 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4 /m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] Underfull \hbox (badness 3386) in paragraph at lines 1254--1257 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1267] [1268]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 <bates@stat.wisc.edu> \T1/ptm/ m/n/10 and William N. Ven-ables [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283]) (./stats-pkg.tex [1284] Chapter 10. [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] Underfull \hbox (badness 1412) in paragraph at lines 846--848 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] Underfull \hbox (badness 2503) in paragraph at lines 1327--1330 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1306] [1307] [1308] Underfull \hbox (badness 10000) in paragraph at lines 1506--1510 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] Underfull \hbox (badness 3965) in paragraph at lines 2166--2168 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1320] [1321] [1322] [1323] [1324] Underfull \hbox (badness 3965) in paragraph at lines 2508--2510 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] Underfull \hbox (badness 2503) in paragraph at lines 3325--3328 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] Underfull \hbox (badness 3989) in paragraph at lines 4553--4560 []\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 = [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] Underfull \hbox (badness 2556) in paragraph at lines 5164--5167 []\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/ ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p tm/m/n/10 . For Underfull \hbox (badness 2932) in paragraph at lines 5181--5183 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is given by [1368] [1369] [1370] [1371] Underfull \hbox (badness 1142) in paragraph at lines 5422--5434 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1372] [1373] Underfull \hbox (badness 2503) in paragraph at lines 5561--5565 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1374] Underfull \hbox (badness 1168) in paragraph at lines 5622--5627 []\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and [1375] [1376] [1377] [1378] [1379] [1380] [1381] Underfull \hbox (badness 8132) in paragraph at lines 6064--6069 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1382] [1383] [1384] [1385] [1386] Underfull \hbox (badness 7081) in paragraph at lines 6342--6345 []\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6346--6348 []\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1387] [1388] [1389] [1390] [1391] Underfull \vbox (badness 3803) has occurred while \output is active [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] Underfull \hbox (badness 10000) in paragraph at lines 7159--7162 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1400] [1401] Underfull \hbox (badness 10000) in paragraph at lines 7296--7299 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/zi4/m/n/10 ht tps : / / cran . r-[]project . org / web / views / [1402] [1403] [1404] [1405] Underfull \vbox (badness 3803) has occurred while \output is active [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] Underfull \hbox (badness 2626) in paragraph at lines 8794--8797 []\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1427] Underfull \hbox (badness 2503) in paragraph at lines 8894--8898 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1428] [1429] [1430] [1431] [1432] Overfull \hbox (6.88992pt too wide) in paragraph at lines 9228--9230 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] Underfull \hbox (badness 4518) in paragraph at lines 10155--10160 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1448] [1449] [1450] [1451] Underfull \hbox (badness 2142) in paragraph at lines 10497--10500 []\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 ^^@ [1452] Underfull \hbox (badness 1253) in paragraph at lines 10516--10519 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1453] Underfull \hbox (badness 1708) in paragraph at lines 10578--10582 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1454] [1455] [1456] [1457] [1458] [1459] Underfull \hbox (badness 1694) in paragraph at lines 10974--10977 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1867) in paragraph at lines 10993--11002 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 10000) in paragraph at lines 11300--11303 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1465] [1466] [1467]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored <to be read again> \relax l.11454 \aliasA{hat}{influence.measures}{hat} [1468] [1469] Underfull \hbox (badness 1484) in paragraph at lines 11577--11579 []\T1/ptm/m/n/10 The func-tion \T1/zi4/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 [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] Underfull \hbox (badness 4441) in paragraph at lines 12135--12137 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12142--12144 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1479] [1480] [1481] [1482] [1483] [1484] Underfull \hbox (badness 2894) in paragraph at lines 12476--12480 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1485] [1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494] [1495] [1496] Underfull \hbox (badness 4518) in paragraph at lines 13171--13176 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] Underfull \hbox (badness 4518) in paragraph at lines 13818--13823 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1506] [1507] [1508] Underfull \hbox (badness 10000) in paragraph at lines 13956--13960 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 13963--13965 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] [1523] [1524] [1525] Underfull \hbox (badness 2503) in paragraph at lines 15025--15029 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] Underfull \hbox (badness 1418) in paragraph at lines 15534--15540 []\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1 /ptm/m/n/10 and [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] Underfull \hbox (badness 2359) in paragraph at lines 17158--17160 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1560] [1561] Underfull \vbox (badness 10000) has occurred while \output is active [1562] Underfull \vbox (badness 10000) has occurred while \output is active [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] Underfull \hbox (badness 1377) in paragraph at lines 18069--18074 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) in paragraph at lines 18074--18077 []\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 1184) in paragraph at lines 18087--18091 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18095--18099 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1576] [1577] [1578] Underfull \vbox (badness 10000) has occurred while \output is active [1579] [1580] [1581] [1582] [1583] [1584] [1585] Underfull \hbox (badness 1337) in paragraph at lines 18711--18714 []\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 [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] Underfull \hbox (badness 5563) in paragraph at lines 19441--19443 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19444--19447 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1599] [1600] [1601] [1602] [1603] [1604] Underfull \hbox (badness 2503) in paragraph at lines 19811--19814 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1605] Underfull \hbox (badness 10000) in paragraph at lines 19838--19840 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] Underfull \hbox (badness 10000) in paragraph at lines 20863--20869 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] Underfull \hbox (badness 1337) in paragraph at lines 22198--22204 []\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 [1645] [1646] [1647] [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] Underfull \hbox (badness 10000) in paragraph at lines 22991--22994 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] Underfull \hbox (badness 10000) in paragraph at lines 23568--23571 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1667] Underfull \hbox (badness 3690) in paragraph at lines 23619--23623 [][][]\T1/zi4/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 [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] Underfull \hbox (badness 3439) in paragraph at lines 24089--24095 [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1 0 , [1676] [1677] [1678] Underfull \hbox (badness 1867) in paragraph at lines 24286--24288 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to [1679] Underfull \hbox (badness 10000) in paragraph at lines 24299--24301 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and [1680] [1681] [1682] [1683] [1684] [1685] [1686] Underfull \hbox (badness 10000) in paragraph at lines 24757--24762 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1687] [1688] [1689] Underfull \vbox (badness 3803) has occurred while \output is active [1690] [1691] [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] Underfull \vbox (badness 10000) has occurred while \output is active [1702] Underfull \hbox (badness 3514) in paragraph at lines 25775--25780 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1703] Underfull \hbox (badness 3514) in paragraph at lines 25837--25842 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1704] Underfull \hbox (badness 3514) in paragraph at lines 25894--25899 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1705] Underfull \hbox (badness 3514) in paragraph at lines 25955--25961 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1706] [1707] [1708] [1709] Underfull \hbox (badness 3514) in paragraph at lines 26168--26173 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1710] Underfull \hbox (badness 3514) in paragraph at lines 26224--26229 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1711] Underfull \hbox (badness 3514) in paragraph at lines 26281--26286 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1712] Underfull \hbox (badness 3514) in paragraph at lines 26336--26341 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1713] Underfull \hbox (badness 6691) in paragraph at lines 26405--26410 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] [1722] Underfull \hbox (badness 10000) in paragraph at lines 26929--26932 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 26929--26932 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732] Underfull \hbox (badness 5431) in paragraph at lines 27535--27537 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1733] [1734] [1735] Underfull \hbox (badness 5431) in paragraph at lines 27745--27748 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1736] [1737] [1738] [1739] [1740] [1741] Underfull \hbox (badness 1337) in paragraph at lines 28057--28061 []\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 [1742] [1743] Underfull \hbox (badness 10000) in paragraph at lines 28174--28177 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1744] [1745] Underfull \hbox (badness 1616) in paragraph at lines 28357--28360 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1746] [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] [1763] [1764] Underfull \hbox (badness 10000) in paragraph at lines 29483--29487 []\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect [1765] [1766] [1767] Underfull \vbox (badness 10000) has occurred while \output is active [1768] [1769] [1770] Underfull \hbox (badness 1337) in paragraph at lines 29847--29851 []\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 [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] Underfull \hbox (badness 1337) in paragraph at lines 30331--30335 []\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 [1779] Underfull \hbox (badness 5161) in paragraph at lines 30424--30426 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1780] [1781] [1782] [1783] [1784] [1785] Underfull \hbox (badness 10000) in paragraph at lines 30788--30793 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1786] [1787] [1788]) (./stats4-pkg.tex Chapter 11. [1789] [1790] [1791] [1792] [1793] [1794]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored <to be read again> \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1795] [1796] [1797] [1798]) (./tcltk-pkg.tex Chapter 12. [1799] [1800] [1801] [1802] [1803] [1804] [1805] Underfull \vbox (badness 10000) has occurred while \output is active [1806] Underfull \vbox (badness 10000) has occurred while \output is active [1807] Underfull \hbox (badness 1546) in paragraph at lines 664--671 []\T1/zi4/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 [1808] [1809] [1810] [1811] [1812] [1813] [1814] [1815] [1816] [1817] [1818] Underfull \hbox (badness 3375) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the OS X GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh ose [1819]) (./tools-pkg.tex [1820] Chapter 13. [1821] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1822] Underfull \hbox (badness 3039) in paragraph at lines 164--167 []\T1/zi4/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 [1823] [1824] Underfull \hbox (badness 1308) 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 types Underfull \hbox (badness 4967) in paragraph at lines 285--298 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1825] [1826] Underfull \hbox (badness 3039) in paragraph at lines 389--391 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] [1835] [1836] [1837] Underfull \hbox (badness 1635) in paragraph at lines 1050--1052 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1838] Underfull \hbox (badness 4441) in paragraph at lines 1126--1136 \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- [1839] Underfull \hbox (badness 1014) in paragraph at lines 1148--1150 []\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 1154--1156 []\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 1185--1188 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1185--1188 \T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1840] [1841] [1842] Underfull \hbox (badness 10000) in paragraph at lines 1348--1350 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1843] [1844] [1845] Underfull \hbox (badness 7981) in paragraph at lines 1518--1523 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 1082) in paragraph at lines 1525--1527 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1846] [1847] [1848] [1849]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored <to be read again> \relax l.1722 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1850] Underfull \hbox (badness 1137) in paragraph at lines 1807--1809 []\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 Underfull \hbox (badness 5726) in paragraph at lines 1836--1841 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/n/10 De pendsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 1836--1841 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1851] [1852] [1853] [1854] [1855] [1856] Overfull \hbox (17.88089pt too wide) in paragraph at lines 2173--2173 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1857] [1858] [1859] [1860] Underfull \hbox (badness 7981) in paragraph at lines 2376--2382 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1861] [1862] [1863] [1864] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2660. [1865] [1866] [1867] [1868] Underfull \hbox (badness 1424) in paragraph at lines 2942--2944 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1869] [1870] [1871] [1872] [1873] [1874] [1875] [1876] [1877] [1878] [1879] [1880] Underfull \hbox (badness 10000) in paragraph at lines 3638--3640 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1881] [1882] Underfull \hbox (badness 10000) in paragraph at lines 3777--3780 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1883] [1884] [1885] [1886] Underfull \hbox (badness 1838) in paragraph at lines 4037--4043 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4037--4043 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1887] [1888] Underfull \hbox (badness 5726) in paragraph at lines 4117--4122 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4117--4122 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1889] [1890] Underfull \hbox (badness 1688) in paragraph at lines 4260--4272 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/zi4/m/sl/10 PACKAGES\T1/ptm/m/n/10 ' and [1891] [1892] [1893] [1894]) (./utils-pkg.tex Chapter 14. [1895] Underfull \hbox (badness 2556) 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/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1896] [1897] Underfull \hbox (badness 1454) in paragraph at lines 197--200 []\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive , \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 by de- Underfull \hbox (badness 1540) in paragraph at lines 213--216 []\T1/zi4/m/sl/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for the same task as \T1/zi4/m/sl/10 apropos\T1/ptm/m/n/10 . How-ever, by de-fault [1898] [1899] [1900] [1901] [1902] [1903] Underfull \hbox (badness 10000) in paragraph at lines 543--549 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 543--549 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1904] Underfull \hbox (badness 5847) in paragraph at lines 657--663 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 657--663 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1905] Underfull \hbox (badness 3861) in paragraph at lines 725--730 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1906] [1907] [1908] [1909] [1910] Underfull \vbox (badness 10000) has occurred while \output is active [1911] [1912] [1913] [1914] [1915] Underfull \hbox (badness 1371) in paragraph at lines 1321--1323 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1916] [1917] [1918] [1919] [1920] [1921] [1922] Underfull \hbox (badness 2057) in paragraph at lines 1807--1809 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1923] [1924] Underfull \hbox (badness 10000) in paragraph at lines 1901--1903 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1925] Underfull \hbox (badness 5189) in paragraph at lines 1991--1993 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1926] [1927] [1928] [1929] Underfull \hbox (badness 1661) in paragraph at lines 2209--2216 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1990) in paragraph at lines 2226--2229 []\T1/ptm/m/n/10 a [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1930] [1931] [1932] [1933] [1934] [1935] Underfull \hbox (badness 10000) in paragraph at lines 2635--2639 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing [1936] Overfull \hbox (64.10922pt too wide) in paragraph at lines 2640--2643 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1937] [1938] [1939] [1940] [1941] [1942] [1943] [1944] Underfull \hbox (badness 1412) in paragraph at lines 3220--3225 []\T1/ptm/m/n/10 The \T1/zi4/m/sl/10 "libcurl" \T1/ptm/m/n/10 and \T1/zi4/m/sl/ 10 "wget" \T1/ptm/m/n/10 meth-ods fol-low `\T1/zi4/m/sl/10 http://\T1/ptm/m/n/1 0 ' and `\T1/zi4/m/sl/10 https://\T1/ptm/m/n/10 ' redi-rec-tions: the [1945] Underfull \hbox (badness 1430) in paragraph at lines 3246--3254 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 1231) in paragraph at lines 3289--3295 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1946] [1947] [1948] [1949] [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] [1958] [1959]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored <to be read again> \relax l.4109 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored <to be read again> \relax l.4109 ...mat Unordered and Ordered Lists}{format} [1960] [1961] [1962] [1963] [1964] [1965] [1966] [1967] [1968] [1969] [1970] [1971] [1972] [1973] [1974] Underfull \hbox (badness 1371) in paragraph at lines 5062--5064 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1975] Underfull \hbox (badness 1502) in paragraph at lines 5151--5156 []\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 5151--5156 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1976] [1977] [1978] Underfull \hbox (badness 10000) in paragraph at lines 5324--5333 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [1979] Underfull \hbox (badness 2150) in paragraph at lines 5387--5390 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [1980] [1981] Underfull \hbox (badness 3118) in paragraph at lines 5524--5526 []\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 [1982] Underfull \hbox (badness 2409) in paragraph at lines 5557--5561 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [1983] Underfull \hbox (badness 1325) in paragraph at lines 5665--5669 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [1984] Underfull \hbox (badness 10000) in paragraph at lines 5748--5751 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 5748--5751 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [1985] Underfull \hbox (badness 3219) in paragraph at lines 5821--5828 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 5821--5828 \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 5821--5828 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [1986] Underfull \hbox (badness 10000) in paragraph at lines 5901--5906 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] Underfull \hbox (badness 10000) in paragraph at lines 7203--7205 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7208--7213 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2008] [2009] [2010] [2011] [2012] [2013] [2014] [2015] [2016] Underfull \hbox (badness 1789) in paragraph at lines 7758--7760 []\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 [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] Underfull \hbox (badness 1097) in paragraph at lines 8583--8586 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2030] Underfull \hbox (badness 3000) in paragraph at lines 8719--8724 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] Underfull \hbox (badness 2134) in paragraph at lines 9302--9307 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2040] [2041] [2042] [2043] [2044] [2045] [2046] Underfull \hbox (badness 5077) in paragraph at lines 9727--9731 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 9727--9731 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 9739--9743 []\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia , The Free En-cy-clo-pe-dia. Underfull \hbox (badness 3428) in paragraph at lines 9739--9743 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2047] [2048] [2049] [2050] [2051] [2052] Underfull \hbox (badness 10000) in paragraph at lines 10093--10095 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. 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The de-fault is the cur-rently ac-t ive [2073] [2074] [2075] Underfull \hbox (badness 10000) in paragraph at lines 11529--11531 []\T1/ptm/m/n/10 Options other than \T1/zi4/m/sl/10 memory = "none" \T1/ptm/m/n /10 ap-ply only to files pro-duced by [2076] [2077] [2078] [2079] [2080] [2081] Underfull \hbox (badness 10000) in paragraph at lines 11930--11933 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 11930--11933 \T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2082] [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] Underfull \hbox (badness 10000) in paragraph at lines 12460--12462 []\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 1052) in paragraph at lines 12463--12465 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2091] Underfull \hbox (badness 10000) in paragraph at lines 12493--12498 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined see Underfull \hbox (badness 10000) in paragraph at lines 12493--12498 [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 av ailable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 10000) in paragraph at lines 12522--12525 [][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n /10 , [2092] [2093] [2094] [2095] Overfull \hbox (25.86961pt too wide) in paragraph at lines 12764--12767 [][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi -gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](<basename>, package = "<pkg >") [2096] [2097] Underfull \hbox (badness 1454) in paragraph at lines 12841--12845 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, [2098] Underfull \hbox (badness 10000) in paragraph at lines 12911--12913 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion [2099] [2100] [2101]) [2102] (./refman.ind [2103] [2104] [2105] [2106] [2107] [2108] [2109] [2110] [2111] [2112] [2113] [2114] [2115] [2116] [2117] [2118] [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131] [2132] [2133] [2134] [2135] [2136] [2137] [2138] [2139] [2140] [2141] [2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163] Overfull \hbox (5.8567pt too wide) in paragraph at lines 11267--11269 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_depends Overfull \hbox (5.8567pt too wide) in paragraph at lines 11269--11271 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_results Overfull \hbox (5.8567pt too wide) in paragraph at lines 11271--11273 []\T1/zi4/m/it/10 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Transcript written on refman.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-admin.texi This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/«PKGBUILDDIR»/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-02-05.07.deb3]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/«PKGBUILDDIR»/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/«PKGBUILDDIR»/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/«PKGBUILDDIR»/doc/manual/version.texi) [1{/var/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 [1] Chapter 2 [2] Cross reference values unknown; you must run TeX again. [3] [4] [5] [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] [15] [16] [17] [18] Chapter 4 [19] Underfull \hbox (badness 7047) in paragraph at lines 1713--1717 [][][]@smallrm The in-staller as puts links to @smalltt R[] @smallrm and @small tt Rscript[] @smallrm in @smalltt /usr/bin[] @smallrm (Mav-er-icks, Yosemite) o r [20] Underfull \hbox (badness 10000) in paragraph at lines 1775--1784 @texttt org.r-project.R.x86_64.GUI.pkg[]@textrm , @texttt org.r-project.x86_64. tcltk.x11[] @textrm and [21] Chapter 5 [22] Chapter 6 [23] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1916--1916 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [24] [25] Underfull \hbox (badness 6842) in paragraph at lines 2108--2119 []@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age s. No ad-di- [26] Overfull \hbox (50.73642pt too wide) in paragraph at lines 2213--2224 []@textrm The de-fault com-pil-ers spec-i-fied in @texttt /Library/Frameworks/R .framework/Resources/etc/Makeconf[] [27] [28] [29] [30] [31] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2546--2546 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text tt --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2566--2566 []@texttt .../bin/i386/Rcmd check -l @textttsl lib-dir @texttt --extra-arch -- install=check:@textttsl pkg@texttt .log @textttsl pkg[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2567--2567 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [32] [33] [34] Chapter 8 [35] Chapter 9 [36] [37] [38] Appendix A [39] [40] Overfull \hbox (43.6852pt too wide) in paragraph at lines 3199--3199 []@texttt /configure --enable-utf --enable-unicode-properties --enable-jit --d isable-cpp[] [41] [42] [43] [44] [45] [46] [47] Overfull \hbox (26.43913pt too wide) in paragraph at lines 3799--3799 []@texttt ln -s /opt/acml5.1.0/gfortran64_mp/lib/libacml_mp.so @textttsl R_HOM E@texttt /lib/libRblas.so[] [48] Appendix B [49] [50] [51] [52] [53] [54] Appendix C [55] [56] [57] [58] Overfull \hbox (22.38167pt too wide) in paragraph at lines 4660--4664 []@textrm Others have re-ported suc-cess with ver-sions 10.x and 11.x. % https: //stat.ethz.ch/pipermail/r- [59] [60] [61] Overfull \hbox (106.92076pt too wide) in paragraph at lines 4803--4803 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [62] Underfull \hbox (badness 10000) in paragraph at lines 4955--4960 []@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled , run [63] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4978--4978 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_72.jdk/Contents /Home[] [64] [65] Underfull \hbox (badness 10000) in paragraph at lines 5135--5141 @texttt LDFLAGS=-L/usr/local/lib/sparcv9[] @textrm or @texttt LDFLAGS=-L/usr/lo cal/lib/amd64[] @textrm as Overfull \hbox (14.94176pt too wide) in paragraph at lines 5144--5144 []@texttt PKG_CONFIG_PATH=/opt/csw/lib/sparcv9/pkgconfig:/usr/lib/sparcv9/pkgc onfig[] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5151--5151 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s olaris"[] [66] [67] [68] [69] [70] [71] Appendix D [72] [73] [74] (Function and variable index) [75] (Concept index) [76] (Environment variable index) [77] [78] ) (see the transcript file for additional information)</usr/share/texlive/texmf-d ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu blic/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am sfonts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c m/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.p fb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></u sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/s hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/t exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive /texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf -dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb> Output written on R-admin.pdf (81 pages, 453479 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/«PKGBUILDDIR»/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-02-05.07.deb3]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/«PKGBUILDDIR»/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/«PKGBUILDDIR»/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/«PKGBUILDDIR»/doc/manual/version.texi) [1{/var/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] (/«PKGBUILDDIR»/doc/manual/R-admin.toc [-1] [-2]) [-3] (/«PKGBUILDDIR»/doc/manual/R-admin.toc) (/«PKGBUILDDIR»/doc/manual/R-admin.toc) Chapter 1 (/«PKGBUILDDIR»/doc/manual/R-admin.aux) [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] [15] [16] [17] [18] Chapter 4 [19] Underfull \hbox (badness 7047) in paragraph at lines 1713--1717 [][][]@smallrm The in-staller as puts links to @smalltt R[] @smallrm and @small tt Rscript[] @smallrm in @smalltt /usr/bin[] @smallrm (Mav-er-icks, Yosemite) o r [20] Underfull \hbox (badness 10000) in paragraph at lines 1775--1784 @texttt org.r-project.R.x86_64.GUI.pkg[]@textrm , @texttt org.r-project.x86_64. tcltk.x11[] @textrm and [21] Chapter 5 [22] Chapter 6 [23] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1916--1916 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [24] [25] Underfull \hbox (badness 6842) in paragraph at lines 2108--2119 []@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age s. No ad-di- [26] Overfull \hbox (50.73642pt too wide) in paragraph at lines 2213--2224 []@textrm The de-fault com-pil-ers spec-i-fied in @texttt /Library/Frameworks/R .framework/Resources/etc/Makeconf[] [27] [28] [29] [30] [31] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2546--2546 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text tt --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2566--2566 []@texttt .../bin/i386/Rcmd check -l @textttsl lib-dir @texttt --extra-arch -- install=check:@textttsl pkg@texttt .log @textttsl pkg[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2567--2567 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [32] [33] [34] Chapter 8 [35] Chapter 9 [36] [37] [38] Appendix A [39] [40] Overfull \hbox (43.6852pt too wide) in paragraph at lines 3199--3199 []@texttt /configure --enable-utf --enable-unicode-properties --enable-jit --d isable-cpp[] [41] [42] [43] [44] [45] [46] [47] Overfull \hbox (26.43913pt too wide) in paragraph at lines 3799--3799 []@texttt ln -s /opt/acml5.1.0/gfortran64_mp/lib/libacml_mp.so @textttsl R_HOM E@texttt /lib/libRblas.so[] [48] Appendix B [49] [50] [51] [52] [53] [54] Appendix C [55] [56] [57] [58] Overfull \hbox (22.38167pt too wide) in paragraph at lines 4660--4664 []@textrm Others have re-ported suc-cess with ver-sions 10.x and 11.x. % https: //stat.ethz.ch/pipermail/r- [59] [60] [61] Overfull \hbox (106.92076pt too wide) in paragraph at lines 4803--4803 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [62] Underfull \hbox (badness 10000) in paragraph at lines 4955--4960 []@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled , run [63] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4978--4978 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_72.jdk/Contents /Home[] [64] [65] Underfull \hbox (badness 10000) in paragraph at lines 5135--5141 @texttt LDFLAGS=-L/usr/local/lib/sparcv9[] @textrm or @texttt LDFLAGS=-L/usr/lo cal/lib/amd64[] @textrm as Overfull \hbox (14.94176pt too wide) in paragraph at lines 5144--5144 []@texttt PKG_CONFIG_PATH=/opt/csw/lib/sparcv9/pkgconfig:/usr/lib/sparcv9/pkgc onfig[] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5151--5151 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s olaris"[] [66] [67] [68] [69] [70] [71] Appendix D [72] [73] [74] (Function and variable index) [75] (Concept index) [76] (Environment variable index) [77] [78] ) (see the transcript file for additional information)</usr/share/texlive/texmf-d ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu blic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a msfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont s/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cm r10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb> </usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/sh are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texl ive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/te xmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf- dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/f onts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts/t ype1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/p ublic/amsfonts/cm/cmtt9.pfb> Output written on R-admin.pdf (83 pages, 499264 bytes). Transcript written on R-admin.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-data.texi This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/«PKGBUILDDIR»/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-02-05.07.deb3]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/«PKGBUILDDIR»/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/«PKGBUILDDIR»/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/«PKGBUILDDIR»/doc/manual/version.texi) [1{/var/lib/texmf/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 hdf5 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 (10.24956pt too wide) in paragraph at lines 91--91 @texttt package=hdf5[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf ncdf 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 (13.29123pt too wide) in paragraph at lines 92--92 @texttt package=ncdf[]@textrm )[][], Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf ncdf4 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=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf rJava 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=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RJDBC 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 (15.99825pt too wide) in paragraph at lines 94--94 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RMySQL 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 (21.74693pt too wide) in paragraph at lines 95--95 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RNetCDF 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 (27.49562pt too wide) in paragraph at lines 96--96 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf RODBC 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 (15.99825pt too wide) in paragraph at lines 97--97 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 98--98 [][]@textbf ROracle 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 (27.49562pt too wide) in paragraph at lines 98--98 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 99--99 [][]@textbf RPostgreSQL Underfull \hbox (badness 10000) in paragraph at lines 99--99 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 99--99 @texttt org / Overfull \hbox (50.49037pt too wide) in paragraph at lines 99--99 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 102--102 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 102--102 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 102--102 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 102--102 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf WriteXLS 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 (33.24431pt too wide) in paragraph at lines 104--104 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XLConnect 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 (38.993pt too wide) in paragraph at lines 105--105 @texttt package=XLConnect[]@textrm )[][]| Overfull \hbox (2.49414pt too wide) in paragraph at lines 106--106 [][]@textbf xlsReadWrite Underfull \hbox (badness 10000) in paragraph at lines 106--106 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 106--106 @texttt org / Overfull \hbox (56.23906pt too wide) in paragraph at lines 106--106 @texttt package=xlsReadWrite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 107--107 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 107--107 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 107--107 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 107--107 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] Cross reference values unknown; you must run TeX again. [4] [5] [6] [7] Chapter 2 [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15] [16] Chapter 4 [17] [18] [19] [20] [21] [22] [23] Chapter 5 [24] Chapter 6 [25] Chapter 7 [26] [27] [28] [29] [30] Chapter 8 [31] Chapter 9 [32] Appendix A [33] (Function and variable index) [34] (Concept index) [35] [36] ) (see the transcript file for additional information)</usr/share/texlive/texmf-d ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub lic/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams fonts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm /cmr9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt1 0.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb> </usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/ share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/ texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texliv e/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb> Output written on R-data.pdf (39 pages, 274403 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/«PKGBUILDDIR»/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-02-05.07.deb3]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/«PKGBUILDDIR»/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/«PKGBUILDDIR»/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/«PKGBUILDDIR»/doc/manual/version.texi) [1{/var/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] (/«PKGBUILDDIR»/doc/manual/R-data.toc [-1]) [-2] (/«PKGBUILDDIR»/doc/manual/R-data.toc) (/«PKGBUILDDIR»/doc/manual/R-data.toc) (Acknowledgements) (/«PKGBUILDDIR»/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 hdf5 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 (10.24956pt too wide) in paragraph at lines 91--91 @texttt package=hdf5[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf ncdf 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 (13.29123pt too wide) in paragraph at lines 92--92 @texttt package=ncdf[]@textrm )[][], Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf ncdf4 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=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf rJava 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=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RJDBC 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 (15.99825pt too wide) in paragraph at lines 94--94 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RMySQL 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 (21.74693pt too wide) in paragraph at lines 95--95 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RNetCDF 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 (27.49562pt too wide) in paragraph at lines 96--96 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf RODBC 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 (15.99825pt too wide) in paragraph at lines 97--97 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 98--98 [][]@textbf ROracle 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 (27.49562pt too wide) in paragraph at lines 98--98 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 99--99 [][]@textbf RPostgreSQL Underfull \hbox (badness 10000) in paragraph at lines 99--99 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 99--99 @texttt org / Overfull \hbox (50.49037pt too wide) in paragraph at lines 99--99 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 102--102 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 102--102 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 102--102 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 102--102 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf WriteXLS 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 (33.24431pt too wide) in paragraph at lines 104--104 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XLConnect 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 (38.993pt too wide) in paragraph at lines 105--105 @texttt package=XLConnect[]@textrm )[][]| Overfull \hbox (2.49414pt too wide) in paragraph at lines 106--106 [][]@textbf xlsReadWrite Underfull \hbox (badness 10000) in paragraph at lines 106--106 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 106--106 @texttt org / Overfull \hbox (56.23906pt too wide) in paragraph at lines 106--106 @texttt package=xlsReadWrite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 107--107 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 107--107 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 107--107 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 107--107 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] [4] [5] [6] [7] Chapter 2 [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15] [16] Chapter 4 [17] [18] [19] [20] [21] [22] [23] Chapter 5 [24] Chapter 6 [25] Chapter 7 [26] [27] [28] [29] [30] Chapter 8 [31] Chapter 9 [32] Appendix A [33] (Function and variable index) [34] [35] (Concept index) [36] [37] ) (see the transcript file for additional information)</usr/share/texlive/texmf-d ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub lic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am sfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/ cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7 .pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></u sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/s hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/t exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive /texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf -dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/ fonts/type1/public/amsfonts/cm/cmtt9.pfb> Output written on R-data.pdf (41 pages, 313679 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/«PKGBUILDDIR»/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-02-05.07.deb3]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/«PKGBUILDDIR»/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/«PKGBUILDDIR»/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/«PKGBUILDDIR»/doc/manual/version.texi) [1{/var/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] (/«PKGBUILDDIR»/doc/manual/R-data.toc [-1]) [-2] (/«PKGBUILDDIR»/doc/manual/R-data.toc) (/«PKGBUILDDIR»/doc/manual/R-data.toc) (Acknowledgements) (/«PKGBUILDDIR»/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 hdf5 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 (10.24956pt too wide) in paragraph at lines 91--91 @texttt package=hdf5[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf ncdf 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 (13.29123pt too wide) in paragraph at lines 92--92 @texttt package=ncdf[]@textrm )[][], Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf ncdf4 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=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf rJava 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=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RJDBC 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 (15.99825pt too wide) in paragraph at lines 94--94 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RMySQL 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 (21.74693pt too wide) in paragraph at lines 95--95 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RNetCDF 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 (27.49562pt too wide) in paragraph at lines 96--96 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf RODBC 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 (15.99825pt too wide) in paragraph at lines 97--97 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 98--98 [][]@textbf ROracle 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 (27.49562pt too wide) in paragraph at lines 98--98 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 99--99 [][]@textbf RPostgreSQL Underfull \hbox (badness 10000) in paragraph at lines 99--99 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 99--99 @texttt org / Overfull \hbox (50.49037pt too wide) in paragraph at lines 99--99 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 102--102 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 102--102 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 102--102 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 102--102 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf WriteXLS 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 (33.24431pt too wide) in paragraph at lines 104--104 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XLConnect 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 (38.993pt too wide) in paragraph at lines 105--105 @texttt package=XLConnect[]@textrm )[][]| Overfull \hbox (2.49414pt too wide) in paragraph at lines 106--106 [][]@textbf xlsReadWrite Underfull \hbox (badness 10000) in paragraph at lines 106--106 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 106--106 @texttt org / Overfull \hbox (56.23906pt too wide) in paragraph at lines 106--106 @texttt package=xlsReadWrite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 107--107 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 107--107 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 107--107 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 107--107 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] [4] [5] [6] [7] Chapter 2 [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15] [16] Chapter 4 [17] [18] [19] [20] [21] [22] [23] Chapter 5 [24] Chapter 6 [25] Chapter 7 [26] [27] [28] [29] [30] Chapter 8 [31] Chapter 9 [32] Appendix A [33] (Function and variable index) [34] [35] (Concept index) [36] [37] ) (see the transcript file for additional information)</usr/share/texlive/texmf-d ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub lic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am sfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/ cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7 .pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></u sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/s hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/t exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive /texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf -dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/ fonts/type1/public/amsfonts/cm/cmtt9.pfb> Output written on R-data.pdf (41 pages, 313679 bytes). Transcript written on R-data.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-exts.texi This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/«PKGBUILDDIR»/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-02-05.07.deb3]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/«PKGBUILDDIR»/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/«PKGBUILDDIR»/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/«PKGBUILDDIR»/doc/manual/version.texi) [1{/var/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Chapter 1 [1] Cross reference values unknown; you must run TeX again. [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 494--497 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1882--1882 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [24] [25] [26] [27] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2190--2190 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (53.60722pt too wide) in paragraph at lines 2192--2192 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [28] [29] [30] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2331--2331 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [31] [32] [33] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2564--2566 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4490--4490 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [58] [59] [60] [61] [62] Overfull \hbox (13.62822pt too wide) in paragraph at lines 4865--4865 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [63] [64] [65] Chapter 2 [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 6119--6126 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [80] [81] [82] [83] Underfull \hbox (badness 10000) in paragraph at lines 6438--6442 []@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file [84] [85] Chapter 3 [86] [87] [88] [89] [90] [91] Overfull \hbox (20.69044pt too wide) in paragraph at lines 7040--7040 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [92] [93] [94] Chapter 4 [95] [96] [97] Overfull \hbox (14.94176pt too wide) in paragraph at lines 7413--7413 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [98] Overfull \hbox (25.25755pt too wide) in paragraph at lines 7453--7453 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [99] Overfull \hbox (20.53261pt too wide) in paragraph at lines 7557--7557 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] [100] Overfull \hbox (38.96663pt too wide) in paragraph at lines 7587--7596 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [101] [102] [103] [104] [105] Overfull \hbox (78.17732pt too wide) in paragraph at lines 7977--7977 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Overfull \hbox (29.50735pt too wide) in paragraph at lines 8009--8011 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] [106] [107] Overfull \hbox (72.42863pt too wide) in paragraph at lines 8154--8154 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [108] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8203--8203 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8206--8206 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [109] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8285--8285 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [110] [111] Chapter 5 [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] [125] Overfull \hbox (37.93651pt too wide) in paragraph at lines 9472--9472 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [126] [127] [128] [129] [130] [131] [132] [133] [134] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10244--10244 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [135] Underfull \hbox (badness 10000) in paragraph at lines 10305--10307 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [136] [137] [138] [139] [140] [141] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10814--10814 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [142] [143] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10937--10937 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [144] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10942--10942 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10997--10997 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11009--11009 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [145] [146] [147] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11234--11234 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [148] Overfull \hbox (43.6852pt too wide) in paragraph at lines 11316--11316 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [149] [150] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11403--11403 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] Underfull \hbox (badness 10000) in paragraph at lines 12561--12565 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [164] Warning: unbalanced parentheses in @def... [165] [166] [167] [168] [169] [170] Chapter 7 [171] [172] Chapter 8 [173] [174] [175] Overfull \hbox (43.6852pt too wide) in paragraph at lines 13433--13433 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [176] Overfull \hbox (20.69044pt too wide) in paragraph at lines 13465--13465 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 13481--13481 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [177] [178] [179] [180] Underfull \hbox (badness 10000) in paragraph at lines 13724--13731 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [181] [182] [183] [184] [185] Underfull \hbox (badness 10000) in paragraph at lines 14113--14117 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+3/600 --dpi 603 ecrm1095 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+3/600; nonstopmode; input ecrm1095 This is METAFONT, Version 2.7182818 (TeX Live 2015/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm1095.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.07599pt) Font metrics written on ecrm1095.tfm. 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(Function and variable index) [186] (Concept index) [187] [188] ) (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 </home/buildd/.texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1095.603pk></usr/shar e/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texli ve/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/tex mf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dis t/fonts/type1/public/amsfonts/cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts /type1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/ public/amsfonts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a msfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/ cm/cmr9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl1 0.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pf b></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmss10.pfb></us r/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/shar e/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/share/texli ve/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9.pfb></usr/share/texlive/texm f-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist /fonts/type1/public/amsfonts/cm/cmti9.pfb></usr/share/texlive/texmf-dist/fonts/ type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/ public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public /amsfonts/cm/cmtt9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfon ts/latxfont/lcircle1.pfb> Output written on R-exts.pdf (191 pages, 845838 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/«PKGBUILDDIR»/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-02-05.07.deb3]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/«PKGBUILDDIR»/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/«PKGBUILDDIR»/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/«PKGBUILDDIR»/doc/manual/version.texi) [1{/var/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] (/«PKGBUILDDIR»/doc/manual/R-exts.toc [-1] [-2] [-3] [-4]) [-5] (/«PKGBUILDDIR»/doc/manual/R-exts.toc) (/«PKGBUILDDIR»/doc/manual/R-exts.toc) (Acknowledgements) (/«PKGBUILDDIR»/doc/manual/R-exts.aux) Chapter 1 [1] [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 494--497 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1882--1882 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [24] [25] [26] [27] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2190--2190 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (53.60722pt too wide) in paragraph at lines 2192--2192 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [28] [29] [30] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2331--2331 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [31] [32] [33] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2564--2566 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4490--4490 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [58] [59] [60] [61] [62] Overfull \hbox (13.62822pt too wide) in paragraph at lines 4865--4865 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [63] [64] [65] Chapter 2 [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 6119--6126 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [80] [81] [82] [83] Underfull \hbox (badness 10000) in paragraph at lines 6438--6442 []@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file [84] [85] Chapter 3 [86] [87] [88] [89] [90] [91] Overfull \hbox (20.69044pt too wide) in paragraph at lines 7040--7040 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [92] [93] [94] Chapter 4 [95] [96] [97] Overfull \hbox (14.94176pt too wide) in paragraph at lines 7413--7413 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [98] Overfull \hbox (25.25755pt too wide) in paragraph at lines 7453--7453 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [99] Overfull \hbox (20.53261pt too wide) in paragraph at lines 7557--7557 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] [100] Overfull \hbox (38.96663pt too wide) in paragraph at lines 7587--7596 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [101] [102] [103] [104] [105] Overfull \hbox (78.17732pt too wide) in paragraph at lines 7977--7977 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Overfull \hbox (29.50735pt too wide) in paragraph at lines 8009--8011 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] [106] [107] Overfull \hbox (72.42863pt too wide) in paragraph at lines 8154--8154 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [108] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8203--8203 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8206--8206 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [109] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8285--8285 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [110] [111] Chapter 5 [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] [125] Overfull \hbox (37.93651pt too wide) in paragraph at lines 9472--9472 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [126] [127] [128] [129] [130] [131] [132] [133] [134] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10244--10244 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [135] Underfull \hbox (badness 10000) in paragraph at lines 10305--10307 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [136] [137] [138] [139] [140] [141] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10814--10814 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [142] [143] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10937--10937 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [144] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10942--10942 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10997--10997 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11009--11009 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [145] [146] [147] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11234--11234 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [148] Overfull \hbox (43.6852pt too wide) in paragraph at lines 11316--11316 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [149] [150] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11403--11403 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] Underfull \hbox (badness 10000) in paragraph at lines 12561--12565 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [164] Warning: unbalanced parentheses in @def... [165] [166] [167] [168] [169] [170] Chapter 7 [171] [172] Chapter 8 [173] [174] [175] Overfull \hbox (43.6852pt too wide) in paragraph at lines 13433--13433 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [176] Overfull \hbox (20.69044pt too wide) in paragraph at lines 13465--13465 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 13481--13481 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [177] [178] [179] [180] Underfull \hbox (badness 10000) in paragraph at lines 13724--13731 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [181] [182] [183] [184] [185] Underfull \hbox (badness 10000) in paragraph at lines 14113--14117 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [186] [187] [188] (Concept index) [189] [190] [191] ) (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 </home/buildd/.texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1095.603pk></usr/shar e/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texli ve/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/tex mf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dis t/fonts/type1/public/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/font s/type1/public/amsfonts/cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1 /public/amsfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public /amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfon ts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cm r8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb>< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/s hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share /texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmss10.pfb></usr/share/texli ve/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/tex mf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/share/texlive/texmf-dist /fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts /type1/public/amsfonts/cm/cmti9.pfb></usr/share/texlive/texmf-dist/fonts/type1/ public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public /amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo nts/cm/cmtt9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/lat xfont/lcircle1.pfb> Output written on R-exts.pdf (198 pages, 903788 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/«PKGBUILDDIR»/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-02-05.07.deb3]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/«PKGBUILDDIR»/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/«PKGBUILDDIR»/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/«PKGBUILDDIR»/doc/manual/version.texi) [1{/var/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] (/«PKGBUILDDIR»/doc/manual/R-exts.toc [-1] [-2] [-3] [-4]) [-5] (/«PKGBUILDDIR»/doc/manual/R-exts.toc) (/«PKGBUILDDIR»/doc/manual/R-exts.toc) (Acknowledgements) (/«PKGBUILDDIR»/doc/manual/R-exts.aux) Chapter 1 [1] [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 494--497 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1882--1882 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [24] [25] [26] [27] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2190--2190 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (53.60722pt too wide) in paragraph at lines 2192--2192 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [28] [29] [30] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2331--2331 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [31] [32] [33] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2564--2566 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4490--4490 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [58] [59] [60] [61] [62] Overfull \hbox (13.62822pt too wide) in paragraph at lines 4865--4865 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [63] [64] [65] Chapter 2 [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 6119--6126 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [80] [81] [82] [83] Underfull \hbox (badness 10000) in paragraph at lines 6438--6442 []@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file [84] [85] Chapter 3 [86] [87] [88] [89] [90] [91] Overfull \hbox (20.69044pt too wide) in paragraph at lines 7040--7040 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [92] [93] [94] Chapter 4 [95] [96] [97] Overfull \hbox (14.94176pt too wide) in paragraph at lines 7413--7413 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [98] Overfull \hbox (25.25755pt too wide) in paragraph at lines 7453--7453 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [99] Overfull \hbox (20.53261pt too wide) in paragraph at lines 7557--7557 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] [100] Overfull \hbox (38.96663pt too wide) in paragraph at lines 7587--7596 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [101] [102] [103] [104] [105] Overfull \hbox (78.17732pt too wide) in paragraph at lines 7977--7977 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Overfull \hbox (29.50735pt too wide) in paragraph at lines 8009--8011 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] [106] [107] Overfull \hbox (72.42863pt too wide) in paragraph at lines 8154--8154 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [108] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8203--8203 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8206--8206 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [109] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8285--8285 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [110] [111] Chapter 5 [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] [125] Overfull \hbox (37.93651pt too wide) in paragraph at lines 9472--9472 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [126] [127] [128] [129] [130] [131] [132] [133] [134] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10244--10244 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [135] Underfull \hbox (badness 10000) in paragraph at lines 10305--10307 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [136] [137] [138] [139] [140] [141] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10814--10814 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [142] [143] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10937--10937 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [144] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10942--10942 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10997--10997 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11009--11009 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [145] [146] [147] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11234--11234 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [148] Overfull \hbox (43.6852pt too wide) in paragraph at lines 11316--11316 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [149] [150] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11403--11403 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] Underfull \hbox (badness 10000) in paragraph at lines 12561--12565 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [164] Warning: unbalanced parentheses in @def... [165] [166] [167] [168] [169] [170] Chapter 7 [171] [172] Chapter 8 [173] [174] [175] Overfull \hbox (43.6852pt too wide) in paragraph at lines 13433--13433 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [176] Overfull \hbox (20.69044pt too wide) in paragraph at lines 13465--13465 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 13481--13481 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [177] [178] [179] [180] Underfull \hbox (badness 10000) in paragraph at lines 13724--13731 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [181] [182] [183] [184] [185] Underfull \hbox (badness 10000) in paragraph at lines 14113--14117 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [186] [187] [188] (Concept index) [189] [190] [191] ) (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 </home/buildd/.texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1095.603pk></usr/shar e/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texli ve/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/tex mf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dis t/fonts/type1/public/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/font s/type1/public/amsfonts/cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1 /public/amsfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public /amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfon ts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cm r8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb>< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/s hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share /texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmss10.pfb></usr/share/texli ve/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/tex mf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/share/texlive/texmf-dist /fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts /type1/public/amsfonts/cm/cmti9.pfb></usr/share/texlive/texmf-dist/fonts/type1/ public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public /amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo nts/cm/cmtt9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/lat xfont/lcircle1.pfb> Output written on R-exts.pdf (198 pages, 903807 bytes). Transcript written on R-exts.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-FAQ.texi This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/«PKGBUILDDIR»/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-02-05.07.deb3]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/«PKGBUILDDIR»/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/tex/texinfo/txi-en.tex) [1{/var/lib/texmf/fonts/map/pdftex/up dmap/pdftex.map}] [-1] Chapter 1 Cross reference values unknown; you must run TeX again. [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [19] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6 [26] [27] Chapter 7 [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3367--3375 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [43] Chapter 8 [44] Chapter 9 [45] [46] Chapter 10 [47] [48] [49] ) (see the transcript file for additional information)</usr/share/texlive/texmf-d ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu blic/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a msfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont s/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/c mmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pf b></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/ share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/te xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/ texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texm f-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist /fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts /type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1 /public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi c/amsfonts/cm/cmtt9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo nts/latxfont/lcircle1.pfb> Output written on R-FAQ.pdf (51 pages, 366909 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/«PKGBUILDDIR»/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-02-05.07.deb3]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/«PKGBUILDDIR»/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/tex/texinfo/txi-en.tex) [1{/var/lib/texmf/fonts/map/pdftex/up dmap/pdftex.map}] (/«PKGBUILDDIR»/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/«PKGBUILDDIR»/doc/manual/R-FAQ.toc) (/«PKGBUILDDIR»/doc/manual/R-FAQ.toc) Chapter 1 (/«PKGBUILDDIR»/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [19] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6 [26] [27] Chapter 7 [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3367--3375 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [43] Chapter 8 [44] Chapter 9 [45] [46] Chapter 10 [47] [48] [49] ) (see the transcript file for additional information)</usr/share/texlive/texmf-d ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu blic/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a msfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont s/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/c mmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pf b></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/ share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/te xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/ texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texm f-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist /fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts /type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1 /public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi c/amsfonts/cm/cmtt9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo nts/latxfont/lcircle1.pfb> Output written on R-FAQ.pdf (53 pages, 383569 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/«PKGBUILDDIR»/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-02-05.07.deb3]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/«PKGBUILDDIR»/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/tex/texinfo/txi-en.tex) [1{/var/lib/texmf/fonts/map/pdftex/up dmap/pdftex.map}] (/«PKGBUILDDIR»/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/«PKGBUILDDIR»/doc/manual/R-FAQ.toc) (/«PKGBUILDDIR»/doc/manual/R-FAQ.toc) Chapter 1 (/«PKGBUILDDIR»/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [19] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6 [26] [27] Chapter 7 [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3367--3375 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [43] Chapter 8 [44] Chapter 9 [45] [46] Chapter 10 [47] [48] [49] ) (see the transcript file for additional information)</usr/share/texlive/texmf-d ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ e1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu blic/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a msfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont s/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/c mmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pf b></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/ share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/te xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/ texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texm f-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist /fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts /type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1 /public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi c/amsfonts/cm/cmtt9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo nts/latxfont/lcircle1.pfb> Output written on R-FAQ.pdf (53 pages, 383561 bytes). Transcript written on R-FAQ.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/«PKGBUILDDIR»/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-02-05.07.deb3]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/«PKGBUILDDIR»/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/«PKGBUILDDIR»/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/«PKGBUILDDIR»/doc/manual/version.texi) [1{/var/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Preface) Cross reference values unknown; you must run TeX again. Chapter 1 [1] [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] [15] Chapter 4 [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Chapter 6 [28] [29] [30] [31] Chapter 7 [32] [33] [34] Chapter 8 [35] [36] [37] </«PKGBUILDDIR»/doc/manual/images/hist.pdf> < /«PKGBUILDDIR»/doc/manual/images/ecdf.pdf> [38] </build/r-ba se-asNdei/r-base-3.3.0/doc/manual/images/QQ.pdf> [39] </«BUILDDIR»/r-b ase-3.3.0/doc/manual/images/ice.pdf> [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Chapter 11 [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] Chapter 12 [67] [68] [69] [70] [71] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5743--5743 []@texttt > text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{ n-x})))[] [72] [73] [74] [75] [76] </«PKGBUILDDIR»/doc/manual/images/f ig11.pdf> [77] </«PKGBUILDDIR»/doc/manual/images/fig12.pdf> [78] [79] [80] [81] Chapter 13 [82] Underfull \hbox (badness 10000) in paragraph at lines 6449--6454 []@textrm Users con-nected to the In-ter-net can use the @texttt install.packag es()[] @textrm and [83] Chapter 14 [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 6650--6655 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and [86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95] [96] [97] [98] Appendix C [99] [100] Appendix D [101] Appendix E [102] Appendix F [103] [104] ) (see the transcript file for additional information) </home/buildd/.texmf-var/f onts/pk/ljfour/jknappen/ec/ecrm1095.603pk></usr/share/texlive/texmf-dist/fonts/ type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type1/p ublic/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ amsfonts/cm/cmbx7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont s/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/ cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10 .pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi7.pfb></ usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi9.pfb></usr/sha re/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texl ive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/share/texlive/texm f-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dist/f onts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texlive/texmf-dist/fonts/typ e1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub lic/amsfonts/cm/cmsl9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams fonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont s/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/c msy7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9.pf b></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></us r/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti9.pfb></usr/share /texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texli ve/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/tex mf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb></usr/share/texlive/texmf-dist /fonts/type1/public/amsfonts/latxfont/lcircle1.pfb> Output written on R-intro.pdf (107 pages, 584454 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/«PKGBUILDDIR»/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-02-05.07.deb3]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/«PKGBUILDDIR»/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/«PKGBUILDDIR»/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/«PKGBUILDDIR»/doc/manual/version.texi) [1{/var/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] (/«PKGBUILDDIR»/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/«PKGBUILDDIR»/doc/manual/R-intro.toc) (/«PKGBUILDDIR»/doc/manual/R-intro.toc) (Preface) (/«PKGBUILDDIR»/doc/manual/R-intro.aux) Chapter 1 [1] [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] [15] Chapter 4 [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Chapter 6 [28] [29] [30] [31] Chapter 7 [32] [33] [34] Chapter 8 [35] [36] [37] </«PKGBUILDDIR»/doc/manual/images/h ist.pdf> </«PKGBUILDDIR»/doc/manual/images/ecdf.pdf> [38] </«PKGBUILDDIR»/doc/manual/images/QQ.pdf> [39] </build/ r-base-asNdei/r-base-3.3.0/doc/manual/images/ice.pdf> [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Chapter 11 [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] Chapter 12 [67] [68] [69] [70] [71] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5743--5743 []@texttt > text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{ n-x})))[] [72] [73] [74] [75] [76] </«PKGBUILDDIR»/doc/manual/images/f ig11.pdf> [77] </«PKGBUILDDIR»/doc/manual/images/fig12.pdf> [78] [79] [80] [81] Chapter 13 [82] Underfull \hbox (badness 10000) in paragraph at lines 6449--6454 []@textrm Users con-nected to the In-ter-net can use the @texttt install.packag es()[] @textrm and [83] Chapter 14 [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 6650--6655 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and [86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95] [96] [97] [98] Appendix C [99] [100] Appendix D [101] [102] [103] Appendix E [104] [105] Appendix F [106] [107] ) (see the transcript file for additional information) </home/buildd/.texmf-var/f onts/pk/ljfour/jknappen/ec/ecrm1095.603pk></usr/share/texlive/texmf-dist/fonts/ type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type1/p ublic/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ amsfonts/cm/cmbx7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont s/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/ cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10 .pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi12.pfb>< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi7.pfb></usr/sh are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi9.pfb></usr/share/tex live/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/te xmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/share/texlive/texmf-dist /fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/t ype1/public/amsfonts/cm/cmr9.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub lic/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am sfonts/cm/cmsl9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/ cm/cmsltt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/c msy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.p fb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></u sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti9.pfb></usr/shar e/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texl ive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/te xmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb></usr/share/texlive/texmf-dis t/fonts/type1/public/amsfonts/latxfont/lcircle1.pfb> Output written on R-intro.pdf (113 pages, 634192 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/«PKGBUILDDIR»/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-02-05.07.deb3]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/«PKGBUILDDIR»/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/«PKGBUILDDIR»/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/«PKGBUILDDIR»/doc/manual/version.texi) [1{/var/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] (/«PKGBUILDDIR»/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/«PKGBUILDDIR»/doc/manual/R-intro.toc) (/«PKGBUILDDIR»/doc/manual/R-intro.toc) (Preface) (/«PKGBUILDDIR»/doc/manual/R-intro.aux) Chapter 1 [1] [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] [15] Chapter 4 [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Chapter 6 [28] [29] [30] [31] Chapter 7 [32] [33] [34] Chapter 8 [35] [36] [37] </«PKGBUILDDIR»/doc/manual/images/h ist.pdf> </«PKGBUILDDIR»/doc/manual/images/ecdf.pdf> [38] </«PKGBUILDDIR»/doc/manual/images/QQ.pdf> [39] </build/ r-base-asNdei/r-base-3.3.0/doc/manual/images/ice.pdf> [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Chapter 11 [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] Chapter 12 [67] [68] [69] [70] [71] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5743--5743 []@texttt > text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{ n-x})))[] [72] [73] [74] [75] [76] </«PKGBUILDDIR»/doc/manual/images/f ig11.pdf> [77] </«PKGBUILDDIR»/doc/manual/images/fig12.pdf> [78] [79] [80] [81] Chapter 13 [82] Underfull \hbox (badness 10000) in paragraph at lines 6449--6454 []@textrm Users con-nected to the In-ter-net can use the @texttt install.packag es()[] @textrm and [83] Chapter 14 [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 6650--6655 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and [86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95] [96] [97] [98] Appendix C [99] [100] Appendix D [101] [102] [103] Appendix E [104] [105] Appendix F [106] [107] ) (see the transcript file for additional information) </home/buildd/.texmf-var/f onts/pk/ljfour/jknappen/ec/ecrm1095.603pk></usr/share/texlive/texmf-dist/fonts/ type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type1/p ublic/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ amsfonts/cm/cmbx7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont s/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/ cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10 .pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi12.pfb>< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi7.pfb></usr/sh are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi9.pfb></usr/share/tex live/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/te xmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/share/texlive/texmf-dist /fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/t ype1/public/amsfonts/cm/cmr9.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub lic/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am sfonts/cm/cmsl9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/ cm/cmsltt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/c msy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.p fb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></u sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti9.pfb></usr/shar e/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texl ive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/te xmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb></usr/share/texlive/texmf-dis t/fonts/type1/public/amsfonts/latxfont/lcircle1.pfb> Output written on R-intro.pdf (113 pages, 634289 bytes). Transcript written on R-intro.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-ints.texi This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/«PKGBUILDDIR»/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-02-05.07.deb3]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/«PKGBUILDDIR»/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/«PKGBUILDDIR»/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/«PKGBUILDDIR»/doc/manual/version.texi) [1{/var/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Chapter 2 [24] [25] Overfull \hbox (26.43913pt too wide) in paragraph at lines 1970--1970 [] @texttt if (!is.character(x)) x <- structure(as.character(x), names = na mes(x))[] [26] [27] [28] [29] Chapter 3 [30] [31] Chapter 4 [32] [33] Chapter 5 [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] Chapter 7 [48] Underfull \hbox (badness 10000) in paragraph at lines 3617--3626 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3617--3626 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [49] Chapter 8 [50] [51] [52] [53] [54] Underfull \hbox (badness 10000) in paragraph at lines 3991--3999 @texttt CRAN . R-project . org / package=codetools[]@textrm )[][] func-tions u sed for Underfull \hbox (badness 7869) in paragraph at lines 3991--3999 @textrm an-a-lyz-ing pack-age code. E.g., use @texttt _R_CHECK_CODETOOLS_PROFI LE_ Underfull \hbox (badness 10000) in paragraph at lines 3991--3999 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [55] [56] Chapter 9 [57] [58] Chapter 10 [59] Chapter 11 [60] Chapter 12 [61] [62] (Function and variable index) [63] [64] (Concept index) [65] [66] ) (see the transcript file for additional information) </home/buildd/.texmf-var/f onts/pk/ljfour/jknappen/ec/ecrm1095.603pk></usr/share/texlive/texmf-dist/fonts/ type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type1/p ublic/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfont s/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr 8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></ usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/sh are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/ texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texliv e/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texm f-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist /fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts /type1/public/amsfonts/cm/cmtt9.pfb> Output written on R-ints.pdf (69 pages, 383089 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/«PKGBUILDDIR»/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-02-05.07.deb3]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/«PKGBUILDDIR»/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/«PKGBUILDDIR»/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/«PKGBUILDDIR»/doc/manual/version.texi) [1{/var/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] (/«PKGBUILDDIR»/doc/manual/R-ints.toc [-1] [-2]) [-3] (/«PKGBUILDDIR»/doc/manual/R-ints.toc) (/«PKGBUILDDIR»/doc/manual/R-ints.toc) Chapter 1 (/«PKGBUILDDIR»/doc/manual/R-ints.aux) [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Chapter 2 [24] [25] Overfull \hbox (26.43913pt too wide) in paragraph at lines 1970--1970 [] @texttt if (!is.character(x)) x <- structure(as.character(x), names = na mes(x))[] [26] [27] [28] [29] Chapter 3 [30] [31] Chapter 4 [32] [33] Chapter 5 [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] Chapter 7 [48] Underfull \hbox (badness 10000) in paragraph at lines 3617--3626 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3617--3626 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [49] Chapter 8 [50] [51] [52] [53] [54] Underfull \hbox (badness 10000) in paragraph at lines 3991--3999 @texttt CRAN . R-project . org / package=codetools[]@textrm )[][] func-tions u sed for Underfull \hbox (badness 7869) in paragraph at lines 3991--3999 @textrm an-a-lyz-ing pack-age code. E.g., use @texttt _R_CHECK_CODETOOLS_PROFI LE_ Underfull \hbox (badness 10000) in paragraph at lines 3991--3999 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [55] [56] Chapter 9 [57] [58] Chapter 10 [59] Chapter 11 [60] Chapter 12 [61] [62] (Function and variable index) [63] [64] [65] (Concept index) [66] [67] ) (see the transcript file for additional information) </home/buildd/.texmf-var/f onts/pk/ljfour/jknappen/ec/ecrm1095.603pk></usr/share/texlive/texmf-dist/fonts/ type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type1/p ublic/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfon ts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/ cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.p fb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr /share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/t exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texlive/t exmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texmf-d ist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-dist/ fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/ type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts/type1/ public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public /amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo nts/cm/cmtt9.pfb> Output written on R-ints.pdf (72 pages, 431209 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/«PKGBUILDDIR»/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-02-05.07.deb3]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/«PKGBUILDDIR»/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/«PKGBUILDDIR»/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/«PKGBUILDDIR»/doc/manual/version.texi) [1{/var/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] (/«PKGBUILDDIR»/doc/manual/R-ints.toc [-1] [-2]) [-3] (/«PKGBUILDDIR»/doc/manual/R-ints.toc) (/«PKGBUILDDIR»/doc/manual/R-ints.toc) Chapter 1 (/«PKGBUILDDIR»/doc/manual/R-ints.aux) [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Chapter 2 [24] [25] Overfull \hbox (26.43913pt too wide) in paragraph at lines 1970--1970 [] @texttt if (!is.character(x)) x <- structure(as.character(x), names = na mes(x))[] [26] [27] [28] [29] Chapter 3 [30] [31] Chapter 4 [32] [33] Chapter 5 [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] Chapter 7 [48] Underfull \hbox (badness 10000) in paragraph at lines 3617--3626 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3617--3626 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [49] Chapter 8 [50] [51] [52] [53] [54] Underfull \hbox (badness 10000) in paragraph at lines 3991--3999 @texttt CRAN . R-project . org / package=codetools[]@textrm )[][] func-tions u sed for Underfull \hbox (badness 7869) in paragraph at lines 3991--3999 @textrm an-a-lyz-ing pack-age code. E.g., use @texttt _R_CHECK_CODETOOLS_PROFI LE_ Underfull \hbox (badness 10000) in paragraph at lines 3991--3999 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [55] [56] Chapter 9 [57] [58] Chapter 10 [59] Chapter 11 [60] Chapter 12 [61] [62] (Function and variable index) [63] [64] [65] (Concept index) [66] [67] ) (see the transcript file for additional information) </home/buildd/.texmf-var/f onts/pk/ljfour/jknappen/ec/ecrm1095.603pk></usr/share/texlive/texmf-dist/fonts/ type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fonts/type1/p ublic/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfon ts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/ cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.p fb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr /share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/t exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></usr/share/texlive/t exmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texmf-d ist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-dist/ fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/ type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf-dist/fonts/type1/ public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public /amsfonts/cm/cmtt12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo nts/cm/cmtt9.pfb> Output written on R-ints.pdf (72 pages, 431212 bytes). Transcript written on R-ints.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-lang.texi This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/«PKGBUILDDIR»/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-02-05.07.deb3]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/«PKGBUILDDIR»/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/«PKGBUILDDIR»/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/«PKGBUILDDIR»/doc/manual/version.texi) [1{/var/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 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] [8] Chapter 3 [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Chapter 4 [24] [25] [26] [27] [28] Chapter 5 [29] [30] [31] [32] [33] [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] Chapter 7 [44] [45] Chapter 8 [46] [47] Chapter 9 [48] [49] [50] Chapter 10 [51] [52] [53] [54] [55] [56] [57] [58] (Function and Variable Index) [59] (Concept Index) [60] Appendix A [61] [62] ) (see the transcript file for additional information)</usr/share/texlive/texmf-d ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub lic/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams fonts/cm/cmr7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm /cmr9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10. pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb> </usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/ share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9.pfb></usr/share/t exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive /texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf -dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb> Output written on R-lang.pdf (65 pages, 330635 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/«PKGBUILDDIR»/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-02-05.07.deb3]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/«PKGBUILDDIR»/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/«PKGBUILDDIR»/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/«PKGBUILDDIR»/doc/manual/version.texi) [1{/var/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] (/«PKGBUILDDIR»/doc/manual/R-lang.toc [-1] [-2]) [-3] (/«PKGBUILDDIR»/doc/manual/R-lang.toc) (/«PKGBUILDDIR»/doc/manual/R-lang.toc) Chapter 1 (/«PKGBUILDDIR»/doc/manual/R-lang.aux) Chapter 2 [1] [2] Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [4] [5] [6] [7] [8] Chapter 3 [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Chapter 4 [24] [25] [26] [27] [28] Chapter 5 [29] [30] [31] [32] [33] [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] Chapter 7 [44] [45] Chapter 8 [46] [47] Chapter 9 [48] [49] [50] Chapter 10 [51] [52] [53] [54] [55] [56] [57] [58] (Function and Variable Index) [59] [60] (Concept Index) [61] Appendix A [62] Overfull \vbox (26.25688pt too high) has occurred while \output is active [63] [64] ) (see the transcript file for additional information)</usr/share/texlive/texmf-d ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub lic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am sfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/ cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7 .pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></u sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/sha re/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/t exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive /texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf -dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/ fonts/type1/public/amsfonts/cm/cmtt9.pfb> Output written on R-lang.pdf (69 pages, 379064 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/«PKGBUILDDIR»/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-02-05.07.deb3]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/«PKGBUILDDIR»/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/«PKGBUILDDIR»/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/«PKGBUILDDIR»/doc/manual/version.texi) [1{/var/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] (/«PKGBUILDDIR»/doc/manual/R-lang.toc [-1] [-2]) [-3] (/«PKGBUILDDIR»/doc/manual/R-lang.toc) (/«PKGBUILDDIR»/doc/manual/R-lang.toc) Chapter 1 (/«PKGBUILDDIR»/doc/manual/R-lang.aux) Chapter 2 [1] [2] Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [4] [5] [6] [7] [8] Chapter 3 [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Chapter 4 [24] [25] [26] [27] [28] Chapter 5 [29] [30] [31] [32] [33] [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] Chapter 7 [44] [45] Chapter 8 [46] [47] Chapter 9 [48] [49] [50] Chapter 10 [51] [52] [53] [54] [55] [56] [57] [58] (Function and Variable Index) [59] [60] (Concept Index) [61] Appendix A [62] Overfull \vbox (26.25688pt too high) has occurred while \output is active [63] [64] ) (see the transcript file for additional information)</usr/share/texlive/texmf-d ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub lic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am sfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/ cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7 .pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb></u sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb></usr/sha re/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr/share/t exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive /texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive/texmf -dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/ fonts/type1/public/amsfonts/cm/cmtt9.pfb> Output written on R-lang.pdf (69 pages, 379063 bytes). Transcript written on R-lang.log. make[1]: Leaving directory '/«PKGBUILDDIR»/doc/manual' /usr/bin/make -k pdf make[1]: Entering directory '/«PKGBUILDDIR»' make[2]: Entering directory '/«PKGBUILDDIR»/doc' make[3]: Entering directory '/«PKGBUILDDIR»/doc/manual' PDF/LaTeX documentation: full reference index ... This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./fullrefman.tex LaTeX2e <2016/02/01> Babel <3.9q> and hyphenation patterns for 3 language(s) loaded. 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(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) Underfull \hbox (badness 4595) in paragraph at lines 40--43 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [1] [2] Underfull \hbox (badness 1960) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is 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 [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 296--300 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 381--384 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 524--530 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/n/10 insertions\T1/ptm/m/n/10 ', [9] [10] [11] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 2671) in paragraph at lines 1135--1138 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] [22] Underfull \hbox (badness 4072) in paragraph at lines 1369--1375 []\T1/zi4/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/zi4/m/n/10 x mod y \T1/ptm/m /n/10 and \T1/zi4/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I t is guar-an-teed that [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.88089pt too wide) in paragraph at lines 1894--1894 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2079--2081 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3580--3582 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] Underfull \hbox (badness 2521) in paragraph at lines 4782--4784 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] Overfull \hbox (7.0809pt too wide) in paragraph at lines 5909--5909 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [93] [94] [95] Underfull \hbox (badness 2096) in paragraph at lines 6090--6103 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [96] [97] [98] Overfull \hbox (58.35893pt too wide) in paragraph at lines 6293--6295 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [99] [100] Underfull \hbox (badness 10000) in paragraph at lines 6434--6437 []\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is [101] [102] Underfull \hbox (badness 1442) in paragraph at lines 6599--6605 []\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/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6599--6605 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6599--6605 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [103] Underfull \hbox (badness 3568) in paragraph at lines 6660--6667 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [104] [105] Underfull \vbox (badness 10000) has occurred while \output is active [106] [107] [108] [109] [110] [111] [112] [113] Underfull \hbox (badness 2096) in paragraph at lines 7298--7302 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [114] Underfull \hbox (badness 4595) in paragraph at lines 7355--7358 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [115] Underfull \hbox (badness 3000) in paragraph at lines 7391--7393 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7416--7419 [][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [116] [117] [118] [119] Underfull \hbox (badness 10000) in paragraph at lines 7671--7682 []\T1/zi4/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 [120] [121] Underfull \hbox (badness 4479) in paragraph at lines 7743--7752 [][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), Underfull \hbox (badness 2469) in paragraph at lines 7743--7752 [][]\T1/zi4/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods, [][]\T1/zi4/m/n/10 Math.data.frame[][][] \T1/ptm/m/n/10 etc, about \T1/ptm/m/i t/10 Group \T1/ptm/m/n/10 meth-ods for [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] Underfull \hbox (badness 1394) in paragraph at lines 9355--9360 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [146] [147] [148] [149] [150] Underfull \hbox (badness 1052) in paragraph at lines 9698--9703 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 9698--9703 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [151] [152] Underfull \hbox (badness 1735) in paragraph at lines 9836--9840 \T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ zi4/m/n/10 https : / / en . wikipedia . [153] [154] [155] [156] [157] [158] Underfull \hbox (badness 2150) in paragraph at lines 10240--10243 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse [159] Underfull \hbox (badness 6396) in paragraph at lines 10254--10262 []\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 2409) in paragraph at lines 10295--10302 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] Underfull \hbox (badness 4569) in paragraph at lines 11341--11345 []\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 11341--11345 \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 [176] [177] [178] [179] [180] [181] [182] [183] Underfull \hbox (badness 2698) in paragraph at lines 11917--11926 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 11917--11926 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] Underfull \hbox (badness 6236) in paragraph at lines 12561--12564 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [194] [195] [196] [197] [198] [199] Underfull \hbox (badness 2253) in paragraph at lines 12939--12941 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [200] Underfull \hbox (badness 1565) in paragraph at lines 13010--13014 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and [201] Underfull \hbox (badness 10000) in paragraph at lines 13054--13056 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with [202] [203] Underfull \hbox (badness 1466) in paragraph at lines 13195--13198 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ zi4/m/n/10 file.copy \T1/ptm/m/n/10 and [204] [205] Underfull \hbox (badness 10000) in paragraph at lines 13303--13307 [][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13314--13317 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [206] [207] [208] [209] Underfull \hbox (badness 3965) in paragraph at lines 13577--13581 []\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, [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] Underfull \hbox (badness 4429) in paragraph at lines 14338--14341 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [222] Underfull \hbox (badness 10000) in paragraph at lines 14430--14432 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14436--14440 []\T1/zi4/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 [223] Underfull \hbox (badness 10000) in paragraph at lines 14478--14482 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 14478--14482 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [224] Underfull \vbox (badness 3803) has occurred while \output is active [225] [226] [227] [228] [229] [230] [231] [232] Underfull \hbox (badness 2452) in paragraph at lines 15058--15062 []\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 15058--15062 \T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_ WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and [233] [234] [235] Underfull \hbox (badness 1092) in paragraph at lines 15231--15236 [][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [236] [237] [238] [239] Underfull \hbox (badness 6741) in paragraph at lines 15479--15483 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [240] [241] [242] [243] Underfull \hbox (badness 1867) in paragraph at lines 15785--15792 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [244] [245] [246] [247] Underfull \vbox (badness 10000) has occurred while \output is active [248] [249] Underfull \hbox (badness 3679) in paragraph at lines 16166--16168 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [250] [251] [252] [253] [254] [255] [256] [257] Underfull \hbox (badness 1478) in paragraph at lines 16711--16714 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [258] [259] [260] [261] Underfull \hbox (badness 10000) in paragraph at lines 16964--16966 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [262] [263] [264] [265] [266] [267] [268] [269] [270] Underfull \hbox (badness 1442) in paragraph at lines 17527--17529 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [271] Underfull \hbox (badness 2452) in paragraph at lines 17619--17635 [][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [272] [273] [274] [275] [276] [277] [278] Underfull \hbox (badness 1248) in paragraph at lines 18033--18036 []\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/ m/n/10 , [279] [280] [281] [282] Underfull \hbox (badness 4739) in paragraph at lines 18291--18293 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] Underfull \hbox (badness 1360) in paragraph at lines 19249--19254 \T1/zi4/m/n/10 "none"\T1/ptm/m/n/10 . It is in-tended for the ver-sion of OpenS SL used, but not all Underfull \hbox (badness 10000) in paragraph at lines 19272--19278 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / Underfull \hbox (badness 1127) in paragraph at lines 19272--19278 \T1/zi4/m/n/10 ssl-[]compared . html$[][] \T1/ptm/m/n/10 for more de-tails on S SL ver-sions. Nor-mally \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 used with \T1/phv /m/n/10 R [299] Underfull \hbox (badness 10000) in paragraph at lines 19345--19349 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 19345--19349 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [300] [301] Underfull \hbox (badness 1509) in paragraph at lines 19480--19487 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1354) in paragraph at lines 19480--19487 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19496--19501 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313] Underfull \hbox (badness 1264) in paragraph at lines 20227--20232 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] Underfull \hbox (badness 10000) in paragraph at lines 20981--20983 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] Underfull \hbox (badness 1077) in paragraph at lines 21979--21985 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [341] [342] [343] Underfull \hbox (badness 1484) in paragraph at lines 22140--22148 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [344] [345] [346] [347] Underfull \hbox (badness 2790) in paragraph at lines 22411--22414 []\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 22411--22414 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [348] [349] [350] [351] Underfull \hbox (badness 1194) in paragraph at lines 22692--22695 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 . It calls [352] [353] [354] [355] Underfull \hbox (badness 10000) in paragraph at lines 22898--22904 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 5862) in paragraph at lines 22898--22904 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 22908--22911 []\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 22908--22911 \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 [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] [367] [368] [369] Underfull \hbox (badness 10000) in paragraph at lines 23839--23841 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [370] [371] [372] [373] Underfull \hbox (badness 1199) in paragraph at lines 24066--24072 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24066--24072 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [374] [375] [376] [377] [378] [379] [380] [381] Underfull \hbox (badness 1038) in paragraph at lines 24645--24653 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 1881) in paragraph at lines 24654--24657 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 24673--24675 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [382] Underfull \hbox (badness 10000) in paragraph at lines 24745--24755 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 24756--24762 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able Underfull \hbox (badness 1968) in paragraph at lines 24769--24774 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 24779--24781 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [383] [384] Underfull \vbox (badness 10000) has occurred while \output is active [385] Underfull \hbox (badness 10000) in paragraph at lines 25034--25040 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/zi4/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25034--25040 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 25034--25040 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by [386] Underfull \hbox (badness 10000) in paragraph at lines 25047--25050 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 25071--25073 []\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 25103--25108 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 25109--25120 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 25121--25124 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and [387] Underfull \hbox (badness 4084) in paragraph at lines 25131--25143 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN OS X build), Underfull \hbox (badness 10000) in paragraph at lines 25131--25143 \T1/zi4/m/n/10 "mac.binary."\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.maveric ks" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for C RAN Underfull \hbox (badness 7397) in paragraph at lines 25131--25143 \T1/ptm/m/n/10 OS X builds). Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m /n/10 . (\T1/zi4/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 25145--25152 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 25145--25152 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 25145--25152 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1082) in paragraph at lines 25145--25152 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [388] [389] [390] [391] [392] Underfull \hbox (badness 10000) in paragraph at lines 25491--25495 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 25491--25495 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [393] [394] [395] [396] [397] Underfull \hbox (badness 1735) in paragraph at lines 25809--25813 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [398] [399] [400] [401] [402] [403] [404] [405] [406] Underfull \hbox (badness 2726) in paragraph at lines 26369--26372 []\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] [418] [419] Underfull \hbox (badness 1052) in paragraph at lines 27186--27191 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [420] [421] [422] [423] [424] Underfull \vbox (badness 10000) has occurred while \output is active [425] [426] [427] [428] [429] [430] [431] Underfull \hbox (badness 1533) in paragraph at lines 27995--27998 []\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 [432] [433] [434] Underfull \hbox (badness 1163) in paragraph at lines 28157--28168 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] Underfull \hbox (badness 10000) in paragraph at lines 29676--29680 []\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 29676--29680 \T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. Underfull \hbox (badness 6188) in paragraph at lines 29698--29700 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [459] [460] [461] [462] [463] [464] [465] [466] [467] Underfull \hbox (badness 1655) in paragraph at lines 30246--30248 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm /m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for [468] [469] [470] [471] [472] [473] [474] [475] [476] [477] [478] Underfull \hbox (badness 10000) in paragraph at lines 30914--30918 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [479] [480] [481] Underfull \hbox (badness 2302) in paragraph at lines 31154--31161 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 31154--31161 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 2980) in paragraph at lines 31154--31161 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 31154--31161 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [482] [483] [484] Underfull \hbox (badness 2261) in paragraph at lines 31310--31315 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if Underfull \hbox (badness 10000) in paragraph at lines 31337--31343 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [485] Underfull \hbox (badness 10000) in paragraph at lines 31413--31418 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [486] [487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] Underfull \hbox (badness 1072) in paragraph at lines 34333--34337 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 34338--34342 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 34366--34372 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 34366--34372 \T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 34366--34372 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in Underfull \hbox (badness 3343) in paragraph at lines 34379--34386 \T1/ptm/m/n/10 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 34379--34386 \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 Underfull \hbox (badness 1917) in paragraph at lines 34379--34386 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [532] [533] [534] [535] [536] Underfull \hbox (badness 10000) in paragraph at lines 34670--34676 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1152) in paragraph at lines 34670--34676 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] Underfull \hbox (badness 3333) in paragraph at lines 36500--36505 []\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] Underfull \hbox (badness 1472) in paragraph at lines 37120--37123 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [576] [577] [578] [579] [580] [581] [582] [583] [584] [585] [586] Underfull \hbox (badness 2671) in paragraph at lines 37785--37788 []\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/zi4/m/n/10 ...\T1/pt m/m/n/10 . If set to \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies [587] [588] [589] [590] [591] [592] Underfull \hbox (badness 10000) in paragraph at lines 38200--38203 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [593] [594] Underfull \hbox (badness 10000) in paragraph at lines 38318--38322 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [595] Underfull \hbox (badness 10000) in paragraph at lines 38380--38384 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614] [615] Underfull \hbox (badness 1990) in paragraph at lines 39706--39714 []\T1/zi4/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 4846) in paragraph at lines 39706--39714 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [616] [617] [618] [619] Underfull \hbox (badness 1515) in paragraph at lines 39978--39983 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0 [620] [621] [622] [623] Underfull \hbox (badness 1917) in paragraph at lines 40208--40215 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [624] [625] [626] [627] [628] [629] [630] [631] [632] [633] Underfull \hbox (badness 3668) in paragraph at lines 40869--40871 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [634] [635] Underfull \hbox (badness 2401) in paragraph at lines 40974--40978 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [636] [637] Underfull \hbox (badness 2111) in paragraph at lines 41143--41148 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. [638] Underfull \hbox (badness 6542) in paragraph at lines 41159--41164 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [639] [640] [641] [642] [643] [644] [645] Underfull \hbox (badness 10000) in paragraph at lines 41604--41609 []\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu nc-tion than [][]\T1/zi4/m/n/10 rank[][][] Underfull \hbox (badness 10000) in paragraph at lines 41604--41609 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to [646] Underfull \hbox (badness 5417) in paragraph at lines 41696--41700 []\T1/zi4/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 [647] Underfull \hbox (badness 10000) in paragraph at lines 41757--41761 []\T1/zi4/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 [648] [649]) (./compiler-pkg.tex [650] Chapter 2. [651] [652] [653] [654]) (./datasets-pkg.tex Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple te list, use [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] Underfull \vbox (badness 1515) has occurred while \output is active [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] Underfull \hbox (badness 6658) in paragraph at lines 3940--3942 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h ttp : / / www . ltrr . arizona . edu / ~hallman / [722] Underfull \vbox (badness 10000) has occurred while \output is active [723] [724] [725] [726] Underfull \vbox (badness 10000) has occurred while \output is active [727] Underfull \vbox (badness 10000) has occurred while \output is active [728] [729] [730] [731] [732] [733] [734] [735]) (./grDevices-pkg.tex [736] Chapter 4. [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] Underfull \hbox (badness 5175) in paragraph at lines 1071--1073 []\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 [754] [755] [756] [757] Underfull \hbox (badness 1852) in paragraph at lines 1268--1271 []\T1/zi4/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 [758] [759] [760] Underfull \hbox (badness 1490) in paragraph at lines 1474--1479 \T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and [761] Underfull \hbox (badness 2698) in paragraph at lines 1528--1531 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture, oth-er-wise a ma-trix of color names (for [762] Underfull \hbox (badness 10000) in paragraph at lines 1597--1601 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [763] [764] [765] [766] Underfull \hbox (badness 1325) in paragraph at lines 1880--1890 \T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/ 10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1 /ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 , [767] [768] Underfull \hbox (badness 10000) in paragraph at lines 1985--1987 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [769] [770] [771] Underfull \hbox (badness 6758) in paragraph at lines 2146--2149 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [772] [773] [774] [775] [776] [777] [778] [779] [780] Underfull \hbox (badness 10000) in paragraph at lines 2712--2713 [781] [782] [783] [784] [785] [786] [787] Underfull \hbox (badness 1152) in paragraph at lines 3150--3152 []\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/zi4/m/n/10 nr, nc \T1/ptm/m /n/10 giv-ing the num-ber of rows and columns, ful-fill-ing [788] [789] [790] [791] [792] Underfull \hbox (badness 2856) in paragraph at lines 3470--3473 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3484--3486 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [793] [794] Underfull \hbox (badness 1173) in paragraph at lines 3600--3610 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 paper \T1/ptm/m/n/10 ar-gu-ment sets the `\ T1/zi4/m/n/10 /MediaBox\T1/ptm/m/n/10 ' en-try in the file, which de-faults to \T1/zi4/m/n/10 width \T1/ptm/m/n/10 by [795] [796] [797] [798] [799] [800] [801] [802] [803] [804] [805] Underfull \hbox (badness 1067) in paragraph at lines 4307--4314 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [806] [807] Underfull \hbox (badness 3364) in paragraph at lines 4468--4470 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$ \T1/zi4/m/n/10 https : / / partners . adobe . com / public / [808] Underfull \hbox (badness 1789) in paragraph at lines 4545--4547 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [809] Underfull \hbox (badness 1377) in paragraph at lines 4595--4600 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [810] Underfull \hbox (badness 2671) in paragraph at lines 4622--4630 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4671--4678 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4679--4688 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4679--4688 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4689--4691 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [811] [812] Underfull \hbox (badness 1057) in paragraph at lines 4800--4805 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/zi4/m/n/10 "rgb"\T1/ptm/m/n/10 ) (which is RGB+gray) and [813] Underfull \hbox (badness 7344) in paragraph at lines 4860--4862 []\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 [814] [815] Underfull \hbox (badness 2035) in paragraph at lines 4984--4993 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 10000) in paragraph at lines 4984--4993 \T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 4984--4993 \T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [816] Underfull \hbox (badness 10000) in paragraph at lines 5053--5060 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5053--5060 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [817] [818] [819] Underfull \hbox (badness 1546) in paragraph at lines 5195--5203 []\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/ n/10 , [820] Underfull \hbox (badness 1648) in paragraph at lines 5272--5276 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [821] [822] [823] [824] [825] [826] [827] Underfull \hbox (badness 10000) in paragraph at lines 5724--5727 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [828] [829] [830] [831] [832] [833] Underfull \hbox (badness 1189) in paragraph at lines 6121--6123 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [834] [835] Underfull \hbox (badness 10000) in paragraph at lines 6219--6221 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [836] [837] [838] [839] Underfull \hbox (badness 3780) in paragraph at lines 6510--6516 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [840] [841] [842] Underfull \hbox (badness 2680) in paragraph at lines 6706--6708 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [843] [844] [845]) (./graphics-pkg.tex [846] Chapter 5. [847] [848] [849] [850] [851] [852] [853] [854] [855] [856] [857] Underfull \hbox (badness 10000) in paragraph at lines 683--690 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [858] [859] [860] [861] Underfull \vbox (badness 3803) has occurred while \output is active [862] [863] [864] [865] [866] Underfull \hbox (badness 4634) in paragraph at lines 1246--1249 [][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [867] [868] [869] [870] [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] [883] Underfull \hbox (badness 1009) in paragraph at lines 2280--2287 \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 [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] Underfull \vbox (badness 10000) has occurred while \output is active [906] Underfull \vbox (badness 10000) has occurred while \output is active [907] [908] [909] [910] Underfull \hbox (badness 1867) in paragraph at lines 3912--3916 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [911] [912] [913] [914] [915] [916] [917] Underfull \hbox (badness 1924) in paragraph at lines 4359--4364 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain [918] Underfull \hbox (badness 2529) in paragraph at lines 4390--4393 []\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 [919] [920] [921] [922] [923] Underfull \hbox (badness 10000) in paragraph at lines 4740--4746 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4740--4746 \T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that [924] Underfull \hbox (badness 10000) in paragraph at lines 4871--4874 [925] </«PKGBUILDDIR»/library/graphics/help/figures/mai.pdf, id=15 314, 289.08pt x 289.08pt> <use /«PKGBUILDDIR»/library/graphics/help/figures/mai.pdf> [926 </«PKGBUILDDIR»/library/graphics/help/figures/mai.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 4932--4934 </«PKGBUILDDIR»/library/graphics/help/figures/oma.pdf, id=15 327, 259.97125pt x 332.24126pt> <use /«PKGBUILDDIR»/library/graphics/help/figures/oma.pdf> [927 </«PKGBUILDDIR»/library/graphics/help/figures/oma.pdf>] [928] Underfull \hbox (badness 10000) in paragraph at lines 5122--5124 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [929] [930] [931] [932] [933] Underfull \vbox (badness 10000) has occurred while \output is active [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] </«PKGBUILDDIR»/library/graphics/help/figures/pch.pdf, id=15 774, 361.35pt x 50.1875pt> <use /«PKGBUILDDIR»/library/graphics/help/figures/pch.pdf> Overfull \hbox (31.57222pt too wide) in paragraph at lines 6592--6593 [][] [953 </«PKGBUILDDIR»/library/graphics/help/figures/pch.pdf>] [954] Underfull \vbox (badness 10000) has occurred while \output is active [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] Underfull \hbox (badness 1048) in paragraph at lines 7301--7306 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [965] Underfull \hbox (badness 1038) in paragraph at lines 7417--7420 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [966] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] Underfull \hbox (badness 10000) in paragraph at lines 8653--8655 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8655--8657 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [988]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored <to be read again> \relax l.8735 \HeaderA{units}{Graphical Units}{units} [989] [990] [991] [992]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [993] [994] [995] [996] [997] [998] Underfull \hbox (badness 2680) in paragraph at lines 390--393 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] Underfull \hbox (badness 4279) in paragraph at lines 970--979 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] Underfull \vbox (badness 3803) has occurred while \output is active [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] Underfull \hbox (badness 1067) in paragraph at lines 4340--4343 []\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 [1066] [1067] [1068] [1069] Underfull \hbox (badness 7256) in paragraph at lines 4583--4585 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] Underfull \hbox (badness 10000) in paragraph at lines 5860--5866 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] Underfull \hbox (badness 7649) in paragraph at lines 6334--6337 []\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 [1100] [1101] [1102] [1103]) (./methods-pkg.tex [1104] Chapter 7. [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] Underfull \hbox (badness 2237) in paragraph at lines 1454--1456 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1125] [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] Underfull \hbox (badness 10000) in paragraph at lines 2050--2055 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 2050--2055 \T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] Underfull \hbox (badness 10000) in paragraph at lines 2655--2658 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1142] [1143] Underfull \hbox (badness 1132) in paragraph at lines 2795--2799 []\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in [1144] Underfull \hbox (badness 1033) in paragraph at lines 2827--2832 \T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1145] [1146] [1147] [1148] [1149] [1150] [1151] Underfull \hbox (badness 1102) in paragraph at lines 3339--3341 []\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1152] [1153] [1154] [1155] [1156] Underfull \hbox (badness 10000) in paragraph at lines 3667--3672 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Underfull \hbox (badness 10000) in paragraph at lines 3675--3684 []\T1/ptm/m/n/10 The [1157] [1158] [1159] [1160] [1161] [1162] Underfull \vbox (badness 10000) has occurred while \output is active [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] Underfull \hbox (badness 1436) in paragraph at lines 4580--4583 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4609--4615 []\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4609--4615 \T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1171] [1172] [1173] [1174] [1175] [1176] Underfull \vbox (badness 2452) has occurred while \output is active [1177] [1178] Underfull \vbox (badness 10000) has occurred while \output is active [1179] [1180] Underfull \hbox (badness 1092) in paragraph at lines 5281--5288 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 5281--5288 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and Underfull \hbox (badness 4036) in paragraph at lines 5329--5332 []\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1181] [1182] [1183] [1184] [1185] Underfull \hbox (badness 1087) in paragraph at lines 5649--5654 []\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 [1186] [1187] [1188] [1189] Underfull \hbox (badness 2221) in paragraph at lines 5878--5883 []\T1/ptm/m/n/10 Two op-tional method names are in-ter-preted spe-cially, \T1/z i4/m/n/10 initialize \T1/ptm/m/n/10 and [1190] [1191] [1192] [1193] [1194] Underfull \hbox (badness 1675) in paragraph at lines 6345--6351 \T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1195] [1196] [1197] [1198] Underfull \vbox (badness 10000) has occurred while \output is active [1199] [1200]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4} ) has been already used, duplicate ignored <to be read again> \relax l.6828 \aliasA{S4}{S3Part}{S4} [1201] [1202] [1203] [1204]pdfTeX warning (ext4) : destination with the same identifier (name{Rfn.Complex}) has been already use d, duplicate ignored <to be read again> \relax l.7096 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored <to be read again> \relax l.7098 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red <to be read again> \relax l.7099 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored <to be read again> \relax l.7101 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed <to be read again> \relax l.7102 \aliasA{Summary}{S4groupGeneric}{Summary} [1205] Underfull \hbox (badness 2050) in paragraph at lines 7163--7167 []\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 [1206] [1207] [1208] Underfull \hbox (badness 1286) in paragraph at lines 7348--7350 []\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] Underfull \hbox (badness 1852) in paragraph at lines 9765--9769 []\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., [1243] [1244] [1245] [1246]) (./parallel-pkg.tex Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 15--17 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4 /m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] Underfull \hbox (badness 3386) in paragraph at lines 1254--1257 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1267] [1268]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 <bates@stat.wisc.edu> \T1/ptm/ m/n/10 and William N. Ven-ables [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283]) (./stats-pkg.tex [1284] Chapter 10. [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] Underfull \hbox (badness 1412) in paragraph at lines 846--848 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] Underfull \hbox (badness 2503) in paragraph at lines 1327--1330 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1306] [1307] [1308] Underfull \hbox (badness 10000) in paragraph at lines 1506--1510 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] Underfull \hbox (badness 3965) in paragraph at lines 2166--2168 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1320] [1321] [1322] [1323] [1324] Underfull \hbox (badness 3965) in paragraph at lines 2508--2510 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] Underfull \hbox (badness 2503) in paragraph at lines 3325--3328 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] Underfull \hbox (badness 3989) in paragraph at lines 4553--4560 []\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 = [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] Underfull \hbox (badness 2556) in paragraph at lines 5164--5167 []\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/ ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p tm/m/n/10 . For Underfull \hbox (badness 2932) in paragraph at lines 5181--5183 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is given by [1368] [1369] [1370] [1371] Underfull \hbox (badness 1142) in paragraph at lines 5422--5434 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1372] [1373] Underfull \hbox (badness 2503) in paragraph at lines 5561--5565 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1374] Underfull \hbox (badness 1168) in paragraph at lines 5622--5627 []\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and [1375] [1376] [1377] [1378] [1379] [1380] [1381] Underfull \hbox (badness 8132) in paragraph at lines 6064--6069 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1382] [1383] [1384] [1385] [1386] Underfull \hbox (badness 7081) in paragraph at lines 6342--6345 []\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6346--6348 []\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1387] [1388] [1389] [1390] [1391] Underfull \vbox (badness 3803) has occurred while \output is active [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] Underfull \hbox (badness 10000) in paragraph at lines 7159--7162 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1400] [1401] Underfull \hbox (badness 10000) in paragraph at lines 7296--7299 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/zi4/m/n/10 ht tps : / / cran . r-[]project . org / web / views / [1402] [1403] [1404] [1405] Underfull \vbox (badness 3803) has occurred while \output is active [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] Underfull \hbox (badness 2626) in paragraph at lines 8794--8797 []\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1427] Underfull \hbox (badness 2503) in paragraph at lines 8894--8898 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1428] [1429] [1430] [1431] [1432] Overfull \hbox (6.88992pt too wide) in paragraph at lines 9228--9230 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] Underfull \hbox (badness 4518) in paragraph at lines 10155--10160 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1448] [1449] [1450] [1451] Underfull \hbox (badness 2142) in paragraph at lines 10497--10500 []\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 ^^@ [1452] Underfull \hbox (badness 1253) in paragraph at lines 10516--10519 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1453] Underfull \hbox (badness 1708) in paragraph at lines 10578--10582 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1454] [1455] [1456] [1457] [1458] [1459] Underfull \hbox (badness 1694) in paragraph at lines 10974--10977 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1867) in paragraph at lines 10993--11002 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 10000) in paragraph at lines 11300--11303 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1465] [1466] [1467]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored <to be read again> \relax l.11454 \aliasA{hat}{influence.measures}{hat} [1468] [1469] Underfull \hbox (badness 1484) in paragraph at lines 11577--11579 []\T1/ptm/m/n/10 The func-tion \T1/zi4/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 [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] Underfull \hbox (badness 4441) in paragraph at lines 12135--12137 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12142--12144 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1479] [1480] [1481] [1482] [1483] [1484] Underfull \hbox (badness 2894) in paragraph at lines 12476--12480 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1485] [1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494] [1495] [1496] Underfull \hbox (badness 4518) in paragraph at lines 13171--13176 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] Underfull \hbox (badness 4518) in paragraph at lines 13818--13823 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1506] [1507] [1508] Underfull \hbox (badness 10000) in paragraph at lines 13956--13960 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 13963--13965 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] [1523] [1524] [1525] Underfull \hbox (badness 2503) in paragraph at lines 15025--15029 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] Underfull \hbox (badness 1418) in paragraph at lines 15534--15540 []\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1 /ptm/m/n/10 and [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] Underfull \hbox (badness 2359) in paragraph at lines 17158--17160 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1560] [1561] Underfull \vbox (badness 10000) has occurred while \output is active [1562] Underfull \vbox (badness 10000) has occurred while \output is active [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] Underfull \hbox (badness 1377) in paragraph at lines 18069--18074 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) in paragraph at lines 18074--18077 []\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 1184) in paragraph at lines 18087--18091 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18095--18099 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1576] [1577] [1578] Underfull \vbox (badness 10000) has occurred while \output is active [1579] [1580] [1581] [1582] [1583] [1584] [1585] Underfull \hbox (badness 1337) in paragraph at lines 18711--18714 []\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 [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] Underfull \hbox (badness 5563) in paragraph at lines 19441--19443 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19444--19447 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1599] [1600] [1601] [1602] [1603] [1604] Underfull \hbox (badness 2503) in paragraph at lines 19811--19814 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1605] Underfull \hbox (badness 10000) in paragraph at lines 19838--19840 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] Underfull \hbox (badness 10000) in paragraph at lines 20863--20869 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] Underfull \hbox (badness 1337) in paragraph at lines 22198--22204 []\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 [1645] [1646] [1647] [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] Underfull \hbox (badness 10000) in paragraph at lines 22991--22994 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] Underfull \hbox (badness 10000) in paragraph at lines 23568--23571 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1667] Underfull \hbox (badness 3690) in paragraph at lines 23619--23623 [][][]\T1/zi4/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 [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] Underfull \hbox (badness 3439) in paragraph at lines 24089--24095 [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1 0 , [1676] [1677] [1678] Underfull \hbox (badness 1867) in paragraph at lines 24286--24288 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to [1679] Underfull \hbox (badness 10000) in paragraph at lines 24299--24301 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and [1680] [1681] [1682] [1683] [1684] [1685] [1686] Underfull \hbox (badness 10000) in paragraph at lines 24757--24762 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1687] [1688] [1689] Underfull \vbox (badness 3803) has occurred while \output is active [1690] [1691] [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] Underfull \vbox (badness 10000) has occurred while \output is active [1702] Underfull \hbox (badness 3514) in paragraph at lines 25775--25780 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1703] Underfull \hbox (badness 3514) in paragraph at lines 25837--25842 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1704] Underfull \hbox (badness 3514) in paragraph at lines 25894--25899 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1705] Underfull \hbox (badness 3514) in paragraph at lines 25955--25961 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1706] [1707] [1708] [1709] Underfull \hbox (badness 3514) in paragraph at lines 26168--26173 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1710] Underfull \hbox (badness 3514) in paragraph at lines 26224--26229 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1711] Underfull \hbox (badness 3514) in paragraph at lines 26281--26286 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1712] Underfull \hbox (badness 3514) in paragraph at lines 26336--26341 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1713] Underfull \hbox (badness 6691) in paragraph at lines 26405--26410 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] [1722] Underfull \hbox (badness 10000) in paragraph at lines 26929--26932 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 26929--26932 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732] Underfull \hbox (badness 5431) in paragraph at lines 27535--27537 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1733] [1734] [1735] Underfull \hbox (badness 5431) in paragraph at lines 27745--27748 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1736] [1737] [1738] [1739] [1740] [1741] Underfull \hbox (badness 1337) in paragraph at lines 28057--28061 []\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 [1742] [1743] Underfull \hbox (badness 10000) in paragraph at lines 28174--28177 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1744] [1745] Underfull \hbox (badness 1616) in paragraph at lines 28357--28360 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1746] [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] [1763] [1764] Underfull \hbox (badness 10000) in paragraph at lines 29483--29487 []\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect [1765] [1766] [1767] Underfull \vbox (badness 10000) has occurred while \output is active [1768] [1769] [1770] Underfull \hbox (badness 1337) in paragraph at lines 29847--29851 []\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 [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] Underfull \hbox (badness 1337) in paragraph at lines 30331--30335 []\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 [1779] Underfull \hbox (badness 5161) in paragraph at lines 30424--30426 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1780] [1781] [1782] [1783] [1784] [1785] Underfull \hbox (badness 10000) in paragraph at lines 30788--30793 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1786] [1787] [1788]) (./stats4-pkg.tex Chapter 11. [1789] [1790] [1791] [1792] [1793] [1794]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored <to be read again> \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1795] [1796] [1797] [1798]) (./tcltk-pkg.tex Chapter 12. [1799] [1800] [1801] [1802] [1803] [1804] [1805] Underfull \vbox (badness 10000) has occurred while \output is active [1806] Underfull \vbox (badness 10000) has occurred while \output is active [1807] Underfull \hbox (badness 1546) in paragraph at lines 664--671 []\T1/zi4/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 [1808] [1809] [1810] [1811] [1812] [1813] [1814] [1815] [1816] [1817] [1818] Underfull \hbox (badness 3375) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the OS X GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh ose [1819]) (./tools-pkg.tex [1820] Chapter 13. [1821] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1822] Underfull \hbox (badness 3039) in paragraph at lines 164--167 []\T1/zi4/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 [1823] [1824] Underfull \hbox (badness 1308) 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 types Underfull \hbox (badness 4967) in paragraph at lines 285--298 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1825] [1826] Underfull \hbox (badness 3039) in paragraph at lines 389--391 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] [1835] [1836] [1837] Underfull \hbox (badness 1635) in paragraph at lines 1050--1052 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1838] Underfull \hbox (badness 4441) in paragraph at lines 1126--1136 \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- [1839] Underfull \hbox (badness 1014) in paragraph at lines 1148--1150 []\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 1154--1156 []\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 1185--1188 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1185--1188 \T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1840] [1841] [1842] Underfull \hbox (badness 10000) in paragraph at lines 1348--1350 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1843] [1844] [1845] Underfull \hbox (badness 7981) in paragraph at lines 1518--1523 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 1082) in paragraph at lines 1525--1527 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1846] [1847] [1848] [1849]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored <to be read again> \relax l.1722 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1850] Underfull \hbox (badness 1137) in paragraph at lines 1807--1809 []\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 Underfull \hbox (badness 5726) in paragraph at lines 1836--1841 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/n/10 De pendsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 1836--1841 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1851] [1852] [1853] [1854] [1855] [1856] Overfull \hbox (17.88089pt too wide) in paragraph at lines 2173--2173 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1857] [1858] [1859] [1860] Underfull \hbox (badness 7981) in paragraph at lines 2376--2382 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1861] [1862] [1863] [1864] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2660. [1865] [1866] [1867] [1868] Underfull \hbox (badness 1424) in paragraph at lines 2942--2944 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1869] [1870] [1871] [1872] [1873] [1874] [1875] [1876] [1877] [1878] [1879] [1880] Underfull \hbox (badness 10000) in paragraph at lines 3638--3640 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1881] [1882] Underfull \hbox (badness 10000) in paragraph at lines 3777--3780 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1883] [1884] [1885] [1886] Underfull \hbox (badness 1838) in paragraph at lines 4037--4043 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4037--4043 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1887] [1888] Underfull \hbox (badness 5726) in paragraph at lines 4117--4122 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4117--4122 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1889] [1890] Underfull \hbox (badness 1688) in paragraph at lines 4260--4272 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/zi4/m/sl/10 PACKAGES\T1/ptm/m/n/10 ' and [1891] [1892] [1893] [1894]) (./utils-pkg.tex Chapter 14. [1895] Underfull \hbox (badness 2556) 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/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1896] [1897] Underfull \hbox (badness 1454) in paragraph at lines 197--200 []\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive , \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 by de- Underfull \hbox (badness 1540) in paragraph at lines 213--216 []\T1/zi4/m/sl/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for the same task as \T1/zi4/m/sl/10 apropos\T1/ptm/m/n/10 . How-ever, by de-fault [1898] [1899] [1900] [1901] [1902] [1903] Underfull \hbox (badness 10000) in paragraph at lines 543--549 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 543--549 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1904] Underfull \hbox (badness 5847) in paragraph at lines 657--663 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 657--663 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1905] Underfull \hbox (badness 3861) in paragraph at lines 725--730 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1906] [1907] [1908] [1909] [1910] Underfull \vbox (badness 10000) has occurred while \output is active [1911] [1912] [1913] [1914] [1915] Underfull \hbox (badness 1371) in paragraph at lines 1321--1323 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1916] [1917] [1918] [1919] [1920] [1921] [1922] Underfull \hbox (badness 2057) in paragraph at lines 1807--1809 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1923] [1924] Underfull \hbox (badness 10000) in paragraph at lines 1901--1903 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1925] Underfull \hbox (badness 5189) in paragraph at lines 1991--1993 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1926] [1927] [1928] [1929] Underfull \hbox (badness 1661) in paragraph at lines 2209--2216 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1990) in paragraph at lines 2226--2229 []\T1/ptm/m/n/10 a [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1930] [1931] [1932] [1933] [1934] [1935] Underfull \hbox (badness 10000) in paragraph at lines 2635--2639 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing [1936] Overfull \hbox (64.10922pt too wide) in paragraph at lines 2640--2643 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1937] [1938] [1939] [1940] [1941] [1942] [1943] [1944] Underfull \hbox (badness 1412) in paragraph at lines 3220--3225 []\T1/ptm/m/n/10 The \T1/zi4/m/sl/10 "libcurl" \T1/ptm/m/n/10 and \T1/zi4/m/sl/ 10 "wget" \T1/ptm/m/n/10 meth-ods fol-low `\T1/zi4/m/sl/10 http://\T1/ptm/m/n/1 0 ' and `\T1/zi4/m/sl/10 https://\T1/ptm/m/n/10 ' redi-rec-tions: the [1945] Underfull \hbox (badness 1430) in paragraph at lines 3246--3254 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 1231) in paragraph at lines 3289--3295 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1946] [1947] [1948] [1949] [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] [1958] [1959]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored <to be read again> \relax l.4109 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored <to be read again> \relax l.4109 ...mat Unordered and Ordered Lists}{format} [1960] [1961] [1962] [1963] [1964] [1965] [1966] [1967] [1968] [1969] [1970] [1971] [1972] [1973] [1974] Underfull \hbox (badness 1371) in paragraph at lines 5062--5064 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1975] Underfull \hbox (badness 1502) in paragraph at lines 5151--5156 []\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 5151--5156 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1976] [1977] [1978] Underfull \hbox (badness 10000) in paragraph at lines 5324--5333 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [1979] Underfull \hbox (badness 2150) in paragraph at lines 5387--5390 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [1980] [1981] Underfull \hbox (badness 3118) in paragraph at lines 5524--5526 []\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 [1982] Underfull \hbox (badness 2409) in paragraph at lines 5557--5561 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [1983] Underfull \hbox (badness 1325) in paragraph at lines 5665--5669 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [1984] Underfull \hbox (badness 10000) in paragraph at lines 5748--5751 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 5748--5751 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [1985] Underfull \hbox (badness 3219) in paragraph at lines 5821--5828 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 5821--5828 \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 5821--5828 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [1986] Underfull \hbox (badness 10000) in paragraph at lines 5901--5906 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] Underfull \hbox (badness 10000) in paragraph at lines 7203--7205 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7208--7213 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2008] [2009] [2010] [2011] [2012] [2013] [2014] [2015] [2016] Underfull \hbox (badness 1789) in paragraph at lines 7758--7760 []\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 [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] Underfull \hbox (badness 1097) in paragraph at lines 8583--8586 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2030] Underfull \hbox (badness 3000) in paragraph at lines 8719--8724 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] Underfull \hbox (badness 2134) in paragraph at lines 9302--9307 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2040] [2041] [2042] [2043] [2044] [2045] [2046] Underfull \hbox (badness 5077) in paragraph at lines 9727--9731 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 9727--9731 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 9739--9743 []\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia , The Free En-cy-clo-pe-dia. Underfull \hbox (badness 3428) in paragraph at lines 9739--9743 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2047] [2048] [2049] [2050] [2051] [2052] Underfull \hbox (badness 10000) in paragraph at lines 10093--10095 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][] []\T1/ptm/m/n/10 s are nicely viewed via [2053] [2054] [2055] Underfull \hbox (badness 2150) in paragraph at lines 10269--10271 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2056] [2057] [2058] Underfull \hbox (badness 10000) in paragraph at lines 10447--10451 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 10478--10484 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2059] [2060] Underfull \hbox (badness 2096) in paragraph at lines 10596--10599 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 10600--10603 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether JPEG fig-ures should be gen-er-ated. Ig-nored if [2061] Underfull \hbox (badness 1009) in paragraph at lines 10666--10677 []\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 [2062] [2063] [2064] [2065] [2066] Underfull \hbox (badness 3780) in paragraph at lines 10965--10969 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 10981--10984 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2067] [2068] [2069] [2070] [2071] [2072] Underfull \hbox (badness 5970) in paragraph at lines 11350--11353 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2073] [2074] [2075] Underfull \hbox (badness 10000) in paragraph at lines 11529--11531 []\T1/ptm/m/n/10 Options other than \T1/zi4/m/sl/10 memory = "none" \T1/ptm/m/n /10 ap-ply only to files pro-duced by [2076] [2077] [2078] [2079] [2080] [2081] Underfull \hbox (badness 10000) in paragraph at lines 11930--11933 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 11930--11933 \T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2082] [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] Underfull \hbox (badness 10000) in paragraph at lines 12460--12462 []\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 1052) in paragraph at lines 12463--12465 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. 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Transcript written on fullrefman.log. This is makeindex, version 2.15 [TeX Live 2015] (kpathsea + Thai support). Scanning input file fullrefman.idx.................done (13047 entries accepted, 33 rejected). Sorting entries.......................................................................................................................................done (197084 comparisons). Generating output file fullrefman.ind................done (12956 lines written, 50 warnings). Output written in fullrefman.ind. Transcript written in fullrefman.ilg. This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./fullrefman.tex LaTeX2e <2016/02/01> Babel <3.9q> and hyphenation patterns for 3 language(s) loaded. 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Underfull \hbox (badness 4595) in paragraph at lines 40--43 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [1] [2] Underfull \hbox (badness 1960) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is 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 [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 296--300 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 381--384 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? 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I t is guar-an-teed that [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.88089pt too wide) in paragraph at lines 1894--1894 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2079--2081 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3580--3582 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] Underfull \hbox (badness 2521) in paragraph at lines 4782--4784 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] Overfull \hbox (7.0809pt too wide) in paragraph at lines 5909--5909 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [93] [94] [95] Underfull \hbox (badness 2096) in paragraph at lines 6090--6103 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [96] [97] [98] Overfull \hbox (58.35893pt too wide) in paragraph at lines 6293--6295 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [99] [100] Underfull \hbox (badness 10000) in paragraph at lines 6434--6437 []\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is [101] [102] Underfull \hbox (badness 1442) in paragraph at lines 6599--6605 []\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/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6599--6605 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6599--6605 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [103] Underfull \hbox (badness 3568) in paragraph at lines 6660--6667 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [104] [105] Underfull \vbox (badness 10000) has occurred while \output is active [106] [107] [108] [109] [110] [111] [112] [113] Underfull \hbox (badness 2096) in paragraph at lines 7298--7302 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [114] Underfull \hbox (badness 4595) in paragraph at lines 7355--7358 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [115] Underfull \hbox (badness 3000) in paragraph at lines 7391--7393 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7416--7419 [][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [116] [117] [118] [119] Underfull \hbox (badness 10000) in paragraph at lines 7671--7682 []\T1/zi4/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 [120] [121] Underfull \hbox (badness 4479) in paragraph at lines 7743--7752 [][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), Underfull \hbox (badness 2469) in paragraph at lines 7743--7752 [][]\T1/zi4/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods, [][]\T1/zi4/m/n/10 Math.data.frame[][][] \T1/ptm/m/n/10 etc, about \T1/ptm/m/i t/10 Group \T1/ptm/m/n/10 meth-ods for [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] Underfull \hbox (badness 1394) in paragraph at lines 9355--9360 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [146] [147] [148] [149] [150] Underfull \hbox (badness 1052) in paragraph at lines 9698--9703 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 9698--9703 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [151] [152] Underfull \hbox (badness 1735) in paragraph at lines 9836--9840 \T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ zi4/m/n/10 https : / / en . wikipedia . [153] [154] [155] [156] [157] [158] Underfull \hbox (badness 2150) in paragraph at lines 10240--10243 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse [159] Underfull \hbox (badness 6396) in paragraph at lines 10254--10262 []\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 2409) in paragraph at lines 10295--10302 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] Underfull \hbox (badness 4569) in paragraph at lines 11341--11345 []\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 11341--11345 \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 [176] [177] [178] [179] [180] [181] [182] [183] Underfull \hbox (badness 2698) in paragraph at lines 11917--11926 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 11917--11926 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] Underfull \hbox (badness 6236) in paragraph at lines 12561--12564 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [194] [195] [196] [197] [198] [199] Underfull \hbox (badness 2253) in paragraph at lines 12939--12941 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [200] Underfull \hbox (badness 1565) in paragraph at lines 13010--13014 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and [201] Underfull \hbox (badness 10000) in paragraph at lines 13054--13056 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with [202] [203] Underfull \hbox (badness 1466) in paragraph at lines 13195--13198 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ zi4/m/n/10 file.copy \T1/ptm/m/n/10 and [204] [205] Underfull \hbox (badness 10000) in paragraph at lines 13303--13307 [][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13314--13317 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [206] [207] [208] [209] Underfull \hbox (badness 3965) in paragraph at lines 13577--13581 []\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, [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] Underfull \hbox (badness 4429) in paragraph at lines 14338--14341 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [222] Underfull \hbox (badness 10000) in paragraph at lines 14430--14432 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14436--14440 []\T1/zi4/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 [223] Underfull \hbox (badness 10000) in paragraph at lines 14478--14482 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 14478--14482 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [224] Underfull \vbox (badness 3803) has occurred while \output is active [225] [226] [227] [228] [229] [230] [231] [232] Underfull \hbox (badness 2452) in paragraph at lines 15058--15062 []\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 15058--15062 \T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_ WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and [233] [234] [235] Underfull \hbox (badness 1092) in paragraph at lines 15231--15236 [][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [236] [237] [238] [239] Underfull \hbox (badness 6741) in paragraph at lines 15479--15483 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [240] [241] [242] [243] Underfull \hbox (badness 1867) in paragraph at lines 15785--15792 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [244] [245] [246] [247] Underfull \vbox (badness 10000) has occurred while \output is active [248] [249] Underfull \hbox (badness 3679) in paragraph at lines 16166--16168 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [250] [251] [252] [253] [254] [255] [256] [257] Underfull \hbox (badness 1478) in paragraph at lines 16711--16714 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [258] [259] [260] [261] Underfull \hbox (badness 10000) in paragraph at lines 16964--16966 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [262] [263] [264] [265] [266] [267] [268] [269] [270] Underfull \hbox (badness 1442) in paragraph at lines 17527--17529 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [271] Underfull \hbox (badness 2452) in paragraph at lines 17619--17635 [][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [272] [273] [274] [275] [276] [277] [278] Underfull \hbox (badness 1248) in paragraph at lines 18033--18036 []\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/ m/n/10 , [279] [280] [281] [282] Underfull \hbox (badness 4739) in paragraph at lines 18291--18293 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] Underfull \hbox (badness 1360) in paragraph at lines 19249--19254 \T1/zi4/m/n/10 "none"\T1/ptm/m/n/10 . It is in-tended for the ver-sion of OpenS SL used, but not all Underfull \hbox (badness 10000) in paragraph at lines 19272--19278 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / Underfull \hbox (badness 1127) in paragraph at lines 19272--19278 \T1/zi4/m/n/10 ssl-[]compared . html$[][] \T1/ptm/m/n/10 for more de-tails on S SL ver-sions. Nor-mally \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 used with \T1/phv /m/n/10 R [299] Underfull \hbox (badness 10000) in paragraph at lines 19345--19349 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 19345--19349 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [300] [301] Underfull \hbox (badness 1509) in paragraph at lines 19480--19487 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1354) in paragraph at lines 19480--19487 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19496--19501 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313] Underfull \hbox (badness 1264) in paragraph at lines 20227--20232 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] Underfull \hbox (badness 10000) in paragraph at lines 20981--20983 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] Underfull \hbox (badness 1077) in paragraph at lines 21979--21985 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [341] [342] [343] Underfull \hbox (badness 1484) in paragraph at lines 22140--22148 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [344] [345] [346] [347] Underfull \hbox (badness 2790) in paragraph at lines 22411--22414 []\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 22411--22414 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [348] [349] [350] [351] Underfull \hbox (badness 1194) in paragraph at lines 22692--22695 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 . It calls [352] [353] [354] [355] Underfull \hbox (badness 10000) in paragraph at lines 22898--22904 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 5862) in paragraph at lines 22898--22904 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 22908--22911 []\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 22908--22911 \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 [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] [367] [368] [369] Underfull \hbox (badness 10000) in paragraph at lines 23839--23841 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [370] [371] [372] [373] Underfull \hbox (badness 1199) in paragraph at lines 24066--24072 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24066--24072 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [374] [375] [376] [377] [378] [379] [380] [381] Underfull \hbox (badness 1038) in paragraph at lines 24645--24653 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 1881) in paragraph at lines 24654--24657 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 24673--24675 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [382] Underfull \hbox (badness 10000) in paragraph at lines 24745--24755 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 24756--24762 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able Underfull \hbox (badness 1968) in paragraph at lines 24769--24774 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 24779--24781 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [383] [384] Underfull \vbox (badness 10000) has occurred while \output is active [385] Underfull \hbox (badness 10000) in paragraph at lines 25034--25040 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/zi4/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25034--25040 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 25034--25040 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by [386] Underfull \hbox (badness 10000) in paragraph at lines 25047--25050 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 25071--25073 []\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 25103--25108 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 25109--25120 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 25121--25124 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and [387] Underfull \hbox (badness 4084) in paragraph at lines 25131--25143 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN OS X build), Underfull \hbox (badness 10000) in paragraph at lines 25131--25143 \T1/zi4/m/n/10 "mac.binary."\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.maveric ks" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for C RAN Underfull \hbox (badness 7397) in paragraph at lines 25131--25143 \T1/ptm/m/n/10 OS X builds). Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m /n/10 . (\T1/zi4/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 25145--25152 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 25145--25152 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 25145--25152 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1082) in paragraph at lines 25145--25152 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [388] [389] [390] [391] [392] Underfull \hbox (badness 10000) in paragraph at lines 25491--25495 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 25491--25495 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [393] [394] [395] [396] [397] Underfull \hbox (badness 1735) in paragraph at lines 25809--25813 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [398] [399] [400] [401] [402] [403] [404] [405] [406] Underfull \hbox (badness 2726) in paragraph at lines 26369--26372 []\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] [418] [419] Underfull \hbox (badness 1052) in paragraph at lines 27186--27191 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [420] [421] [422] [423] [424] Underfull \vbox (badness 10000) has occurred while \output is active [425] [426] [427] [428] [429] [430] [431] Underfull \hbox (badness 1533) in paragraph at lines 27995--27998 []\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 [432] [433] [434] Underfull \hbox (badness 1163) in paragraph at lines 28157--28168 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] Underfull \hbox (badness 10000) in paragraph at lines 29676--29680 []\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 29676--29680 \T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. Underfull \hbox (badness 6188) in paragraph at lines 29698--29700 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [459] [460] [461] [462] [463] [464] [465] [466] [467] Underfull \hbox (badness 1655) in paragraph at lines 30246--30248 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm /m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for [468] [469] [470] [471] [472] [473] [474] [475] [476] [477] [478] Underfull \hbox (badness 10000) in paragraph at lines 30914--30918 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [479] [480] [481] Underfull \hbox (badness 2302) in paragraph at lines 31154--31161 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 31154--31161 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 2980) in paragraph at lines 31154--31161 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 31154--31161 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [482] [483] [484] Underfull \hbox (badness 2261) in paragraph at lines 31310--31315 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if Underfull \hbox (badness 10000) in paragraph at lines 31337--31343 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [485] Underfull \hbox (badness 10000) in paragraph at lines 31413--31418 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [486] [487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] Underfull \hbox (badness 1072) in paragraph at lines 34333--34337 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 34338--34342 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 34366--34372 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 34366--34372 \T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 34366--34372 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in Underfull \hbox (badness 3343) in paragraph at lines 34379--34386 \T1/ptm/m/n/10 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 34379--34386 \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 Underfull \hbox (badness 1917) in paragraph at lines 34379--34386 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [532] [533] [534] [535] [536] Underfull \hbox (badness 10000) in paragraph at lines 34670--34676 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1152) in paragraph at lines 34670--34676 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] Underfull \hbox (badness 3333) in paragraph at lines 36500--36505 []\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] Underfull \hbox (badness 1472) in paragraph at lines 37120--37123 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [576] [577] [578] [579] [580] [581] [582] [583] [584] [585] [586] Underfull \hbox (badness 2671) in paragraph at lines 37785--37788 []\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/zi4/m/n/10 ...\T1/pt m/m/n/10 . If set to \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies [587] [588] [589] [590] [591] [592] Underfull \hbox (badness 10000) in paragraph at lines 38200--38203 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [593] [594] Underfull \hbox (badness 10000) in paragraph at lines 38318--38322 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [595] Underfull \hbox (badness 10000) in paragraph at lines 38380--38384 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614] [615] Underfull \hbox (badness 1990) in paragraph at lines 39706--39714 []\T1/zi4/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 4846) in paragraph at lines 39706--39714 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [616] [617] [618] [619] Underfull \hbox (badness 1515) in paragraph at lines 39978--39983 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0 [620] [621] [622] [623] Underfull \hbox (badness 1917) in paragraph at lines 40208--40215 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [624] [625] [626] [627] [628] [629] [630] [631] [632] [633] Underfull \hbox (badness 3668) in paragraph at lines 40869--40871 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [634] [635] Underfull \hbox (badness 2401) in paragraph at lines 40974--40978 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [636] [637] Underfull \hbox (badness 2111) in paragraph at lines 41143--41148 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. [638] Underfull \hbox (badness 6542) in paragraph at lines 41159--41164 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [639] [640] [641] [642] [643] [644] [645] Underfull \hbox (badness 10000) in paragraph at lines 41604--41609 []\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu nc-tion than [][]\T1/zi4/m/n/10 rank[][][] Underfull \hbox (badness 10000) in paragraph at lines 41604--41609 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to [646] Underfull \hbox (badness 5417) in paragraph at lines 41696--41700 []\T1/zi4/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 [647] Underfull \hbox (badness 10000) in paragraph at lines 41757--41761 []\T1/zi4/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 [648] [649]) (./compiler-pkg.tex [650] Chapter 2. [651] [652] [653] [654]) (./datasets-pkg.tex Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple te list, use [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] Underfull \vbox (badness 1515) has occurred while \output is active [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] Underfull \hbox (badness 6658) in paragraph at lines 3940--3942 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h ttp : / / www . ltrr . arizona . edu / ~hallman / [722] Underfull \vbox (badness 10000) has occurred while \output is active [723] [724] [725] [726] Underfull \vbox (badness 10000) has occurred while \output is active [727] Underfull \vbox (badness 10000) has occurred while \output is active [728] [729] [730] [731] [732] [733] [734] [735]) (./grDevices-pkg.tex [736] Chapter 4. [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] Underfull \hbox (badness 5175) in paragraph at lines 1071--1073 []\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 [754] [755] [756] [757] Underfull \hbox (badness 1852) in paragraph at lines 1268--1271 []\T1/zi4/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 [758] [759] [760] Underfull \hbox (badness 1490) in paragraph at lines 1474--1479 \T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and [761] Underfull \hbox (badness 2698) in paragraph at lines 1528--1531 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture, oth-er-wise a ma-trix of color names (for [762] Underfull \hbox (badness 10000) in paragraph at lines 1597--1601 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [763] [764] [765] [766] Underfull \hbox (badness 1325) in paragraph at lines 1880--1890 \T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/ 10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1 /ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 , [767] [768] Underfull \hbox (badness 10000) in paragraph at lines 1985--1987 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [769] [770] [771] Underfull \hbox (badness 6758) in paragraph at lines 2146--2149 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [772] [773] [774] [775] [776] [777] [778] [779] [780] Underfull \hbox (badness 10000) in paragraph at lines 2712--2713 [781] [782] [783] [784] [785] [786] [787] Underfull \hbox (badness 1152) in paragraph at lines 3150--3152 []\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/zi4/m/n/10 nr, nc \T1/ptm/m /n/10 giv-ing the num-ber of rows and columns, ful-fill-ing [788] [789] [790] [791] [792] Underfull \hbox (badness 2856) in paragraph at lines 3470--3473 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3484--3486 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [793] [794] Underfull \hbox (badness 1173) in paragraph at lines 3600--3610 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 paper \T1/ptm/m/n/10 ar-gu-ment sets the `\ T1/zi4/m/n/10 /MediaBox\T1/ptm/m/n/10 ' en-try in the file, which de-faults to \T1/zi4/m/n/10 width \T1/ptm/m/n/10 by [795] [796] [797] [798] [799] [800] [801] [802] [803] [804] [805] Underfull \hbox (badness 1067) in paragraph at lines 4307--4314 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [806] [807] Underfull \hbox (badness 3364) in paragraph at lines 4468--4470 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$ \T1/zi4/m/n/10 https : / / partners . adobe . com / public / [808] Underfull \hbox (badness 1789) in paragraph at lines 4545--4547 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [809] Underfull \hbox (badness 1377) in paragraph at lines 4595--4600 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [810] Underfull \hbox (badness 2671) in paragraph at lines 4622--4630 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4671--4678 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4679--4688 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4679--4688 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4689--4691 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [811] [812] Underfull \hbox (badness 1057) in paragraph at lines 4800--4805 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/zi4/m/n/10 "rgb"\T1/ptm/m/n/10 ) (which is RGB+gray) and [813] Underfull \hbox (badness 7344) in paragraph at lines 4860--4862 []\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 [814] [815] Underfull \hbox (badness 2035) in paragraph at lines 4984--4993 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 10000) in paragraph at lines 4984--4993 \T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 4984--4993 \T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [816] Underfull \hbox (badness 10000) in paragraph at lines 5053--5060 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5053--5060 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [817] [818] [819] Underfull \hbox (badness 1546) in paragraph at lines 5195--5203 []\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/ n/10 , [820] Underfull \hbox (badness 1648) in paragraph at lines 5272--5276 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [821] [822] [823] [824] [825] [826] [827] Underfull \hbox (badness 10000) in paragraph at lines 5724--5727 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [828] [829] [830] [831] [832] [833] Underfull \hbox (badness 1189) in paragraph at lines 6121--6123 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [834] [835] Underfull \hbox (badness 10000) in paragraph at lines 6219--6221 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [836] [837] [838] [839] Underfull \hbox (badness 3780) in paragraph at lines 6510--6516 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [840] [841] [842] Underfull \hbox (badness 2680) in paragraph at lines 6706--6708 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [843] [844] [845]) (./graphics-pkg.tex [846] Chapter 5. [847] [848] [849] [850] [851] [852] [853] [854] [855] [856] [857] Underfull \hbox (badness 10000) in paragraph at lines 683--690 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [858] [859] [860] [861] Underfull \vbox (badness 3803) has occurred while \output is active [862] [863] [864] [865] [866] Underfull \hbox (badness 4634) in paragraph at lines 1246--1249 [][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [867] [868] [869] [870] [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] [883] Underfull \hbox (badness 1009) in paragraph at lines 2280--2287 \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 [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] Underfull \vbox (badness 10000) has occurred while \output is active [906] Underfull \vbox (badness 10000) has occurred while \output is active [907] [908] [909] [910] Underfull \hbox (badness 1867) in paragraph at lines 3912--3916 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [911] [912] [913] [914] [915] [916] [917] Underfull \hbox (badness 1924) in paragraph at lines 4359--4364 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain [918] Underfull \hbox (badness 2529) in paragraph at lines 4390--4393 []\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 [919] [920] [921] [922] [923] Underfull \hbox (badness 10000) in paragraph at lines 4740--4746 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4740--4746 \T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that [924] Underfull \hbox (badness 10000) in paragraph at lines 4871--4874 [925] </«PKGBUILDDIR»/library/graphics/help/figures/mai.pdf, id=22 376, 289.08pt x 289.08pt> <use /«PKGBUILDDIR»/library/graphics/help/figures/mai.pdf> [926 </«PKGBUILDDIR»/library/graphics/help/figures/mai.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 4932--4934 </«PKGBUILDDIR»/library/graphics/help/figures/oma.pdf, id=22 389, 259.97125pt x 332.24126pt> <use /«PKGBUILDDIR»/library/graphics/help/figures/oma.pdf> [927 </«PKGBUILDDIR»/library/graphics/help/figures/oma.pdf>] [928] Underfull \hbox (badness 10000) in paragraph at lines 5122--5124 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [929] [930] [931] [932] [933] Underfull \vbox (badness 10000) has occurred while \output is active [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] </«PKGBUILDDIR»/library/graphics/help/figures/pch.pdf, id=22 807, 361.35pt x 50.1875pt> <use /«PKGBUILDDIR»/library/graphics/help/figures/pch.pdf> Overfull \hbox (31.57222pt too wide) in paragraph at lines 6592--6593 [][] [953 </«PKGBUILDDIR»/library/graphics/help/figures/pch.pdf>] [954] Underfull \vbox (badness 10000) has occurred while \output is active [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] Underfull \hbox (badness 1048) in paragraph at lines 7301--7306 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [965] Underfull \hbox (badness 1038) in paragraph at lines 7417--7420 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [966] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] Underfull \hbox (badness 10000) in paragraph at lines 8653--8655 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8655--8657 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [988]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored <to be read again> \relax l.8735 \HeaderA{units}{Graphical Units}{units} [989] [990] [991] [992]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [993] [994] [995] [996] [997] [998] Underfull \hbox (badness 2680) in paragraph at lines 390--393 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] Underfull \hbox (badness 4279) in paragraph at lines 970--979 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] Underfull \vbox (badness 3803) has occurred while \output is active [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] Underfull \hbox (badness 1067) in paragraph at lines 4340--4343 []\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 [1066] [1067] [1068] [1069] Underfull \hbox (badness 7256) in paragraph at lines 4583--4585 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] Underfull \hbox (badness 10000) in paragraph at lines 5860--5866 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] Underfull \hbox (badness 7649) in paragraph at lines 6334--6337 []\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 [1100] [1101] [1102] [1103]) (./methods-pkg.tex [1104] Chapter 7. [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] Underfull \hbox (badness 2237) in paragraph at lines 1454--1456 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1125] [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] Underfull \hbox (badness 10000) in paragraph at lines 2050--2055 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 2050--2055 \T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] Underfull \hbox (badness 10000) in paragraph at lines 2655--2658 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1142] [1143] Underfull \hbox (badness 1132) in paragraph at lines 2795--2799 []\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in [1144] Underfull \hbox (badness 1033) in paragraph at lines 2827--2832 \T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1145] [1146] [1147] [1148] [1149] [1150] [1151] Underfull \hbox (badness 1102) in paragraph at lines 3339--3341 []\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1152] [1153] [1154] [1155] [1156] Underfull \hbox (badness 10000) in paragraph at lines 3667--3672 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Underfull \hbox (badness 10000) in paragraph at lines 3675--3684 []\T1/ptm/m/n/10 The [1157] [1158] [1159] [1160] [1161] [1162] Underfull \vbox (badness 10000) has occurred while \output is active [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] Underfull \hbox (badness 1436) in paragraph at lines 4580--4583 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4609--4615 []\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4609--4615 \T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1171] [1172] [1173] [1174] [1175] [1176] Underfull \vbox (badness 2452) has occurred while \output is active [1177] [1178] Underfull \vbox (badness 10000) has occurred while \output is active [1179] [1180] Underfull \hbox (badness 1092) in paragraph at lines 5281--5288 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 5281--5288 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and Underfull \hbox (badness 4036) in paragraph at lines 5329--5332 []\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1181] [1182] [1183] [1184] [1185] Underfull \hbox (badness 1087) in paragraph at lines 5649--5654 []\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 [1186] [1187] [1188] [1189] Underfull \hbox (badness 2221) in paragraph at lines 5878--5883 []\T1/ptm/m/n/10 Two op-tional method names are in-ter-preted spe-cially, \T1/z i4/m/n/10 initialize \T1/ptm/m/n/10 and [1190] [1191] [1192] [1193] [1194] Underfull \hbox (badness 1675) in paragraph at lines 6345--6351 \T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1195] [1196] [1197] [1198] Underfull \vbox (badness 10000) has occurred while \output is active [1199] [1200]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4} ) has been already used, duplicate ignored <to be read again> \relax l.6828 \aliasA{S4}{S3Part}{S4} [1201] [1202] [1203] [1204]pdfTeX warning (ext4) : destination with the same identifier (name{Rfn.Complex}) has been already use d, duplicate ignored <to be read again> \relax l.7096 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored <to be read again> \relax l.7098 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red <to be read again> \relax l.7099 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored <to be read again> \relax l.7101 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed <to be read again> \relax l.7102 \aliasA{Summary}{S4groupGeneric}{Summary} [1205] Underfull \hbox (badness 2050) in paragraph at lines 7163--7167 []\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 [1206] [1207] [1208] Underfull \hbox (badness 1286) in paragraph at lines 7348--7350 []\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] Underfull \hbox (badness 1852) in paragraph at lines 9765--9769 []\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., [1243] [1244] [1245] [1246]) (./parallel-pkg.tex Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 15--17 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4 /m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] Underfull \hbox (badness 3386) in paragraph at lines 1254--1257 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1267] [1268]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 <bates@stat.wisc.edu> \T1/ptm/ m/n/10 and William N. Ven-ables [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283]) (./stats-pkg.tex [1284] Chapter 10. [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] Underfull \hbox (badness 1412) in paragraph at lines 846--848 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] Underfull \hbox (badness 2503) in paragraph at lines 1327--1330 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1306] [1307] [1308] Underfull \hbox (badness 10000) in paragraph at lines 1506--1510 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] Underfull \hbox (badness 3965) in paragraph at lines 2166--2168 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1320] [1321] [1322] [1323] [1324] Underfull \hbox (badness 3965) in paragraph at lines 2508--2510 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] Underfull \hbox (badness 2503) in paragraph at lines 3325--3328 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] Underfull \hbox (badness 3989) in paragraph at lines 4553--4560 []\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 = [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] Underfull \hbox (badness 2556) in paragraph at lines 5164--5167 []\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/ ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p tm/m/n/10 . For Underfull \hbox (badness 2932) in paragraph at lines 5181--5183 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is given by [1368] [1369] [1370] [1371] Underfull \hbox (badness 1142) in paragraph at lines 5422--5434 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1372] [1373] Underfull \hbox (badness 2503) in paragraph at lines 5561--5565 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1374] Underfull \hbox (badness 1168) in paragraph at lines 5622--5627 []\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and [1375] [1376] [1377] [1378] [1379] [1380] [1381] Underfull \hbox (badness 8132) in paragraph at lines 6064--6069 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1382] [1383] [1384] [1385] [1386] Underfull \hbox (badness 7081) in paragraph at lines 6342--6345 []\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6346--6348 []\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1387] [1388] [1389] [1390] [1391] Underfull \vbox (badness 3803) has occurred while \output is active [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] Underfull \hbox (badness 10000) in paragraph at lines 7159--7162 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1400] [1401] Underfull \hbox (badness 10000) in paragraph at lines 7296--7299 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/zi4/m/n/10 ht tps : / / cran . r-[]project . org / web / views / [1402] [1403] [1404] [1405] Underfull \vbox (badness 3803) has occurred while \output is active [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] Underfull \hbox (badness 2626) in paragraph at lines 8794--8797 []\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1427] Underfull \hbox (badness 2503) in paragraph at lines 8894--8898 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1428] [1429] [1430] [1431] [1432] Overfull \hbox (6.88992pt too wide) in paragraph at lines 9228--9230 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] Underfull \hbox (badness 4518) in paragraph at lines 10155--10160 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1448] [1449] [1450] [1451] Underfull \hbox (badness 2142) in paragraph at lines 10497--10500 []\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 ^^@ [1452] Underfull \hbox (badness 1253) in paragraph at lines 10516--10519 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1453] Underfull \hbox (badness 1708) in paragraph at lines 10578--10582 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1454] [1455] [1456] [1457] [1458] [1459] Underfull \hbox (badness 1694) in paragraph at lines 10974--10977 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1867) in paragraph at lines 10993--11002 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 10000) in paragraph at lines 11300--11303 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1465] [1466] [1467]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored <to be read again> \relax l.11454 \aliasA{hat}{influence.measures}{hat} [1468] [1469] Underfull \hbox (badness 1484) in paragraph at lines 11577--11579 []\T1/ptm/m/n/10 The func-tion \T1/zi4/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 [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] Underfull \hbox (badness 4441) in paragraph at lines 12135--12137 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12142--12144 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1479] [1480] [1481] [1482] [1483] [1484] Underfull \hbox (badness 2894) in paragraph at lines 12476--12480 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1485] [1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494] [1495] [1496] Underfull \hbox (badness 4518) in paragraph at lines 13171--13176 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] Underfull \hbox (badness 4518) in paragraph at lines 13818--13823 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1506] [1507] [1508] Underfull \hbox (badness 10000) in paragraph at lines 13956--13960 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 13963--13965 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] [1523] [1524] [1525] Underfull \hbox (badness 2503) in paragraph at lines 15025--15029 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] Underfull \hbox (badness 1418) in paragraph at lines 15534--15540 []\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1 /ptm/m/n/10 and [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] Underfull \hbox (badness 2359) in paragraph at lines 17158--17160 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1560] [1561] Underfull \vbox (badness 10000) has occurred while \output is active [1562] Underfull \vbox (badness 10000) has occurred while \output is active [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] Underfull \hbox (badness 1377) in paragraph at lines 18069--18074 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) in paragraph at lines 18074--18077 []\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 1184) in paragraph at lines 18087--18091 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18095--18099 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1576] [1577] [1578] Underfull \vbox (badness 10000) has occurred while \output is active [1579] [1580] [1581] [1582] [1583] [1584] [1585] Underfull \hbox (badness 1337) in paragraph at lines 18711--18714 []\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 [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] Underfull \hbox (badness 5563) in paragraph at lines 19441--19443 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19444--19447 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1599] [1600] [1601] [1602] [1603] [1604] Underfull \hbox (badness 2503) in paragraph at lines 19811--19814 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1605] Underfull \hbox (badness 10000) in paragraph at lines 19838--19840 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] Underfull \hbox (badness 10000) in paragraph at lines 20863--20869 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] Underfull \hbox (badness 1337) in paragraph at lines 22198--22204 []\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 [1645] [1646] [1647] [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] Underfull \hbox (badness 10000) in paragraph at lines 22991--22994 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] Underfull \hbox (badness 10000) in paragraph at lines 23568--23571 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1667] Underfull \hbox (badness 3690) in paragraph at lines 23619--23623 [][][]\T1/zi4/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 [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] Underfull \hbox (badness 3439) in paragraph at lines 24089--24095 [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1 0 , [1676] [1677] [1678] Underfull \hbox (badness 1867) in paragraph at lines 24286--24288 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to [1679] Underfull \hbox (badness 10000) in paragraph at lines 24299--24301 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and [1680] [1681] [1682] [1683] [1684] [1685] [1686] Underfull \hbox (badness 10000) in paragraph at lines 24757--24762 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1687] [1688] [1689] Underfull \vbox (badness 3803) has occurred while \output is active [1690] [1691] [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] Underfull \vbox (badness 10000) has occurred while \output is active [1702] Underfull \hbox (badness 3514) in paragraph at lines 25775--25780 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1703] Underfull \hbox (badness 3514) in paragraph at lines 25837--25842 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1704] Underfull \hbox (badness 3514) in paragraph at lines 25894--25899 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1705] Underfull \hbox (badness 3514) in paragraph at lines 25955--25961 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1706] [1707] [1708] [1709] Underfull \hbox (badness 3514) in paragraph at lines 26168--26173 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1710] Underfull \hbox (badness 3514) in paragraph at lines 26224--26229 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1711] Underfull \hbox (badness 3514) in paragraph at lines 26281--26286 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1712] Underfull \hbox (badness 3514) in paragraph at lines 26336--26341 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1713] Underfull \hbox (badness 6691) in paragraph at lines 26405--26410 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] [1722] Underfull \hbox (badness 10000) in paragraph at lines 26929--26932 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 26929--26932 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732] Underfull \hbox (badness 5431) in paragraph at lines 27535--27537 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1733] [1734] [1735] Underfull \hbox (badness 5431) in paragraph at lines 27745--27748 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1736] [1737] [1738] [1739] [1740] [1741] Underfull \hbox (badness 1337) in paragraph at lines 28057--28061 []\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 [1742] [1743] Underfull \hbox (badness 10000) in paragraph at lines 28174--28177 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1744] [1745] Underfull \hbox (badness 1616) in paragraph at lines 28357--28360 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1746] [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] [1763] [1764] Underfull \hbox (badness 10000) in paragraph at lines 29483--29487 []\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect [1765] [1766] [1767] Underfull \vbox (badness 10000) has occurred while \output is active [1768] [1769] [1770] Underfull \hbox (badness 1337) in paragraph at lines 29847--29851 []\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 [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] Underfull \hbox (badness 1337) in paragraph at lines 30331--30335 []\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 [1779] Underfull \hbox (badness 5161) in paragraph at lines 30424--30426 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1780] [1781] [1782] [1783] [1784] [1785] Underfull \hbox (badness 10000) in paragraph at lines 30788--30793 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1786] [1787] [1788]) (./stats4-pkg.tex Chapter 11. [1789] [1790] [1791] [1792] [1793] [1794]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored <to be read again> \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1795] [1796] [1797] [1798]) (./tcltk-pkg.tex Chapter 12. [1799] [1800] [1801] [1802] [1803] [1804] [1805] Underfull \vbox (badness 10000) has occurred while \output is active [1806] Underfull \vbox (badness 10000) has occurred while \output is active [1807] Underfull \hbox (badness 1546) in paragraph at lines 664--671 []\T1/zi4/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 [1808] [1809] [1810] [1811] [1812] [1813] [1814] [1815] [1816] [1817] [1818] Underfull \hbox (badness 3375) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the OS X GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh ose [1819]) (./tools-pkg.tex [1820] Chapter 13. [1821] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1822] Underfull \hbox (badness 3039) in paragraph at lines 164--167 []\T1/zi4/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 [1823] [1824] Underfull \hbox (badness 1308) 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 types Underfull \hbox (badness 4967) in paragraph at lines 285--298 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1825] [1826] Underfull \hbox (badness 3039) in paragraph at lines 389--391 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] [1835] [1836] [1837] Underfull \hbox (badness 1635) in paragraph at lines 1050--1052 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1838] Underfull \hbox (badness 4441) in paragraph at lines 1126--1136 \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- [1839] Underfull \hbox (badness 1014) in paragraph at lines 1148--1150 []\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 1154--1156 []\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 1185--1188 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1185--1188 \T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1840] [1841] [1842] Underfull \hbox (badness 10000) in paragraph at lines 1348--1350 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1843] [1844] [1845] Underfull \hbox (badness 7981) in paragraph at lines 1518--1523 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 1082) in paragraph at lines 1525--1527 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1846] [1847] [1848] [1849]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored <to be read again> \relax l.1722 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1850] Underfull \hbox (badness 1137) in paragraph at lines 1807--1809 []\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 Underfull \hbox (badness 5726) in paragraph at lines 1836--1841 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/n/10 De pendsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 1836--1841 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1851] [1852] [1853] [1854] [1855] [1856] Overfull \hbox (17.88089pt too wide) in paragraph at lines 2173--2173 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1857] [1858] [1859] [1860] Underfull \hbox (badness 7981) in paragraph at lines 2376--2382 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1861] [1862] [1863] [1864] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2660. [1865] [1866] [1867] [1868] Underfull \hbox (badness 1424) in paragraph at lines 2942--2944 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1869] [1870] [1871] [1872] [1873] [1874] [1875] [1876] [1877] [1878] [1879] [1880] Underfull \hbox (badness 10000) in paragraph at lines 3638--3640 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1881] [1882] Underfull \hbox (badness 10000) in paragraph at lines 3777--3780 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1883] [1884] [1885] [1886] Underfull \hbox (badness 1838) in paragraph at lines 4037--4043 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4037--4043 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1887] [1888] Underfull \hbox (badness 5726) in paragraph at lines 4117--4122 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4117--4122 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1889] [1890] Underfull \hbox (badness 1688) in paragraph at lines 4260--4272 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/zi4/m/sl/10 PACKAGES\T1/ptm/m/n/10 ' and [1891] [1892] [1893] [1894]) (./utils-pkg.tex Chapter 14. [1895] Underfull \hbox (badness 2556) 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/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1896] [1897] Underfull \hbox (badness 1454) in paragraph at lines 197--200 []\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive , \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 by de- Underfull \hbox (badness 1540) in paragraph at lines 213--216 []\T1/zi4/m/sl/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for the same task as \T1/zi4/m/sl/10 apropos\T1/ptm/m/n/10 . How-ever, by de-fault [1898] [1899] [1900] [1901] [1902] [1903] Underfull \hbox (badness 10000) in paragraph at lines 543--549 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 543--549 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1904] Underfull \hbox (badness 5847) in paragraph at lines 657--663 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 657--663 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1905] Underfull \hbox (badness 3861) in paragraph at lines 725--730 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1906] [1907] [1908] [1909] [1910] Underfull \vbox (badness 10000) has occurred while \output is active [1911] [1912] [1913] [1914] [1915] Underfull \hbox (badness 1371) in paragraph at lines 1321--1323 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1916] [1917] [1918] [1919] [1920] [1921] [1922] Underfull \hbox (badness 2057) in paragraph at lines 1807--1809 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1923] [1924] Underfull \hbox (badness 10000) in paragraph at lines 1901--1903 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1925] Underfull \hbox (badness 5189) in paragraph at lines 1991--1993 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1926] [1927] [1928] [1929] Underfull \hbox (badness 1661) in paragraph at lines 2209--2216 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1990) in paragraph at lines 2226--2229 []\T1/ptm/m/n/10 a [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1930] [1931] [1932] [1933] [1934] [1935] Underfull \hbox (badness 10000) in paragraph at lines 2635--2639 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing [1936] Overfull \hbox (64.10922pt too wide) in paragraph at lines 2640--2643 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1937] [1938] [1939] [1940] [1941] [1942] [1943] [1944] Underfull \hbox (badness 1412) in paragraph at lines 3220--3225 []\T1/ptm/m/n/10 The \T1/zi4/m/sl/10 "libcurl" \T1/ptm/m/n/10 and \T1/zi4/m/sl/ 10 "wget" \T1/ptm/m/n/10 meth-ods fol-low `\T1/zi4/m/sl/10 http://\T1/ptm/m/n/1 0 ' and `\T1/zi4/m/sl/10 https://\T1/ptm/m/n/10 ' redi-rec-tions: the [1945] Underfull \hbox (badness 1430) in paragraph at lines 3246--3254 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 1231) in paragraph at lines 3289--3295 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1946] [1947] [1948] [1949] [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] [1958] [1959]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored <to be read again> \relax l.4109 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored <to be read again> \relax l.4109 ...mat Unordered and Ordered Lists}{format} [1960] [1961] [1962] [1963] [1964] [1965] [1966] [1967] [1968] [1969] [1970] [1971] [1972] [1973] [1974] Underfull \hbox (badness 1371) in paragraph at lines 5062--5064 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1975] Underfull \hbox (badness 1502) in paragraph at lines 5151--5156 []\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 5151--5156 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1976] [1977] [1978] Underfull \hbox (badness 10000) in paragraph at lines 5324--5333 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [1979] Underfull \hbox (badness 2150) in paragraph at lines 5387--5390 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [1980] [1981] Underfull \hbox (badness 3118) in paragraph at lines 5524--5526 []\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 [1982] Underfull \hbox (badness 2409) in paragraph at lines 5557--5561 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [1983] Underfull \hbox (badness 1325) in paragraph at lines 5665--5669 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [1984] Underfull \hbox (badness 10000) in paragraph at lines 5748--5751 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 5748--5751 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [1985] Underfull \hbox (badness 3219) in paragraph at lines 5821--5828 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 5821--5828 \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 5821--5828 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [1986] Underfull \hbox (badness 10000) in paragraph at lines 5901--5906 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] Underfull \hbox (badness 10000) in paragraph at lines 7203--7205 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7208--7213 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2008] [2009] [2010] [2011] [2012] [2013] [2014] [2015] [2016] Underfull \hbox (badness 1789) in paragraph at lines 7758--7760 []\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 [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] Underfull \hbox (badness 1097) in paragraph at lines 8583--8586 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2030] Underfull \hbox (badness 3000) in paragraph at lines 8719--8724 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] Underfull \hbox (badness 2134) in paragraph at lines 9302--9307 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2040] [2041] [2042] [2043] [2044] [2045] [2046] Underfull \hbox (badness 5077) in paragraph at lines 9727--9731 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 9727--9731 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 9739--9743 []\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia , The Free En-cy-clo-pe-dia. Underfull \hbox (badness 3428) in paragraph at lines 9739--9743 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2047] [2048] [2049] [2050] [2051] [2052] Underfull \hbox (badness 10000) in paragraph at lines 10093--10095 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][] []\T1/ptm/m/n/10 s are nicely viewed via [2053] [2054] [2055] Underfull \hbox (badness 2150) in paragraph at lines 10269--10271 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2056] [2057] [2058] Underfull \hbox (badness 10000) in paragraph at lines 10447--10451 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 10478--10484 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2059] [2060] Underfull \hbox (badness 2096) in paragraph at lines 10596--10599 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. 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Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 524--530 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/n/10 insertions\T1/ptm/m/n/10 ', [9] [10] [11] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 2671) in paragraph at lines 1135--1138 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] [22] Underfull \hbox (badness 4072) in paragraph at lines 1369--1375 []\T1/zi4/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/zi4/m/n/10 x mod y \T1/ptm/m /n/10 and \T1/zi4/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I t is guar-an-teed that [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.88089pt too wide) in paragraph at lines 1894--1894 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2079--2081 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3580--3582 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] Underfull \hbox (badness 2521) in paragraph at lines 4782--4784 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] Overfull \hbox (7.0809pt too wide) in paragraph at lines 5909--5909 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [93] [94] [95] Underfull \hbox (badness 2096) in paragraph at lines 6090--6103 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [96] [97] [98] Overfull \hbox (58.35893pt too wide) in paragraph at lines 6293--6295 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [99] [100] Underfull \hbox (badness 10000) in paragraph at lines 6434--6437 []\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is [101] [102] Underfull \hbox (badness 1442) in paragraph at lines 6599--6605 []\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/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6599--6605 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6599--6605 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [103] Underfull \hbox (badness 3568) in paragraph at lines 6660--6667 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [104] [105] Underfull \vbox (badness 10000) has occurred while \output is active [106] [107] [108] [109] [110] [111] [112] [113] Underfull \hbox (badness 2096) in paragraph at lines 7298--7302 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [114] Underfull \hbox (badness 4595) in paragraph at lines 7355--7358 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [115] Underfull \hbox (badness 3000) in paragraph at lines 7391--7393 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7416--7419 [][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [116] [117] [118] [119] Underfull \hbox (badness 10000) in paragraph at lines 7671--7682 []\T1/zi4/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 [120] [121] Underfull \hbox (badness 4479) in paragraph at lines 7743--7752 [][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), Underfull \hbox (badness 2469) in paragraph at lines 7743--7752 [][]\T1/zi4/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods, [][]\T1/zi4/m/n/10 Math.data.frame[][][] \T1/ptm/m/n/10 etc, about \T1/ptm/m/i t/10 Group \T1/ptm/m/n/10 meth-ods for [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] Underfull \hbox (badness 1394) in paragraph at lines 9355--9360 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [146] [147] [148] [149] [150] Underfull \hbox (badness 1052) in paragraph at lines 9698--9703 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 9698--9703 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [151] [152] Underfull \hbox (badness 1735) in paragraph at lines 9836--9840 \T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ zi4/m/n/10 https : / / en . wikipedia . [153] [154] [155] [156] [157] [158] Underfull \hbox (badness 2150) in paragraph at lines 10240--10243 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse [159] Underfull \hbox (badness 6396) in paragraph at lines 10254--10262 []\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 2409) in paragraph at lines 10295--10302 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] Underfull \hbox (badness 4569) in paragraph at lines 11341--11345 []\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 11341--11345 \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 [176] [177] [178] [179] [180] [181] [182] [183] Underfull \hbox (badness 2698) in paragraph at lines 11917--11926 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 11917--11926 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] Underfull \hbox (badness 6236) in paragraph at lines 12561--12564 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [194] [195] [196] [197] [198] [199] Underfull \hbox (badness 2253) in paragraph at lines 12939--12941 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [200] Underfull \hbox (badness 1565) in paragraph at lines 13010--13014 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and [201] Underfull \hbox (badness 10000) in paragraph at lines 13054--13056 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with [202] [203] Underfull \hbox (badness 1466) in paragraph at lines 13195--13198 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ zi4/m/n/10 file.copy \T1/ptm/m/n/10 and [204] [205] Underfull \hbox (badness 10000) in paragraph at lines 13303--13307 [][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13314--13317 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [206] [207] [208] [209] Underfull \hbox (badness 3965) in paragraph at lines 13577--13581 []\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, [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] Underfull \hbox (badness 4429) in paragraph at lines 14338--14341 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [222] Underfull \hbox (badness 10000) in paragraph at lines 14430--14432 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14436--14440 []\T1/zi4/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 [223] Underfull \hbox (badness 10000) in paragraph at lines 14478--14482 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 14478--14482 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [224] Underfull \vbox (badness 3803) has occurred while \output is active [225] [226] [227] [228] [229] [230] [231] [232] Underfull \hbox (badness 2452) in paragraph at lines 15058--15062 []\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 15058--15062 \T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_ WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and [233] [234] [235] Underfull \hbox (badness 1092) in paragraph at lines 15231--15236 [][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [236] [237] [238] [239] Underfull \hbox (badness 6741) in paragraph at lines 15479--15483 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [240] [241] [242] [243] Underfull \hbox (badness 1867) in paragraph at lines 15785--15792 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [244] [245] [246] [247] Underfull \vbox (badness 10000) has occurred while \output is active [248] [249] Underfull \hbox (badness 3679) in paragraph at lines 16166--16168 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [250] [251] [252] [253] [254] [255] [256] [257] Underfull \hbox (badness 1478) in paragraph at lines 16711--16714 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [258] [259] [260] [261] Underfull \hbox (badness 10000) in paragraph at lines 16964--16966 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [262] [263] [264] [265] [266] [267] [268] [269] [270] Underfull \hbox (badness 1442) in paragraph at lines 17527--17529 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [271] Underfull \hbox (badness 2452) in paragraph at lines 17619--17635 [][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [272] [273] [274] [275] [276] [277] [278] Underfull \hbox (badness 1248) in paragraph at lines 18033--18036 []\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/ m/n/10 , [279] [280] [281] [282] Underfull \hbox (badness 4739) in paragraph at lines 18291--18293 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] Underfull \hbox (badness 1360) in paragraph at lines 19249--19254 \T1/zi4/m/n/10 "none"\T1/ptm/m/n/10 . It is in-tended for the ver-sion of OpenS SL used, but not all Underfull \hbox (badness 10000) in paragraph at lines 19272--19278 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / Underfull \hbox (badness 1127) in paragraph at lines 19272--19278 \T1/zi4/m/n/10 ssl-[]compared . html$[][] \T1/ptm/m/n/10 for more de-tails on S SL ver-sions. Nor-mally \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 used with \T1/phv /m/n/10 R [299] Underfull \hbox (badness 10000) in paragraph at lines 19345--19349 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 19345--19349 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [300] [301] Underfull \hbox (badness 1509) in paragraph at lines 19480--19487 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1354) in paragraph at lines 19480--19487 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19496--19501 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313] Underfull \hbox (badness 1264) in paragraph at lines 20227--20232 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] Underfull \hbox (badness 10000) in paragraph at lines 20981--20983 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] Underfull \hbox (badness 1077) in paragraph at lines 21979--21985 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [341] [342] [343] Underfull \hbox (badness 1484) in paragraph at lines 22140--22148 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [344] [345] [346] [347] Underfull \hbox (badness 2790) in paragraph at lines 22411--22414 []\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 22411--22414 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [348] [349] [350] [351] Underfull \hbox (badness 1194) in paragraph at lines 22692--22695 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 . It calls [352] [353] [354] [355] Underfull \hbox (badness 10000) in paragraph at lines 22898--22904 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 5862) in paragraph at lines 22898--22904 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 22908--22911 []\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 22908--22911 \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 [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] [367] [368] [369] Underfull \hbox (badness 10000) in paragraph at lines 23839--23841 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [370] [371] [372] [373] Underfull \hbox (badness 1199) in paragraph at lines 24066--24072 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24066--24072 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [374] [375] [376] [377] [378] [379] [380] [381] Underfull \hbox (badness 1038) in paragraph at lines 24645--24653 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 1881) in paragraph at lines 24654--24657 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 24673--24675 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [382] Underfull \hbox (badness 10000) in paragraph at lines 24745--24755 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 24756--24762 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able Underfull \hbox (badness 1968) in paragraph at lines 24769--24774 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 24779--24781 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [383] [384] Underfull \vbox (badness 10000) has occurred while \output is active [385] Underfull \hbox (badness 10000) in paragraph at lines 25034--25040 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/zi4/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25034--25040 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 25034--25040 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by [386] Underfull \hbox (badness 10000) in paragraph at lines 25047--25050 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 25071--25073 []\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 25103--25108 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 25109--25120 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 25121--25124 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and [387] Underfull \hbox (badness 4084) in paragraph at lines 25131--25143 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN OS X build), Underfull \hbox (badness 10000) in paragraph at lines 25131--25143 \T1/zi4/m/n/10 "mac.binary."\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.maveric ks" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for C RAN Underfull \hbox (badness 7397) in paragraph at lines 25131--25143 \T1/ptm/m/n/10 OS X builds). Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m /n/10 . (\T1/zi4/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 25145--25152 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 25145--25152 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 25145--25152 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1082) in paragraph at lines 25145--25152 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [388] [389] [390] [391] [392] Underfull \hbox (badness 10000) in paragraph at lines 25491--25495 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 25491--25495 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [393] [394] [395] [396] [397] Underfull \hbox (badness 1735) in paragraph at lines 25809--25813 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [398] [399] [400] [401] [402] [403] [404] [405] [406] Underfull \hbox (badness 2726) in paragraph at lines 26369--26372 []\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [407] [408] [409] [410] [411] [412] [413] [414] [415] [416] [417] [418] [419] Underfull \hbox (badness 1052) in paragraph at lines 27186--27191 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [420] [421] [422] [423] [424] Underfull \vbox (badness 10000) has occurred while \output is active [425] [426] [427] [428] [429] [430] [431] Underfull \hbox (badness 1533) in paragraph at lines 27995--27998 []\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 [432] [433] [434] Underfull \hbox (badness 1163) in paragraph at lines 28157--28168 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] Underfull \hbox (badness 10000) in paragraph at lines 29676--29680 []\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 29676--29680 \T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. Underfull \hbox (badness 6188) in paragraph at lines 29698--29700 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [459] [460] [461] [462] [463] [464] [465] [466] [467] Underfull \hbox (badness 1655) in paragraph at lines 30246--30248 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm /m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for [468] [469] [470] [471] [472] [473] [474] [475] [476] [477] [478] Underfull \hbox (badness 10000) in paragraph at lines 30914--30918 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [479] [480] [481] Underfull \hbox (badness 2302) in paragraph at lines 31154--31161 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 31154--31161 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 2980) in paragraph at lines 31154--31161 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 31154--31161 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [482] [483] [484] Underfull \hbox (badness 2261) in paragraph at lines 31310--31315 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if Underfull \hbox (badness 10000) in paragraph at lines 31337--31343 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [485] Underfull \hbox (badness 10000) in paragraph at lines 31413--31418 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [486] [487] [488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] Underfull \hbox (badness 1072) in paragraph at lines 34333--34337 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 34338--34342 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 34366--34372 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 34366--34372 \T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 34366--34372 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in Underfull \hbox (badness 3343) in paragraph at lines 34379--34386 \T1/ptm/m/n/10 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 34379--34386 \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 Underfull \hbox (badness 1917) in paragraph at lines 34379--34386 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [532] [533] [534] [535] [536] Underfull \hbox (badness 10000) in paragraph at lines 34670--34676 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1152) in paragraph at lines 34670--34676 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] Underfull \hbox (badness 3333) in paragraph at lines 36500--36505 []\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] Underfull \hbox (badness 1472) in paragraph at lines 37120--37123 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [576] [577] [578] [579] [580] [581] [582] [583] [584] [585] [586] Underfull \hbox (badness 2671) in paragraph at lines 37785--37788 []\T1/ptm/m/n/10 levels to re-move for all fac-tors in \T1/zi4/m/n/10 ...\T1/pt m/m/n/10 . If set to \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 , it im-plies [587] [588] [589] [590] [591] [592] Underfull \hbox (badness 10000) in paragraph at lines 38200--38203 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [593] [594] Underfull \hbox (badness 10000) in paragraph at lines 38318--38322 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [595] Underfull \hbox (badness 10000) in paragraph at lines 38380--38384 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614] [615] Underfull \hbox (badness 1990) in paragraph at lines 39706--39714 []\T1/zi4/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 4846) in paragraph at lines 39706--39714 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [616] [617] [618] [619] Underfull \hbox (badness 1515) in paragraph at lines 39978--39983 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. Prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 2.15.0 [620] [621] [622] [623] Underfull \hbox (badness 1917) in paragraph at lines 40208--40215 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [624] [625] [626] [627] [628] [629] [630] [631] [632] [633] Underfull \hbox (badness 3668) in paragraph at lines 40869--40871 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [634] [635] Underfull \hbox (badness 2401) in paragraph at lines 40974--40978 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [636] [637] Underfull \hbox (badness 2111) in paragraph at lines 41143--41148 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. [638] Underfull \hbox (badness 6542) in paragraph at lines 41159--41164 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [639] [640] [641] [642] [643] [644] [645] Underfull \hbox (badness 10000) in paragraph at lines 41604--41609 []\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu nc-tion than [][]\T1/zi4/m/n/10 rank[][][] Underfull \hbox (badness 10000) in paragraph at lines 41604--41609 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to [646] Underfull \hbox (badness 5417) in paragraph at lines 41696--41700 []\T1/zi4/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 [647] Underfull \hbox (badness 10000) in paragraph at lines 41757--41761 []\T1/zi4/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 [648] [649]) (./compiler-pkg.tex [650] Chapter 2. [651] [652] [653] [654]) (./datasets-pkg.tex Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple te list, use [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] Underfull \vbox (badness 1515) has occurred while \output is active [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] Underfull \hbox (badness 6658) in paragraph at lines 3940--3942 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h ttp : / / www . ltrr . arizona . edu / ~hallman / [722] Underfull \vbox (badness 10000) has occurred while \output is active [723] [724] [725] [726] Underfull \vbox (badness 10000) has occurred while \output is active [727] Underfull \vbox (badness 10000) has occurred while \output is active [728] [729] [730] [731] [732] [733] [734] [735]) (./grDevices-pkg.tex [736] Chapter 4. [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] Underfull \hbox (badness 5175) in paragraph at lines 1071--1073 []\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 [754] [755] [756] [757] Underfull \hbox (badness 1852) in paragraph at lines 1268--1271 []\T1/zi4/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 [758] [759] [760] Underfull \hbox (badness 1490) in paragraph at lines 1474--1479 \T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and [761] Underfull \hbox (badness 2698) in paragraph at lines 1528--1531 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture, oth-er-wise a ma-trix of color names (for [762] Underfull \hbox (badness 10000) in paragraph at lines 1597--1601 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [763] [764] [765] [766] Underfull \hbox (badness 1325) in paragraph at lines 1880--1890 \T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/ 10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1 /ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 , [767] [768] Underfull \hbox (badness 10000) in paragraph at lines 1985--1987 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [769] [770] [771] Underfull \hbox (badness 6758) in paragraph at lines 2146--2149 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [772] [773] [774] [775] [776] [777] [778] [779] [780] Underfull \hbox (badness 10000) in paragraph at lines 2712--2713 [781] [782] [783] [784] [785] [786] [787] Underfull \hbox (badness 1152) in paragraph at lines 3150--3152 []\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/zi4/m/n/10 nr, nc \T1/ptm/m /n/10 giv-ing the num-ber of rows and columns, ful-fill-ing [788] [789] [790] [791] [792] Underfull \hbox (badness 2856) in paragraph at lines 3470--3473 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3484--3486 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [793] [794] Underfull \hbox (badness 1173) in paragraph at lines 3600--3610 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 paper \T1/ptm/m/n/10 ar-gu-ment sets the `\ T1/zi4/m/n/10 /MediaBox\T1/ptm/m/n/10 ' en-try in the file, which de-faults to \T1/zi4/m/n/10 width \T1/ptm/m/n/10 by [795] [796] [797] [798] [799] [800] [801] [802] [803] [804] [805] Underfull \hbox (badness 1067) in paragraph at lines 4307--4314 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [806] [807] Underfull \hbox (badness 3364) in paragraph at lines 4468--4470 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$ \T1/zi4/m/n/10 https : / / partners . adobe . com / public / [808] Underfull \hbox (badness 1789) in paragraph at lines 4545--4547 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [809] Underfull \hbox (badness 1377) in paragraph at lines 4595--4600 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [810] Underfull \hbox (badness 2671) in paragraph at lines 4622--4630 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4671--4678 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4679--4688 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4679--4688 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4689--4691 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [811] [812] Underfull \hbox (badness 1057) in paragraph at lines 4800--4805 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/zi4/m/n/10 "rgb"\T1/ptm/m/n/10 ) (which is RGB+gray) and [813] Underfull \hbox (badness 7344) in paragraph at lines 4860--4862 []\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 [814] [815] Underfull \hbox (badness 2035) in paragraph at lines 4984--4993 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 10000) in paragraph at lines 4984--4993 \T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 4984--4993 \T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [816] Underfull \hbox (badness 10000) in paragraph at lines 5053--5060 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5053--5060 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [817] [818] [819] Underfull \hbox (badness 1546) in paragraph at lines 5195--5203 []\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/ n/10 , [820] Underfull \hbox (badness 1648) in paragraph at lines 5272--5276 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [821] [822] [823] [824] [825] [826] [827] Underfull \hbox (badness 10000) in paragraph at lines 5724--5727 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [828] [829] [830] [831] [832] [833] Underfull \hbox (badness 1189) in paragraph at lines 6121--6123 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [834] [835] Underfull \hbox (badness 10000) in paragraph at lines 6219--6221 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [836] [837] [838] [839] Underfull \hbox (badness 3780) in paragraph at lines 6510--6516 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [840] [841] [842] Underfull \hbox (badness 2680) in paragraph at lines 6706--6708 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [843] [844] [845]) (./graphics-pkg.tex [846] Chapter 5. [847] [848] [849] [850] [851] [852] [853] [854] [855] [856] [857] Underfull \hbox (badness 10000) in paragraph at lines 683--690 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [858] [859] [860] [861] Underfull \vbox (badness 3803) has occurred while \output is active [862] [863] [864] [865] [866] Underfull \hbox (badness 4634) in paragraph at lines 1246--1249 [][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [867] [868] [869] [870] [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] [883] Underfull \hbox (badness 1009) in paragraph at lines 2280--2287 \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 [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] Underfull \vbox (badness 10000) has occurred while \output is active [906] Underfull \vbox (badness 10000) has occurred while \output is active [907] [908] [909] [910] Underfull \hbox (badness 1867) in paragraph at lines 3912--3916 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [911] [912] [913] [914] [915] [916] [917] Underfull \hbox (badness 1924) in paragraph at lines 4359--4364 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain [918] Underfull \hbox (badness 2529) in paragraph at lines 4390--4393 []\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 [919] [920] [921] [922] [923] Underfull \hbox (badness 10000) in paragraph at lines 4740--4746 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4740--4746 \T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that [924] Underfull \hbox (badness 10000) in paragraph at lines 4871--4874 [925] </«PKGBUILDDIR»/library/graphics/help/figures/mai.pdf, id=22 382, 289.08pt x 289.08pt> <use /«PKGBUILDDIR»/library/graphics/help/figures/mai.pdf> [926 </«PKGBUILDDIR»/library/graphics/help/figures/mai.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 4932--4934 </«PKGBUILDDIR»/library/graphics/help/figures/oma.pdf, id=22 395, 259.97125pt x 332.24126pt> <use /«PKGBUILDDIR»/library/graphics/help/figures/oma.pdf> [927 </«PKGBUILDDIR»/library/graphics/help/figures/oma.pdf>] [928] Underfull \hbox (badness 10000) in paragraph at lines 5122--5124 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [929] [930] [931] [932] [933] Underfull \vbox (badness 10000) has occurred while \output is active [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] </«PKGBUILDDIR»/library/graphics/help/figures/pch.pdf, id=22 813, 361.35pt x 50.1875pt> <use /«PKGBUILDDIR»/library/graphics/help/figures/pch.pdf> Overfull \hbox (31.57222pt too wide) in paragraph at lines 6592--6593 [][] [953 </«PKGBUILDDIR»/library/graphics/help/figures/pch.pdf>] [954] Underfull \vbox (badness 10000) has occurred while \output is active [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] Underfull \hbox (badness 1048) in paragraph at lines 7301--7306 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [965] Underfull \hbox (badness 1038) in paragraph at lines 7417--7420 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [966] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] Underfull \hbox (badness 10000) in paragraph at lines 8653--8655 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8655--8657 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [988]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored <to be read again> \relax l.8735 \HeaderA{units}{Graphical Units}{units} [989] [990] [991] [992]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [993] [994] [995] [996] [997] [998] Underfull \hbox (badness 2680) in paragraph at lines 390--393 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] Underfull \hbox (badness 4279) in paragraph at lines 970--979 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] Underfull \vbox (badness 3803) has occurred while \output is active [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] Underfull \hbox (badness 1067) in paragraph at lines 4340--4343 []\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 [1066] [1067] [1068] [1069] Underfull \hbox (badness 7256) in paragraph at lines 4583--4585 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] Underfull \hbox (badness 10000) in paragraph at lines 5860--5866 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] Underfull \hbox (badness 7649) in paragraph at lines 6334--6337 []\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 [1100] [1101] [1102] [1103]) (./methods-pkg.tex [1104] Chapter 7. [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] Underfull \hbox (badness 2237) in paragraph at lines 1454--1456 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1125] [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] Underfull \hbox (badness 10000) in paragraph at lines 2050--2055 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 2050--2055 \T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] Underfull \hbox (badness 10000) in paragraph at lines 2655--2658 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1142] [1143] Underfull \hbox (badness 1132) in paragraph at lines 2795--2799 []\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in [1144] Underfull \hbox (badness 1033) in paragraph at lines 2827--2832 \T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1145] [1146] [1147] [1148] [1149] [1150] [1151] Underfull \hbox (badness 1102) in paragraph at lines 3339--3341 []\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1152] [1153] [1154] [1155] [1156] Underfull \hbox (badness 10000) in paragraph at lines 3667--3672 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Underfull \hbox (badness 10000) in paragraph at lines 3675--3684 []\T1/ptm/m/n/10 The [1157] [1158] [1159] [1160] [1161] [1162] Underfull \vbox (badness 10000) has occurred while \output is active [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] Underfull \hbox (badness 1436) in paragraph at lines 4580--4583 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4609--4615 []\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4609--4615 \T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1171] [1172] [1173] [1174] [1175] [1176] Underfull \vbox (badness 2452) has occurred while \output is active [1177] [1178] Underfull \vbox (badness 10000) has occurred while \output is active [1179] [1180] Underfull \hbox (badness 1092) in paragraph at lines 5281--5288 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 5281--5288 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and Underfull \hbox (badness 4036) in paragraph at lines 5329--5332 []\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1181] [1182] [1183] [1184] [1185] Underfull \hbox (badness 1087) in paragraph at lines 5649--5654 []\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 [1186] [1187] [1188] [1189] Underfull \hbox (badness 2221) in paragraph at lines 5878--5883 []\T1/ptm/m/n/10 Two op-tional method names are in-ter-preted spe-cially, \T1/z i4/m/n/10 initialize \T1/ptm/m/n/10 and [1190] [1191] [1192] [1193] [1194] Underfull \hbox (badness 1675) in paragraph at lines 6345--6351 \T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1195] [1196] [1197] [1198] Underfull \vbox (badness 10000) has occurred while \output is active [1199] [1200]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4} ) has been already used, duplicate ignored <to be read again> \relax l.6828 \aliasA{S4}{S3Part}{S4} [1201] [1202] [1203] [1204]pdfTeX warning (ext4) : destination with the same identifier (name{Rfn.Complex}) has been already use d, duplicate ignored <to be read again> \relax l.7096 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored <to be read again> \relax l.7098 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red <to be read again> \relax l.7099 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored <to be read again> \relax l.7101 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed <to be read again> \relax l.7102 \aliasA{Summary}{S4groupGeneric}{Summary} [1205] Underfull \hbox (badness 2050) in paragraph at lines 7163--7167 []\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 [1206] [1207] [1208] Underfull \hbox (badness 1286) in paragraph at lines 7348--7350 []\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] Underfull \hbox (badness 1852) in paragraph at lines 9765--9769 []\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., [1243] [1244] [1245] [1246]) (./parallel-pkg.tex Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 15--17 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4 /m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] Underfull \hbox (badness 3386) in paragraph at lines 1254--1257 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1267] [1268]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 <bates@stat.wisc.edu> \T1/ptm/ m/n/10 and William N. Ven-ables [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283]) (./stats-pkg.tex [1284] Chapter 10. [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] Underfull \hbox (badness 1412) in paragraph at lines 846--848 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] Underfull \hbox (badness 2503) in paragraph at lines 1327--1330 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1306] [1307] [1308] Underfull \hbox (badness 10000) in paragraph at lines 1506--1510 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] Underfull \hbox (badness 3965) in paragraph at lines 2166--2168 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1320] [1321] [1322] [1323] [1324] Underfull \hbox (badness 3965) in paragraph at lines 2508--2510 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] Underfull \hbox (badness 2503) in paragraph at lines 3325--3328 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] Underfull \hbox (badness 3989) in paragraph at lines 4553--4560 []\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 = [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] Underfull \hbox (badness 2556) in paragraph at lines 5164--5167 []\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/ ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p tm/m/n/10 . For Underfull \hbox (badness 2932) in paragraph at lines 5181--5183 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is given by [1368] [1369] [1370] [1371] Underfull \hbox (badness 1142) in paragraph at lines 5422--5434 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1372] [1373] Underfull \hbox (badness 2503) in paragraph at lines 5561--5565 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1374] Underfull \hbox (badness 1168) in paragraph at lines 5622--5627 []\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and [1375] [1376] [1377] [1378] [1379] [1380] [1381] Underfull \hbox (badness 8132) in paragraph at lines 6064--6069 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1382] [1383] [1384] [1385] [1386] Underfull \hbox (badness 7081) in paragraph at lines 6342--6345 []\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6346--6348 []\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1387] [1388] [1389] [1390] [1391] Underfull \vbox (badness 3803) has occurred while \output is active [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] Underfull \hbox (badness 10000) in paragraph at lines 7159--7162 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1400] [1401] Underfull \hbox (badness 10000) in paragraph at lines 7296--7299 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/zi4/m/n/10 ht tps : / / cran . r-[]project . org / web / views / [1402] [1403] [1404] [1405] Underfull \vbox (badness 3803) has occurred while \output is active [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] Underfull \hbox (badness 2626) in paragraph at lines 8794--8797 []\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1427] Underfull \hbox (badness 2503) in paragraph at lines 8894--8898 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1428] [1429] [1430] [1431] [1432] Overfull \hbox (6.88992pt too wide) in paragraph at lines 9228--9230 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] Underfull \hbox (badness 4518) in paragraph at lines 10155--10160 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1448] [1449] [1450] [1451] Underfull \hbox (badness 2142) in paragraph at lines 10497--10500 []\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 ^^@ [1452] Underfull \hbox (badness 1253) in paragraph at lines 10516--10519 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1453] Underfull \hbox (badness 1708) in paragraph at lines 10578--10582 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1454] [1455] [1456] [1457] [1458] [1459] Underfull \hbox (badness 1694) in paragraph at lines 10974--10977 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1867) in paragraph at lines 10993--11002 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 10000) in paragraph at lines 11300--11303 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1465] [1466] [1467]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored <to be read again> \relax l.11454 \aliasA{hat}{influence.measures}{hat} [1468] [1469] Underfull \hbox (badness 1484) in paragraph at lines 11577--11579 []\T1/ptm/m/n/10 The func-tion \T1/zi4/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 [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] Underfull \hbox (badness 4441) in paragraph at lines 12135--12137 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12142--12144 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1479] [1480] [1481] [1482] [1483] [1484] Underfull \hbox (badness 2894) in paragraph at lines 12476--12480 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1485] [1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494] [1495] [1496] Underfull \hbox (badness 4518) in paragraph at lines 13171--13176 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] Underfull \hbox (badness 4518) in paragraph at lines 13818--13823 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1506] [1507] [1508] Underfull \hbox (badness 10000) in paragraph at lines 13956--13960 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 13963--13965 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] [1523] [1524] [1525] Underfull \hbox (badness 2503) in paragraph at lines 15025--15029 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] Underfull \hbox (badness 1418) in paragraph at lines 15534--15540 []\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1 /ptm/m/n/10 and [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] Underfull \hbox (badness 2359) in paragraph at lines 17158--17160 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1560] [1561] Underfull \vbox (badness 10000) has occurred while \output is active [1562] Underfull \vbox (badness 10000) has occurred while \output is active [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] Underfull \hbox (badness 1377) in paragraph at lines 18069--18074 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) in paragraph at lines 18074--18077 []\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 1184) in paragraph at lines 18087--18091 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18095--18099 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1576] [1577] [1578] Underfull \vbox (badness 10000) has occurred while \output is active [1579] [1580] [1581] [1582] [1583] [1584] [1585] Underfull \hbox (badness 1337) in paragraph at lines 18711--18714 []\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 [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] Underfull \hbox (badness 5563) in paragraph at lines 19441--19443 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19444--19447 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1599] [1600] [1601] [1602] [1603] [1604] Underfull \hbox (badness 2503) in paragraph at lines 19811--19814 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1605] Underfull \hbox (badness 10000) in paragraph at lines 19838--19840 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] Underfull \hbox (badness 10000) in paragraph at lines 20863--20869 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] Underfull \hbox (badness 1337) in paragraph at lines 22198--22204 []\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 [1645] [1646] [1647] [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] Underfull \hbox (badness 10000) in paragraph at lines 22991--22994 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] Underfull \hbox (badness 10000) in paragraph at lines 23568--23571 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1667] Underfull \hbox (badness 3690) in paragraph at lines 23619--23623 [][][]\T1/zi4/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 [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] Underfull \hbox (badness 3439) in paragraph at lines 24089--24095 [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1 0 , [1676] [1677] [1678] Underfull \hbox (badness 1867) in paragraph at lines 24286--24288 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to [1679] Underfull \hbox (badness 10000) in paragraph at lines 24299--24301 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and [1680] [1681] [1682] [1683] [1684] [1685] [1686] Underfull \hbox (badness 10000) in paragraph at lines 24757--24762 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1687] [1688] [1689] Underfull \vbox (badness 3803) has occurred while \output is active [1690] [1691] [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] Underfull \vbox (badness 10000) has occurred while \output is active [1702] Underfull \hbox (badness 3514) in paragraph at lines 25775--25780 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1703] Underfull \hbox (badness 3514) in paragraph at lines 25837--25842 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1704] Underfull \hbox (badness 3514) in paragraph at lines 25894--25899 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1705] Underfull \hbox (badness 3514) in paragraph at lines 25955--25961 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1706] [1707] [1708] [1709] Underfull \hbox (badness 3514) in paragraph at lines 26168--26173 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1710] Underfull \hbox (badness 3514) in paragraph at lines 26224--26229 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1711] Underfull \hbox (badness 3514) in paragraph at lines 26281--26286 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1712] Underfull \hbox (badness 3514) in paragraph at lines 26336--26341 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1713] Underfull \hbox (badness 6691) in paragraph at lines 26405--26410 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] [1722] Underfull \hbox (badness 10000) in paragraph at lines 26929--26932 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 26929--26932 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732] Underfull \hbox (badness 5431) in paragraph at lines 27535--27537 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1733] [1734] [1735] Underfull \hbox (badness 5431) in paragraph at lines 27745--27748 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1736] [1737] [1738] [1739] [1740] [1741] Underfull \hbox (badness 1337) in paragraph at lines 28057--28061 []\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 [1742] [1743] Underfull \hbox (badness 10000) in paragraph at lines 28174--28177 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1744] [1745] Underfull \hbox (badness 1616) in paragraph at lines 28357--28360 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1746] [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] [1763] [1764] Underfull \hbox (badness 10000) in paragraph at lines 29483--29487 []\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect [1765] [1766] [1767] Underfull \vbox (badness 10000) has occurred while \output is active [1768] [1769] [1770] Underfull \hbox (badness 1337) in paragraph at lines 29847--29851 []\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 [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] Underfull \hbox (badness 1337) in paragraph at lines 30331--30335 []\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 [1779] Underfull \hbox (badness 5161) in paragraph at lines 30424--30426 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1780] [1781] [1782] [1783] [1784] [1785] Underfull \hbox (badness 10000) in paragraph at lines 30788--30793 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1786] [1787] [1788]) (./stats4-pkg.tex Chapter 11. [1789] [1790] [1791] [1792] [1793] [1794]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored <to be read again> \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1795] [1796] [1797] [1798]) (./tcltk-pkg.tex Chapter 12. [1799] [1800] [1801] [1802] [1803] [1804] [1805] Underfull \vbox (badness 10000) has occurred while \output is active [1806] Underfull \vbox (badness 10000) has occurred while \output is active [1807] Underfull \hbox (badness 1546) in paragraph at lines 664--671 []\T1/zi4/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 [1808] [1809] [1810] [1811] [1812] [1813] [1814] [1815] [1816] [1817] [1818] Underfull \hbox (badness 3375) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the OS X GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 (wh ose [1819]) (./tools-pkg.tex [1820] Chapter 13. [1821] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1822] Underfull \hbox (badness 3039) in paragraph at lines 164--167 []\T1/zi4/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 [1823] [1824] Underfull \hbox (badness 1308) 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 types Underfull \hbox (badness 4967) in paragraph at lines 285--298 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1825] [1826] Underfull \hbox (badness 3039) in paragraph at lines 389--391 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] [1835] [1836] [1837] Underfull \hbox (badness 1635) in paragraph at lines 1050--1052 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1838] Underfull \hbox (badness 4441) in paragraph at lines 1126--1136 \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- [1839] Underfull \hbox (badness 1014) in paragraph at lines 1148--1150 []\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 1154--1156 []\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 1185--1188 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1185--1188 \T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1840] [1841] [1842] Underfull \hbox (badness 10000) in paragraph at lines 1348--1350 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1843] [1844] [1845] Underfull \hbox (badness 7981) in paragraph at lines 1518--1523 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 1082) in paragraph at lines 1525--1527 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1846] [1847] [1848] [1849]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored <to be read again> \relax l.1722 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1850] Underfull \hbox (badness 1137) in paragraph at lines 1807--1809 []\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 Underfull \hbox (badness 5726) in paragraph at lines 1836--1841 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/n/10 De pendsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 1836--1841 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1851] [1852] [1853] [1854] [1855] [1856] Overfull \hbox (17.88089pt too wide) in paragraph at lines 2173--2173 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1857] [1858] [1859] [1860] Underfull \hbox (badness 7981) in paragraph at lines 2376--2382 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1861] [1862] [1863] [1864] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2660. [1865] [1866] [1867] [1868] Underfull \hbox (badness 1424) in paragraph at lines 2942--2944 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1869] [1870] [1871] [1872] [1873] [1874] [1875] [1876] [1877] [1878] [1879] [1880] Underfull \hbox (badness 10000) in paragraph at lines 3638--3640 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1881] [1882] Underfull \hbox (badness 10000) in paragraph at lines 3777--3780 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1883] [1884] [1885] [1886] Underfull \hbox (badness 1838) in paragraph at lines 4037--4043 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4037--4043 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1887] [1888] Underfull \hbox (badness 5726) in paragraph at lines 4117--4122 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4117--4122 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1889] [1890] Underfull \hbox (badness 1688) in paragraph at lines 4260--4272 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/zi4/m/sl/10 PACKAGES\T1/ptm/m/n/10 ' and [1891] [1892] [1893] [1894]) (./utils-pkg.tex Chapter 14. [1895] Underfull \hbox (badness 2556) 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/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1896] [1897] Underfull \hbox (badness 1454) in paragraph at lines 197--200 []\T1/ptm/m/n/10 logical in-di-cat-ing if the search should be case-insensitive , \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 by de- Underfull \hbox (badness 1540) in paragraph at lines 213--216 []\T1/zi4/m/sl/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for the same task as \T1/zi4/m/sl/10 apropos\T1/ptm/m/n/10 . How-ever, by de-fault [1898] [1899] [1900] [1901] [1902] [1903] Underfull \hbox (badness 10000) in paragraph at lines 543--549 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 543--549 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1904] Underfull \hbox (badness 5847) in paragraph at lines 657--663 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 657--663 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1905] Underfull \hbox (badness 3861) in paragraph at lines 725--730 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1906] [1907] [1908] [1909] [1910] Underfull \vbox (badness 10000) has occurred while \output is active [1911] [1912] [1913] [1914] [1915] Underfull \hbox (badness 1371) in paragraph at lines 1321--1323 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1916] [1917] [1918] [1919] [1920] [1921] [1922] Underfull \hbox (badness 2057) in paragraph at lines 1807--1809 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1923] [1924] Underfull \hbox (badness 10000) in paragraph at lines 1901--1903 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1925] Underfull \hbox (badness 5189) in paragraph at lines 1991--1993 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1926] [1927] [1928] [1929] Underfull \hbox (badness 1661) in paragraph at lines 2209--2216 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1990) in paragraph at lines 2226--2229 []\T1/ptm/m/n/10 a [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1930] [1931] [1932] [1933] [1934] [1935] Underfull \hbox (badness 10000) in paragraph at lines 2635--2639 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing [1936] Overfull \hbox (64.10922pt too wide) in paragraph at lines 2640--2643 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1937] [1938] [1939] [1940] [1941] [1942] [1943] [1944] Underfull \hbox (badness 1412) in paragraph at lines 3220--3225 []\T1/ptm/m/n/10 The \T1/zi4/m/sl/10 "libcurl" \T1/ptm/m/n/10 and \T1/zi4/m/sl/ 10 "wget" \T1/ptm/m/n/10 meth-ods fol-low `\T1/zi4/m/sl/10 http://\T1/ptm/m/n/1 0 ' and `\T1/zi4/m/sl/10 https://\T1/ptm/m/n/10 ' redi-rec-tions: the [1945] Underfull \hbox (badness 1430) in paragraph at lines 3246--3254 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 1231) in paragraph at lines 3289--3295 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1946] [1947] [1948] [1949] [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] [1958] [1959]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored <to be read again> \relax l.4109 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored <to be read again> \relax l.4109 ...mat Unordered and Ordered Lists}{format} [1960] [1961] [1962] [1963] [1964] [1965] [1966] [1967] [1968] [1969] [1970] [1971] [1972] [1973] [1974] Underfull \hbox (badness 1371) in paragraph at lines 5062--5064 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1975] Underfull \hbox (badness 1502) in paragraph at lines 5151--5156 []\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 5151--5156 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1976] [1977] [1978] Underfull \hbox (badness 10000) in paragraph at lines 5324--5333 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [1979] Underfull \hbox (badness 2150) in paragraph at lines 5387--5390 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [1980] [1981] Underfull \hbox (badness 3118) in paragraph at lines 5524--5526 []\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 [1982] Underfull \hbox (badness 2409) in paragraph at lines 5557--5561 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [1983] Underfull \hbox (badness 1325) in paragraph at lines 5665--5669 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [1984] Underfull \hbox (badness 10000) in paragraph at lines 5748--5751 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 5748--5751 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [1985] Underfull \hbox (badness 3219) in paragraph at lines 5821--5828 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 5821--5828 \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 5821--5828 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [1986] Underfull \hbox (badness 10000) in paragraph at lines 5901--5906 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] Underfull \hbox (badness 10000) in paragraph at lines 7203--7205 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7208--7213 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2008] [2009] [2010] [2011] [2012] [2013] [2014] [2015] [2016] Underfull \hbox (badness 1789) in paragraph at lines 7758--7760 []\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 [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] Underfull \hbox (badness 1097) in paragraph at lines 8583--8586 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2030] Underfull \hbox (badness 3000) in paragraph at lines 8719--8724 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] Underfull \hbox (badness 2134) in paragraph at lines 9302--9307 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2040] [2041] [2042] [2043] [2044] [2045] [2046] Underfull \hbox (badness 5077) in paragraph at lines 9727--9731 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 9727--9731 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 9739--9743 []\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia , The Free En-cy-clo-pe-dia. Underfull \hbox (badness 3428) in paragraph at lines 9739--9743 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2047] [2048] [2049] [2050] [2051] [2052] Underfull \hbox (badness 10000) in paragraph at lines 10093--10095 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][] []\T1/ptm/m/n/10 s are nicely viewed via [2053] [2054] [2055] Underfull \hbox (badness 2150) in paragraph at lines 10269--10271 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2056] [2057] [2058] Underfull \hbox (badness 10000) in paragraph at lines 10447--10451 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 10478--10484 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2059] [2060] Underfull \hbox (badness 2096) in paragraph at lines 10596--10599 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 10600--10603 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether JPEG fig-ures should be gen-er-ated. Ig-nored if [2061] Underfull \hbox (badness 1009) in paragraph at lines 10666--10677 []\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 [2062] [2063] [2064] [2065] [2066] Underfull \hbox (badness 3780) in paragraph at lines 10965--10969 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 10981--10984 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2067] [2068] [2069] [2070] [2071] [2072] Underfull \hbox (badness 5970) in paragraph at lines 11350--11353 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2073] [2074] [2075] Underfull \hbox (badness 10000) in paragraph at lines 11529--11531 []\T1/ptm/m/n/10 Options other than \T1/zi4/m/sl/10 memory = "none" \T1/ptm/m/n /10 ap-ply only to files pro-duced by [2076] [2077] [2078] [2079] [2080] [2081] Underfull \hbox (badness 10000) in paragraph at lines 11930--11933 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 11930--11933 \T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2082] [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] Underfull \hbox (badness 10000) in paragraph at lines 12460--12462 []\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 1052) in paragraph at lines 12463--12465 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2091] Underfull \hbox (badness 10000) in paragraph at lines 12493--12498 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined see Underfull \hbox (badness 10000) in paragraph at lines 12493--12498 [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 av ailable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 10000) in paragraph at lines 12522--12525 [][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n /10 , [2092] [2093] [2094] [2095] Overfull \hbox (25.86961pt too wide) in paragraph at lines 12764--12767 [][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi -gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](<basename>, package = "<pkg >") [2096] [2097] Underfull \hbox (badness 1454) in paragraph at lines 12841--12845 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, [2098] Underfull \hbox (badness 10000) in paragraph at lines 12911--12913 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion [2099] [2100] [2101]) [2102] (./fullrefman.ind [2103] [2104] [2105] [2106] [2107] [2108] [2109] [2110] [2111] [2112] [2113] [2114] [2115] [2116] [2117] [2118] [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131] [2132] [2133] [2134] [2135] [2136] [2137] [2138] [2139] [2140] [2141] [2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163] Overfull \hbox (5.8567pt too wide) in paragraph at lines 11267--11269 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_depends Overfull \hbox (5.8567pt too wide) in paragraph at lines 11269--11271 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_results Overfull \hbox (5.8567pt too wide) in paragraph at lines 11271--11273 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_timings [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172]) (./fullrefman.aux) LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.write.matrix} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.survreg} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.coxph} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.stepAIC} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.rinvGauss} has been referenced but does not exi st, replaced by a fixed one 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Transcript written on fullrefman.log. make[3]: Leaving directory '/«PKGBUILDDIR»/doc/manual' make[2]: Leaving directory '/«PKGBUILDDIR»/doc' make[1]: Leaving directory '/«PKGBUILDDIR»' /usr/bin/make -k vignettes make[1]: Entering directory '/«PKGBUILDDIR»' make[2]: Entering directory '/«PKGBUILDDIR»/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/«PKGBUILDDIR»/m4' make[2]: Entering directory '/«PKGBUILDDIR»/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/«PKGBUILDDIR»/tools' make[2]: Entering directory '/«PKGBUILDDIR»/doc' make[3]: Entering directory '/«PKGBUILDDIR»/doc/html' make[3]: Leaving directory '/«PKGBUILDDIR»/doc/html' make[3]: Entering directory '/«PKGBUILDDIR»/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/«PKGBUILDDIR»/doc/manual' make[2]: Leaving directory '/«PKGBUILDDIR»/doc' make[2]: Entering directory '/«PKGBUILDDIR»/etc' make[2]: Leaving directory '/«PKGBUILDDIR»/etc' make[2]: Entering directory '/«PKGBUILDDIR»/share' make[2]: Leaving directory '/«PKGBUILDDIR»/share' make[2]: Entering directory '/«PKGBUILDDIR»/src' make[3]: Entering directory '/«PKGBUILDDIR»/src/scripts' make[4]: Entering directory '/«PKGBUILDDIR»/src/scripts' make[4]: Leaving directory '/«PKGBUILDDIR»/src/scripts' make[3]: Leaving directory '/«PKGBUILDDIR»/src/scripts' make[3]: Entering directory '/«PKGBUILDDIR»/src/include' make[4]: Entering directory '/«PKGBUILDDIR»/src/include/R_ext' make[4]: Nothing to be done for 'R'. make[4]: Leaving directory '/«PKGBUILDDIR»/src/include/R_ext' make[3]: Leaving directory '/«PKGBUILDDIR»/src/include' make[3]: Entering directory '/«PKGBUILDDIR»/src/extra' make[4]: Entering directory '/«PKGBUILDDIR»/src/extra/tre' make[5]: Entering directory '/«PKGBUILDDIR»/src/extra/tre' make[5]: 'Makedeps' is up to date. make[5]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre' make[5]: Entering directory '/«PKGBUILDDIR»/src/extra/tre' make[5]: 'libtre.a' is up to date. make[5]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre' make[4]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre' make[3]: Leaving directory '/«PKGBUILDDIR»/src/extra' make[3]: Entering directory '/«PKGBUILDDIR»/src/appl' make[4]: Entering directory '/«PKGBUILDDIR»/src/appl' make[4]: 'libappl.a' is up to date. make[4]: Leaving directory '/«PKGBUILDDIR»/src/appl' make[3]: Leaving directory '/«PKGBUILDDIR»/src/appl' make[3]: Entering directory '/«PKGBUILDDIR»/src/nmath' make[4]: Entering directory '/«PKGBUILDDIR»/src/nmath' make[4]: 'libnmath.a' is up to date. make[4]: Leaving directory '/«PKGBUILDDIR»/src/nmath' make[3]: Leaving directory '/«PKGBUILDDIR»/src/nmath' make[3]: Entering directory '/«PKGBUILDDIR»/src/unix' make[4]: Entering directory '/«PKGBUILDDIR»/src/unix' make[4]: 'libunix.a' is up to date. make[4]: Leaving directory '/«PKGBUILDDIR»/src/unix' make[4]: Entering directory '/«PKGBUILDDIR»/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/«PKGBUILDDIR»"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/«PKGBUILDDIR»/src/unix' make[3]: Leaving directory '/«PKGBUILDDIR»/src/unix' make[3]: Entering directory '/«PKGBUILDDIR»/src/main' make[4]: Entering directory '/«PKGBUILDDIR»/src/main' make[5]: Entering directory '/«PKGBUILDDIR»/src/main' /«PKGBUILDDIR»/lib/libR.so is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/main' make[4]: Leaving directory '/«PKGBUILDDIR»/src/main' make[4]: Entering directory '/«PKGBUILDDIR»/src/main' make[5]: Entering directory '/«PKGBUILDDIR»/src/main' /«PKGBUILDDIR»/bin/exec/R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/main' make[4]: Leaving directory '/«PKGBUILDDIR»/src/main' make[3]: Leaving directory '/«PKGBUILDDIR»/src/main' make[3]: Entering directory '/«PKGBUILDDIR»/src/modules' make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/internet' make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/internet' make[5]: 'internet.so' is up to date. make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet' make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet' make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack' make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack' make[5]: 'lapack.so' is up to date. make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack' make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack' make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/X11' make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/X11' make[5]: 'R_X11.so' is up to date. make[5]: 'R_de.so' is up to date. make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11' make[5]: Entering directory '/«PKGBUILDDIR»/src/modules/X11' /«PKGBUILDDIR»/modules/R_X11.so is unchanged /«PKGBUILDDIR»/modules/R_de.so is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11' make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11' make[3]: Leaving directory '/«PKGBUILDDIR»/src/modules' make[3]: Entering directory '/«PKGBUILDDIR»/src/library' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/profile' building system startup profile make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/profile' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/translations' building package 'translations' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/translations' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/translations' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/translations' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base' building package 'base' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/base' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/base' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tools' building package 'tools' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/tools/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/tools/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/tools/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/compiler' building package 'compiler' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/compiler' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/compiler' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/compiler' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tools' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tools' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/utils' building package 'utils' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils' all.R is unchanged make[5]: Nothing to be done for 'iconvlist'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/utils/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/utils/src' ../../../../library/utils/libs/utils.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/utils/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/utils/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/utils' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/utils' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices' building package 'grDevices' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[8]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[9]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[10]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[9]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[8]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src/cairo' make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grDevices' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/grDevices' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/graphics' building package 'graphics' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/graphics/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/graphics' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/stats' building package 'stats' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/stats/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/stats/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/stats/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/stats' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/datasets' building package 'datasets' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/datasets' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/datasets' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/datasets' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/methods' building package 'methods' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/methods/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/methods/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/methods/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/methods' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/methods' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/grid' building package 'grid' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/grid/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/grid/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/grid/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/grid' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/grid' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/splines' building package 'splines' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/splines/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/splines/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/splines/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/splines' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/splines' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/stats4' building package 'stats4' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/stats4' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk/src' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk/src' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/tcltk' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/parallel' building package 'parallel' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel' make[6]: Entering directory '/«PKGBUILDDIR»/src/library/parallel/src' make[7]: Entering directory '/«PKGBUILDDIR»/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel/src' make[6]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel/src' make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel' make[5]: Entering directory '/«PKGBUILDDIR»/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/parallel' make[4]: Entering directory '/«PKGBUILDDIR»/src/library/base' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/«PKGBUILDDIR»/src/library' make[2]: Leaving directory '/«PKGBUILDDIR»/src' make[2]: Entering directory '/«PKGBUILDDIR»/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/«PKGBUILDDIR»/tests' make[2]: Entering directory '/«PKGBUILDDIR»/doc' make[3]: Entering directory '/«PKGBUILDDIR»/doc/manual' make[4]: Entering directory '/«PKGBUILDDIR»/doc/html' make[4]: Leaving directory '/«PKGBUILDDIR»/doc/html' make[3]: Leaving directory '/«PKGBUILDDIR»/doc/manual' make[2]: Leaving directory '/«PKGBUILDDIR»/doc' make[2]: Entering directory '/«PKGBUILDDIR»/src/library' make[3]: Entering directory '/«PKGBUILDDIR»/src/library' installing parsed Rd make[4]: Entering directory '/«PKGBUILDDIR»/src/library' base stats utils methods graphics grDevices datasets grid tools tcltk splines stats4 compiler parallel make[4]: Leaving directory '/«PKGBUILDDIR»/src/library' make[3]: Leaving directory '/«PKGBUILDDIR»/src/library' make[3]: Entering directory '/«PKGBUILDDIR»/src/library' building/updating package metadata ... make[3]: Leaving directory '/«PKGBUILDDIR»/src/library' make[3]: Entering directory '/«PKGBUILDDIR»/src/library' writing package indices make[4]: Entering directory '/«PKGBUILDDIR»/src/library' make[4]: Leaving directory '/«PKGBUILDDIR»/src/library' make[3]: Leaving directory '/«PKGBUILDDIR»/src/library' make[2]: Leaving directory '/«PKGBUILDDIR»/src/library' make[2]: Entering directory '/«PKGBUILDDIR»/src/library/Recommended' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/«PKGBUILDDIR»/src/library/Recommended' make[2]: Entering directory '/«PKGBUILDDIR»/src/library' building/updating vignettes for package 'grid' ... processing 'grid.Rnw' building/updating vignettes for package 'parallel' ... building/updating vignettes for package 'utils' ... make[2]: Leaving directory '/«PKGBUILDDIR»/src/library' make[1]: Leaving directory '/«PKGBUILDDIR»' touch make-indep-stamp *** check *** xvfb-run make check-all make[1]: Entering directory '/«PKGBUILDDIR»' make[2]: Entering directory '/«PKGBUILDDIR»/tests' make[3]: Entering directory '/«PKGBUILDDIR»/tests' make[4]: Entering directory '/«PKGBUILDDIR»/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’ ... files differ in number of lines: 12223a12224,12231 > Warning: namespace 'MASS' is not available and has been replaced > by .GlobalEnv when processing object '' > predict.glmmPQL : > function (object, newdata = NULL, type = c("link", "response"), level = Q, na.action = na.pass, ...) NULL > Warning: namespace 'MASS' is not available and has been replaced > by .GlobalEnv when processing object '' > predict.lda : > function (object, newdata, prior = object$prior, dimen, method = c("plug-in", "predictive", "debiased"), ...) NULL 12227a12236,12243 > Warning: namespace 'MASS' is not available and has been replaced > by .GlobalEnv when processing object '' > predict.lqs : > function (object, newdata, na.action = na.pass, ...) NULL > Warning: namespace 'MASS' is not available and has been replaced > by .GlobalEnv when processing object '' > predict.mca : > function (object, newdata, type = c("row", "factor"), ...) NULL 12239a12256,12259 > Warning: namespace 'MASS' is not available and has been replaced > by .GlobalEnv when processing object '' > predict.polr : > function (object, newdata, type = c("class", "probs"), ...) NULL 12251a12272,12279 > Warning: namespace 'MASS' is not available and has been replaced > by .GlobalEnv when processing object '' > predict.qda : > function (object, newdata, prior = object$prior, method = c("plug-in", "predictive", "debiased", "looCV"), ...) NULL > Warning: namespace 'MASS' is not available and has been replaced > by .GlobalEnv when processing object '' > predict.rlm : > function (object, newdata = NULL, scale = NULL, ...) NULL 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[4]: Leaving directory '/«PKGBUILDDIR»/tests/Examples' make[3]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Entering directory '/«PKGBUILDDIR»/tests' running strict specific tests make[4]: Entering directory '/«PKGBUILDDIR»/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[4]: Leaving directory '/«PKGBUILDDIR»/tests' running sloppy specific tests make[4]: Entering directory '/«PKGBUILDDIR»/tests' running code in 'complex.R' ... OK comparing 'complex.Rout' to './complex.Rout.save' ... OK running code in 'print-tests.R' ... OK comparing 'print-tests.Rout' to './print-tests.Rout.save' ... OK running code in 'lapack.R' ... OK comparing 'lapack.Rout' to './lapack.Rout.save' ...405,409c405,409 < [1,] -0.4023 0.2877 -0.3638 0.5 0.6108 < [2,] -0.5338 -0.3474 -0.5742 -0.5 -0.1207 < [3,] -0.4177 -0.5380 0.6384 0.0 0.3585 < [4,] -0.4959 0.0733 0.1273 0.5 -0.6946 < [5,] -0.3644 0.7084 0.3378 -0.5 0.0369 --- > [1,] -0.4023 0.2877 0.3638 0.5 0.6108 > [2,] -0.5338 -0.3474 0.5742 -0.5 -0.1207 > [3,] -0.4177 -0.5380 -0.6384 0.0 0.3585 > [4,] -0.4959 0.0733 -0.1273 0.5 -0.6946 > [5,] -0.3644 0.7084 -0.3378 -0.5 0.0369 OK running code in 'datasets.R' ... OK comparing 'datasets.Rout' to './datasets.Rout.save' ... OK running code in 'datetime.R' ... OK comparing 'datetime.Rout' to './datetime.Rout.save' ... OK running code in 'iec60559.R' ... OK comparing 'iec60559.Rout' to './iec60559.Rout.save' ... OK make[4]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Entering directory '/«PKGBUILDDIR»/tests' running regression tests ... make[4]: Entering directory '/«PKGBUILDDIR»/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-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.R' ... OK comparing 'reg-S4.Rout' to './reg-S4.Rout.save' ... OK running code in 'reg-BLAS.R' ... OK make[4]: Leaving directory '/«PKGBUILDDIR»/tests' make[4]: Entering directory '/«PKGBUILDDIR»/tests' 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' ... OK comparing 'reg-plot-latin1.pdf' to './reg-plot-latin1.pdf.save' ... OK make[4]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Entering directory '/«PKGBUILDDIR»/tests' running tests of Internet functions expect some differences make[4]: Entering directory '/«PKGBUILDDIR»/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. > > nrow(available.packages(contrib.url("http://cran.r-project.org"))) > [1] 8269 > > > > # test url connections on http > > zz <- url("http://cran.r-project.org/") > > readLines(zz) > [1] "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Frameset//EN\" \"http://www.w3.org/TR/html4/frameset.dtd\">" > [2] "<html>" > [3] "<head>" > [4] "<title>The Comprehensive R Archive Network</title>" > [5] "<META HTTP-EQUIV=\"content-type\" CONTENT=\"text/html; charset=utf-8\">" > [6] "<link rel=\"icon\" href=\"favicon.ico\" type=\"image/x-icon\">" > [7] "<link rel=\"shortcut icon\" href=\"favicon.ico\" type=\"image/x-icon\">" > [8] "<link rel=\"stylesheet\" type=\"text/css\" href=\"R.css\">" > [9] "</head>" > [10] "" > [11] "<FRAMESET cols=\"1*, 4*\" style=\"border: none;\">" > [12] "<FRAMESET rows=\"120, 1*\">" > [13] "<FRAME src=\"logo.html\" name=\"logo\" frameborder=0>" > [14] "<FRAME src=\"navbar.html\" name=\"contents\" frameborder=0>" > [15] "</FRAMESET>" > [16] "<FRAME src=\"banner.shtml\" name=\"banner\" frameborder=0>" > [17] "<noframes>" > [18] "<h1>The Comprehensive R Archive Network</h1>" > [19] "" > [20] "Your browser seems not to support frames," > [21] "here is the <A href=\"navbar.html\">contents page</A> of CRAN." > [22] "</noframes>" > [23] "</FRAMESET>" > > close(zz) > > > > # and via read.table, test http and ftp. > > > > read.table("http://www.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat") > V1 V2 V3 V4 V5 > 1 1 307 930 36.58 0 > 2 2 307 940 36.73 0 > 3 3 307 950 36.93 0 > 4 4 307 1000 37.15 0 > 5 5 307 1010 37.23 0 > 6 6 307 1020 37.24 0 > 7 7 307 1030 37.24 0 > 8 8 307 1040 36.90 0 > 9 9 307 1050 36.95 0 > 10 10 307 1100 36.89 0 > 11 11 307 1110 36.95 0 > 12 12 307 1120 37.00 0 > 13 13 307 1130 36.90 0 > 14 14 307 1140 36.99 0 > 15 15 307 1150 36.99 0 > 16 16 307 1200 37.01 0 > 17 17 307 1210 37.04 0 > 18 18 307 1220 37.04 0 > 19 19 307 1230 37.14 0 > 20 20 307 1240 37.07 0 > 21 21 307 1250 36.98 0 > 22 22 307 1300 37.01 0 > 23 23 307 1310 36.97 0 > 24 24 307 1320 36.97 0 > 25 25 307 1330 37.12 0 > 26 26 307 1340 37.13 0 > 27 27 307 1350 37.14 0 > 28 28 307 1400 37.15 0 > 29 29 307 1410 37.17 0 > 30 30 307 1420 37.12 0 > 31 31 307 1430 37.12 0 > 32 32 307 1440 37.17 0 > 33 33 307 1450 37.28 0 > 34 34 307 1500 37.28 0 > 35 35 307 1510 37.44 0 > 36 36 307 1520 37.51 0 > 37 37 307 1530 37.64 0 > 38 38 307 1540 37.51 0 > 39 39 307 1550 37.98 1 > 40 40 307 1600 38.02 1 > 41 41 307 1610 38.00 1 > 42 42 307 1620 38.24 1 > 43 43 307 1630 38.10 1 > 44 44 307 1640 38.24 1 > 45 45 307 1650 38.11 1 > 46 46 307 1700 38.02 1 > 47 47 307 1710 38.11 1 > 48 48 307 1720 38.01 1 > 49 49 307 1730 37.91 1 > 50 50 307 1740 37.96 1 > 51 51 307 1750 38.03 1 > 52 52 307 1800 38.17 1 > 53 53 307 1810 38.19 1 > 54 54 307 1820 38.18 1 > 55 55 307 1830 38.15 1 > 56 56 307 1840 38.04 1 > 57 57 307 1850 37.96 1 > 58 58 307 1900 37.84 1 > 59 59 307 1910 37.83 1 > 60 60 307 1920 37.84 1 > 61 61 307 1930 37.74 1 > 62 62 307 1940 37.76 1 > 63 63 307 1950 37.76 1 > 64 64 307 2000 37.64 1 > 65 65 307 2010 37.63 1 > 66 66 307 2020 38.06 1 > 67 67 307 2030 38.19 1 > 68 68 307 2040 38.35 1 > 69 69 307 2050 38.25 1 > 70 70 307 2100 37.86 1 > 71 71 307 2110 37.95 1 > 72 72 307 2120 37.95 1 > 73 73 307 2130 37.76 1 > 74 74 307 2140 37.60 1 > 75 75 307 2150 37.89 1 > 76 76 307 2200 37.86 1 > 77 77 307 2210 37.71 1 > 78 78 307 2220 37.78 1 > 79 79 307 2230 37.82 1 > 80 80 307 2240 37.76 1 > 81 81 307 2250 37.81 1 > 82 82 307 2300 37.84 1 > 83 83 307 2310 38.01 1 > 84 84 307 2320 38.10 1 > 85 85 307 2330 38.15 1 > 86 86 307 2340 37.92 1 > 87 87 307 2350 37.64 1 > 88 88 308 0 37.70 1 > 89 89 308 10 37.46 1 > 90 90 308 20 37.41 1 > 91 91 308 30 37.46 1 > 92 92 308 40 37.56 1 > 93 93 308 50 37.55 1 > 94 94 308 100 37.75 1 > 95 95 308 110 37.76 1 > 96 96 308 120 37.73 1 > 97 97 308 130 37.77 1 > 98 98 308 140 38.01 1 > 99 99 308 150 38.04 1 > 100 100 308 200 38.07 1 > > read.table("ftp://ftp.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat") > V1 V2 V3 V4 V5 > 1 1 307 930 36.58 0 > 2 2 307 940 36.73 0 > 3 3 307 950 36.93 0 > 4 4 307 1000 37.15 0 > 5 5 307 1010 37.23 0 > 6 6 307 1020 37.24 0 > 7 7 307 1030 37.24 0 > 8 8 307 1040 36.90 0 > 9 9 307 1050 36.95 0 > 10 10 307 1100 36.89 0 > 11 11 307 1110 36.95 0 > 12 12 307 1120 37.00 0 > 13 13 307 1130 36.90 0 > 14 14 307 1140 36.99 0 > 15 15 307 1150 36.99 0 > 16 16 307 1200 37.01 0 > 17 17 307 1210 37.04 0 > 18 18 307 1220 37.04 0 > 19 19 307 1230 37.14 0 > 20 20 307 1240 37.07 0 > 21 21 307 1250 36.98 0 > 22 22 307 1300 37.01 0 > 23 23 307 1310 36.97 0 > 24 24 307 1320 36.97 0 > 25 25 307 1330 37.12 0 > 26 26 307 1340 37.13 0 > 27 27 307 1350 37.14 0 > 28 28 307 1400 37.15 0 > 29 29 307 1410 37.17 0 > 30 30 307 1420 37.12 0 > 31 31 307 1430 37.12 0 > 32 32 307 1440 37.17 0 > 33 33 307 1450 37.28 0 > 34 34 307 1500 37.28 0 > 35 35 307 1510 37.44 0 > 36 36 307 1520 37.51 0 > 37 37 307 1530 37.64 0 > 38 38 307 1540 37.51 0 > 39 39 307 1550 37.98 1 > 40 40 307 1600 38.02 1 > 41 41 307 1610 38.00 1 > 42 42 307 1620 38.24 1 > 43 43 307 1630 38.10 1 > 44 44 307 1640 38.24 1 > 45 45 307 1650 38.11 1 > 46 46 307 1700 38.02 1 > 47 47 307 1710 38.11 1 > 48 48 307 1720 38.01 1 > 49 49 307 1730 37.91 1 > 50 50 307 1740 37.96 1 > 51 51 307 1750 38.03 1 > 52 52 307 1800 38.17 1 > 53 53 307 1810 38.19 1 > 54 54 307 1820 38.18 1 > 55 55 307 1830 38.15 1 > 56 56 307 1840 38.04 1 > 57 57 307 1850 37.96 1 > 58 58 307 1900 37.84 1 > 59 59 307 1910 37.83 1 > 60 60 307 1920 37.84 1 > 61 61 307 1930 37.74 1 > 62 62 307 1940 37.76 1 > 63 63 307 1950 37.76 1 > 64 64 307 2000 37.64 1 > 65 65 307 2010 37.63 1 > 66 66 307 2020 38.06 1 > 67 67 307 2030 38.19 1 > 68 68 307 2040 38.35 1 > 69 69 307 2050 38.25 1 > 70 70 307 2100 37.86 1 > 71 71 307 2110 37.95 1 > 72 72 307 2120 37.95 1 > 73 73 307 2130 37.76 1 > 74 74 307 2140 37.60 1 > 75 75 307 2150 37.89 1 > 76 76 307 2200 37.86 1 > 77 77 307 2210 37.71 1 > 78 78 307 2220 37.78 1 > 79 79 307 2230 37.82 1 > 80 80 307 2240 37.76 1 > 81 81 307 2250 37.81 1 > 82 82 307 2300 37.84 1 > 83 83 307 2310 38.01 1 > 84 84 307 2320 38.10 1 > 85 85 307 2330 38.15 1 > 86 86 307 2340 37.92 1 > 87 87 307 2350 37.64 1 > 88 88 308 0 37.70 1 > 89 89 308 10 37.46 1 > 90 90 308 20 37.41 1 > 91 91 308 30 37.46 1 > 92 92 308 40 37.56 1 > 93 93 308 50 37.55 1 > 94 94 308 100 37.75 1 > 95 95 308 110 37.76 1 > 96 96 308 120 37.73 1 > 97 97 308 130 37.77 1 > 98 98 308 140 38.01 1 > 99 99 308 150 38.04 1 > 100 100 308 200 38.07 1 > > OK make[4]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Entering directory '/«PKGBUILDDIR»/tests' running tests of date-time printing expect platform-specific differences make[4]: Entering directory '/«PKGBUILDDIR»/tests' running code in 'datetime2.R' ... OK comparing 'datetime2.Rout' to './datetime2.Rout.save' ...10,11c10,11 < [1] "1890-01-10 13:00:00 CET" "1891-01-10 13:00:00 CET" < [3] "1892-01-10 13:00:00 CET" "1893-01-10 13:00:00 CET" --- > [1] "1890-01-10 12:49:56 RMT" "1891-01-10 12:49:56 RMT" > [3] "1892-01-10 12:49:56 RMT" "1893-01-10 12:49:56 RMT" 24c24 < [1] "1890-01-10 12:09:21 PMT" "1891-01-10 12:09:21 PMT" --- > [1] "1890-01-10 12:09:21 LMT" "1891-01-10 12:09:21 LMT" 37c37 < [1] "1890-01-10 12:09:21 PMT" "1891-01-10 12:09:21 PMT" --- > [1] "1890-01-10 12:09:21 LMT" "1891-01-10 12:09:21 LMT" 68c68 < [1] "1890-01-10 12:09:21 PMT" "1895-01-10 12:09:21 PMT" --- > [1] "1890-01-10 12:09:21 LMT" "1895-01-10 12:09:21 PMT" 78c78 < [1] "1890-01-10 12:09:21 PMT" --- > [1] "1890-01-10 12:09:21 LMT" OK make[4]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Entering directory '/«PKGBUILDDIR»/tests' running tests of documentation examples make[4]: Entering directory '/«PKGBUILDDIR»/tests' running code in 'R-intro.R' ... OK comparing 'R-intro.Rout' to './R-intro.Rout.save' ... OK make[4]: Leaving directory '/«PKGBUILDDIR»/tests' make[4]: Entering directory '/«PKGBUILDDIR»/tests' gcc -std=gnu99 -I/«PKGBUILDDIR»/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R-exts.c -o R-exts.o gcc -std=gnu99 -shared -L/«PKGBUILDDIR»/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o R-exts.so R-exts.o -L/«PKGBUILDDIR»/lib -lR make[4]: Leaving directory '/«PKGBUILDDIR»/tests' make[4]: Entering directory '/«PKGBUILDDIR»/tests' running code in 'R-exts.R' ... OK make[4]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Entering directory '/«PKGBUILDDIR»/tests' running tests of consistency of as/is.* make[4]: Entering directory '/«PKGBUILDDIR»/tests' creating 'isas-tests.R' running code in 'isas-tests.R' ... OK comparing 'isas-tests.Rout' to './isas-tests.Rout.save' ... OK rm isas-tests.R make[4]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Entering directory '/«PKGBUILDDIR»/tests' running tests of random deviate generation make[4]: Entering directory '/«PKGBUILDDIR»/tests' running code in 'p-r-random-tests.R' ... OK comparing 'p-r-random-tests.Rout' to './p-r-random-tests.Rout.save' ... OK make[4]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Entering directory '/«PKGBUILDDIR»/tests' running demos from base and stats make[4]: Entering directory '/«PKGBUILDDIR»/tests' running code in 'demos.R' ... OK comparing 'demos.Rout' to './demos.Rout.save' ... OK running code in 'demos2.R' ... OK make[4]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Entering directory '/«PKGBUILDDIR»/tests' running tests of primitives make[4]: Entering directory '/«PKGBUILDDIR»/tests' running code in 'primitives.R' ... OK make[4]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Entering directory '/«PKGBUILDDIR»/tests' running regexp regression tests make[3]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Entering directory '/«PKGBUILDDIR»/tests' running more Internet and socket tests make[4]: Entering directory '/«PKGBUILDDIR»/tests' running code in 'internet2.R' ... OK running code in 'libcurl.R' ... OK make[4]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Entering directory '/«PKGBUILDDIR»/tests' running tests to possibly trigger segfaults make[4]: Entering directory '/«PKGBUILDDIR»/tests' creating 'no-segfault.R' running code in 'no-segfault.R' ... OK make[4]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Entering directory '/«PKGBUILDDIR»/tests' testing building standalone Rmath make[4]: Entering directory '/«PKGBUILDDIR»/src/nmath/standalone' check output can be found in src/nmath/standalone/check.log make[4]: Leaving directory '/«PKGBUILDDIR»/src/nmath/standalone' make[3]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Entering directory '/«PKGBUILDDIR»/tests' make[4]: Entering directory '/«PKGBUILDDIR»/tests' checking package 'base' * using log directory ‘/«PKGBUILDDIR»/tests/base.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * using option ‘--no-build-vignettes’ * looks like ‘base’ is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Unknown packages ‘date’, ‘chron’, ‘nnet’, ‘survival’ in Rd xrefs * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking examples ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING See ‘/«PKGBUILDDIR»/tests/base.Rcheck/00check.log’ for details. checking package 'tools' * using log directory ‘/«PKGBUILDDIR»/tests/tools.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * using option ‘--no-build-vignettes’ * looks like ‘tools’ is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking R/sysdata.rda ... OK * checking compiled code ... OK * checking examples ... SKIPPED * checking tests ... Running ‘undoc.R’ OK * checking PDF version of manual ... OK * DONE Status: OK checking package 'utils' * using log directory ‘/«PKGBUILDDIR»/tests/utils.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * using option ‘--no-build-vignettes’ * looks like ‘utils’ is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Unknown package ‘MASS’ in Rd xrefs * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking R/sysdata.rda ... OK * checking compiled code ... OK * checking files in ‘vignettes’ ... OK * checking examples ... SKIPPED * checking tests ... Running ‘Sweave-tst.R’ Running ‘completion.R’ OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘Sweave.Rnw’ ... OK OK * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING See ‘/«PKGBUILDDIR»/tests/utils.Rcheck/00check.log’ for details. checking package 'grDevices' * using log directory ‘/«PKGBUILDDIR»/tests/grDevices.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * using option ‘--no-build-vignettes’ * looks like ‘grDevices’ is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Unknown packages ‘KernSmooth’, ‘MASS’ in Rd xrefs * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking compiled code ... OK * checking examples ... SKIPPED * checking tests ... Running ‘ps-tests.R’ Comparing ‘ps-tests.Rout’ to ‘ps-tests.Rout.save’ ... OK Running ‘xfig-tests.R’ Comparing ‘xfig-tests.Rout’ to ‘xfig-tests.Rout.save’ ... OK OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING See ‘/«PKGBUILDDIR»/tests/grDevices.Rcheck/00check.log’ for details. checking package 'graphics' * using log directory ‘/«PKGBUILDDIR»/tests/graphics.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * using option ‘--no-build-vignettes’ * looks like ‘graphics’ is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Unknown packages ‘vcd’, ‘lattice’, ‘MASS’, ‘KernSmooth’ in Rd xrefs * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking compiled code ... OK * checking examples ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING See ‘/«PKGBUILDDIR»/tests/graphics.Rcheck/00check.log’ for details. checking package 'stats' * using log directory ‘/«PKGBUILDDIR»/tests/stats.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * using option ‘--no-build-vignettes’ * looks like ‘stats’ is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Unknown packages ‘coin’, ‘nlme’, ‘cluster’, ‘MASS’, ‘rpart’, ‘Matrix’, ‘pcaPP’, ‘Kendall’, ‘SuppDists’, ‘pspearman’, ‘survival’, ‘multcomp’ in Rd xrefs * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking compiled code ... OK * checking examples ... SKIPPED * checking tests ... Running ‘NLSstClosest.R’ Running ‘arimaML.R’ Running ‘cmdscale.R’ Running ‘drop1-polr.R’ Running ‘glm.R’ Comparing ‘glm.Rout’ to ‘glm.Rout.save’ ... OK Running ‘ig_glm.R’ Running ‘ks-test.R’ Comparing ‘ks-test.Rout’ to ‘ks-test.Rout.save’ ... OK Running ‘nafns.R’ Running ‘nls.R’ Comparing ‘nls.Rout’ to ‘nls.Rout.save’ ...79a80,84 > Waiting for profiling to be done... > 2.5% 97.5% > a 1.00875 1.037847 > b 0.84138 0.914645 > c NA 0.042807 141c146 < 2: 0.00060639084: 0.00517051 0.999153 --- > 2: 0.00060639084: 0.00517053 0.999153 150c155 < b 0.99915 0.00119 841.37 <2e-16 *** --- > b 0.99915 0.00119 841.38 <2e-16 *** 331a337,345 > Waiting for profiling to be done... > 2.5% 97.5% > Asym 2.14936 2.5724 > xmid 1.28535 1.6966 > scal 0.97526 1.1068 > Waiting for profiling to be done... > 2.5% 97.5% > xmid 1.2866 1.6949 > scal 0.9757 1.1063 360a375,377 > Waiting for profiling to be done... > 2.5% 97.5% > 0.68704 0.70281 368a386,388 > Waiting for profiling to be done... > 2.5% 97.5% > 0.68704 0.70281 374a395,398 > Waiting for profiling to be done... > 2.5% 97.5% > a 0.49494 0.50893 > b 0.70019 0.74767 382a407,410 > Waiting for profiling to be done... > 2.5% 97.5% > a 0.49494 0.50893 > b 0.70019 0.74767 388a417,421 > Waiting for profiling to be done... > 2.5% 97.5% > a 0.35006 0.66057 > b 0.45107 0.91473 > logc -0.64627 0.40946 396a430,434 > Waiting for profiling to be done... > 2.5% 97.5% > a 0.35006 0.66057 > b 0.45107 0.91473 > logc -0.64627 0.40946 403a442,446 > 2.5% 97.5% > 0.70019 0.74767 > 2.5% 97.5% > b 0.45105 0.91471 > logc -0.64625 0.40933 473a517,519 > 2.5% 97.5% > a 0.96 5.20 > b NA 1.07 524a571,574 > Waiting for profiling to be done... > 2.5% 97.5% > a 0.907 NA > b NA 0.611 Running ‘offsets.R’ Running ‘ppr.R’ Running ‘simulate.R’ Comparing ‘simulate.Rout’ to ‘simulate.Rout.save’ ...359,364c359,392 < > proc.time() < user system elapsed < 0.346 0.029 0.362 < Warning message: < In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : < there is no package called 'MASS' --- > > > > ## gamma fit, from example(glm) > > clotting <- data.frame(u = c(5,10,15,20,30,40,60,80,100), > + lot1 = c(118,58,42,35,27,25,21,19,18)) > > fit7 <- glm(lot1 ~ log(u), data = clotting, family = Gamma) > > coef(summary(fit7)) > Estimate Std. Error t value Pr(>|t|) > (Intercept) -0.016554 0.00092755 -17.847 4.2791e-07 > log(u) 0.015343 0.00041496 36.975 2.7512e-09 > > set.seed(1) > > ( ys <- simulate(fit7, nsim = 3) ) > sim_1 sim_2 sim_3 > 1 119.451 118.552 123.140 > 2 56.310 51.798 48.747 > 3 42.193 39.456 40.843 > 4 34.581 33.905 35.580 > 5 26.208 26.971 27.210 > 6 25.476 25.840 24.437 > 7 22.287 22.151 21.375 > 8 20.206 20.503 19.626 > 9 18.224 19.094 17.952 > > for(i in seq_len(3)) > + print(coef(summary(update(fit7, ys[, i] ~ .)))) > Estimate Std. Error t value Pr(>|t|) > (Intercept) -0.016008 0.00077887 -20.553 1.6197e-07 > log(u) 0.015044 0.00034611 43.465 8.9084e-10 > Estimate Std. Error t value Pr(>|t|) > (Intercept) -0.015483 0.00050102 -30.903 9.5910e-09 > log(u) 0.014935 0.00021999 67.889 3.9547e-11 > Estimate Std. Error t value Pr(>|t|) > (Intercept) -0.016850 0.00075120 -22.431 8.8554e-08 > log(u) 0.015569 0.00033659 46.256 5.7704e-10 > > > > Running ‘smooth.spline.R’ Running ‘ts-tests.R’ OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING See ‘/«PKGBUILDDIR»/tests/stats.Rcheck/00check.log’ for details. checking package 'datasets' * using log directory ‘/«PKGBUILDDIR»/tests/datasets.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * using option ‘--no-build-vignettes’ * looks like ‘datasets’ is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking examples ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK checking package 'methods' * using log directory ‘/«PKGBUILDDIR»/tests/methods.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * using option ‘--no-build-vignettes’ * looks like ‘methods’ is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.class1’ ‘.missingMethod’ ‘.selectDotsMethod’ ‘.setDummyField’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Unknown package ‘Matrix’ in Rd xrefs * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking compiled code ... OK * checking examples ... SKIPPED * checking tests ... Running ‘S3.R’ Running ‘basicRefClass.R’ Running ‘duplicateClass.R’ Running ‘fieldAssignments.R’ Running ‘mixinInitialize.R’ Running ‘namesAndSlots.R’ Running ‘nextWithDots.R’ Running ‘refClassExample.R’ Running ‘testConditionalIs.R’ Running ‘testGroupGeneric.R’ Running ‘testIs.R’ OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See ‘/«PKGBUILDDIR»/tests/methods.Rcheck/00check.log’ for details. checking package 'grid' * using log directory ‘/«PKGBUILDDIR»/tests/grid.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * using option ‘--no-build-vignettes’ * looks like ‘grid’ is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Unknown package ‘lattice’ in Rd xrefs * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking compiled code ... OK * checking files in ‘vignettes’ ... OK * checking examples ... SKIPPED * checking tests ... Running ‘bugs.R’ Running ‘reg.R’ Running ‘testls.R’ Comparing ‘testls.Rout’ to ‘testls.Rout.save’ ... OK Running ‘units.R’ OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘displaylist.Rnw’ ... OK ‘frame.Rnw’ ... OK ‘grid.Rnw’ ... failed ‘grobs.Rnw’ ... OK ‘interactive.Rnw’ ... OK ‘locndimn.Rnw’ ... OK ‘moveline.Rnw’ ... OK ‘nonfinite.Rnw’ ... OK ‘plotexample.Rnw’ ... OK ‘rotated.Rnw’ ... OK ‘saveload.Rnw’ ... OK ‘sharing.Rnw’ ... OK ‘viewports.Rnw’ ... OK WARNING Errors in running code in vignettes: when running code in ‘grid.Rnw’ ... > leg(legLabels) > popViewport(3) > library(lattice) When sourcing ‘grid.R’: Error: there is no package called ‘lattice’ Execution halted * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs See ‘/«PKGBUILDDIR»/tests/grid.Rcheck/00check.log’ for details. checking package 'splines' * using log directory ‘/«PKGBUILDDIR»/tests/splines.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * using option ‘--no-build-vignettes’ * looks like ‘splines’ is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Unknown package ‘Matrix’ in Rd xrefs * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking compiled code ... OK * checking examples ... SKIPPED * checking tests ... Running ‘sparse-tst.R’ Running ‘spline-tst.R’ OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING See ‘/«PKGBUILDDIR»/tests/splines.Rcheck/00check.log’ for details. checking package 'stats4' * using log directory ‘/«PKGBUILDDIR»/tests/stats4.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * using option ‘--no-build-vignettes’ * looks like ‘stats4’ is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking examples ... SKIPPED * checking tests ... Running ‘confint.R’ OK * checking PDF version of manual ... OK * DONE Status: OK checking package 'tcltk' * using log directory ‘/«PKGBUILDDIR»/tests/tcltk.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * using option ‘--no-build-vignettes’ * looks like ‘tcltk’ is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking compiled code ... OK * checking examples ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK checking package 'compiler' * using log directory ‘/«PKGBUILDDIR»/tests/compiler.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * using option ‘--no-build-vignettes’ * looks like ‘compiler’ is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking examples ... SKIPPED * checking tests ... Running ‘assign.R’ Running ‘basics.R’ Running ‘const.R’ Running ‘envir.R’ Running ‘jit.R’ Running ‘loop.R’ Running ‘switch.R’ OK * checking PDF version of manual ... OK * DONE Status: OK checking package 'parallel' * using log directory ‘/«PKGBUILDDIR»/tests/parallel.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * using option ‘--no-build-vignettes’ * looks like ‘parallel’ is a base package * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking compiled code ... OK * checking files in ‘vignettes’ ... OK * checking examples ... SKIPPED * checking tests ... Running ‘Master.R’ OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘parallel.Rnw’ ... OK NONE * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK make[4]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Entering directory '/«PKGBUILDDIR»/tests' checking package 'MASS' * using log directory ‘/«PKGBUILDDIR»/tests/MASS.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * checking for file ‘MASS/DESCRIPTION’ ... OK * this is package ‘MASS’ version ‘7.3-45’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib: cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib: cannot download all files NOTE Packages suggested but not available for checking: ‘lattice’ ‘nlme’ ‘nnet’ ‘survival’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... WARNING Invalid citation information in ‘inst/CITATION’: Warning message: In utils::packageDescription(basename(dir), dirname(dir)) : no package 'MASS' was found * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... ERROR Loading this package had a fatal error status code 1 Loading log: Error in library(MASS) : there is no package called ‘MASS’ Execution halted * DONE Status: 1 ERROR, 1 WARNING, 1 NOTE See ‘/«PKGBUILDDIR»/tests/MASS.Rcheck/00check.log’ for details. checking package 'lattice' * using log directory ‘/«PKGBUILDDIR»/tests/lattice.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * checking for file ‘lattice/DESCRIPTION’ ... OK * this is package ‘lattice’ version ‘0.20-33’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib: cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib: cannot download all files NOTE Packages suggested but not available for checking: ‘KernSmooth’ ‘MASS’ Package which this enhances but not available for checking: ‘chron’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... WARNING Invalid citation information in ‘inst/CITATION’: Warning message: In utils::packageDescription(basename(dir), dirname(dir)) : no package 'lattice' was found * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... ERROR Loading this package had a fatal error status code 1 Loading log: Error in library(lattice) : there is no package called ‘lattice’ Execution halted * DONE Status: 1 ERROR, 1 WARNING, 1 NOTE See ‘/«PKGBUILDDIR»/tests/lattice.Rcheck/00check.log’ for details. checking package 'Matrix' * using log directory ‘/«PKGBUILDDIR»/tests/Matrix.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * checking for file ‘Matrix/DESCRIPTION’ ... OK * this is package ‘Matrix’ version ‘1.2-6’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib: cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib: cannot download all files ERROR Package required but not available: ‘lattice’ Packages suggested but not available for checking: ‘expm’ ‘MASS’ Packages which this enhances but not available for checking: ‘MatrixModels’ ‘graph’ ‘SparseM’ ‘sfsmisc’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. * DONE Status: 1 ERROR See ‘/«PKGBUILDDIR»/tests/Matrix.Rcheck/00check.log’ for details. checking package 'nlme' * using log directory ‘/«PKGBUILDDIR»/tests/nlme.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * checking for file ‘nlme/DESCRIPTION’ ... OK * this is package ‘nlme’ version ‘3.1-127’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib: cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib: cannot download all files ERROR Package required but not available: ‘lattice’ Packages suggested but not available for checking: ‘Hmisc’ ‘MASS’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. * DONE Status: 1 ERROR See ‘/«PKGBUILDDIR»/tests/nlme.Rcheck/00check.log’ for details. checking package 'survival' * using log directory ‘/«PKGBUILDDIR»/tests/survival.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * checking for file ‘survival/DESCRIPTION’ ... OK * this is package ‘survival’ version ‘2.39-2’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib: cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib: cannot download all files ERROR Package required but not available: ‘Matrix’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. * DONE Status: 1 ERROR See ‘/«PKGBUILDDIR»/tests/survival.Rcheck/00check.log’ for details. checking package 'boot' * using log directory ‘/«PKGBUILDDIR»/tests/boot.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * checking for file ‘boot/DESCRIPTION’ ... OK * this is package ‘boot’ version ‘1.3-18’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib: cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib: cannot download all files NOTE Packages suggested but not available for checking: ‘MASS’ ‘survival’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... WARNING Invalid citation information in ‘inst/CITATION’: Warning message: In utils::packageDescription(basename(dir), dirname(dir)) : no package 'boot' was found * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... ERROR Loading this package had a fatal error status code 1 Loading log: Error in library(boot) : there is no package called ‘boot’ Execution halted * DONE Status: 1 ERROR, 1 WARNING, 1 NOTE See ‘/«PKGBUILDDIR»/tests/boot.Rcheck/00check.log’ for details. checking package 'cluster' * using log directory ‘/«PKGBUILDDIR»/tests/cluster.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * checking for file ‘cluster/DESCRIPTION’ ... OK * this is package ‘cluster’ version ‘2.0.4’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib: cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib: cannot download all files NOTE Package suggested but not available for checking: ‘MASS’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... WARNING Invalid citation information in ‘inst/CITATION’: Warning message: In utils::packageDescription(basename(dir), dirname(dir)) : no package 'cluster' was found * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... ERROR Loading this package had a fatal error status code 1 Loading log: Error in library(cluster) : there is no package called ‘cluster’ Execution halted * DONE Status: 1 ERROR, 1 WARNING, 1 NOTE See ‘/«PKGBUILDDIR»/tests/cluster.Rcheck/00check.log’ for details. checking package 'codetools' * using log directory ‘/«PKGBUILDDIR»/tests/codetools.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * checking for file ‘codetools/DESCRIPTION’ ... OK * this is package ‘codetools’ version ‘0.2-14’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib: cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib: cannot download all files OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... ERROR Loading this package had a fatal error status code 1 Loading log: Error in library(codetools) : there is no package called ‘codetools’ Execution halted * DONE Status: 1 ERROR See ‘/«PKGBUILDDIR»/tests/codetools.Rcheck/00check.log’ for details. checking package 'foreign' * using log directory ‘/«PKGBUILDDIR»/tests/foreign.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * checking for file ‘foreign/DESCRIPTION’ ... OK * this is package ‘foreign’ version ‘0.8-66’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib: cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib: cannot download all files OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... ERROR Loading this package had a fatal error status code 1 Loading log: Error in library(foreign) : there is no package called ‘foreign’ Execution halted * DONE Status: 1 ERROR See ‘/«PKGBUILDDIR»/tests/foreign.Rcheck/00check.log’ for details. checking package 'KernSmooth' * using log directory ‘/«PKGBUILDDIR»/tests/KernSmooth.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * checking for file ‘KernSmooth/DESCRIPTION’ ... OK * this is package ‘KernSmooth’ version ‘2.23-15’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib: cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib: cannot download all files NOTE Package suggested but not available for checking: ‘MASS’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... ERROR Loading this package had a fatal error status code 1 Loading log: Error in library(KernSmooth) : there is no package called ‘KernSmooth’ Execution halted * DONE Status: 1 ERROR, 1 NOTE See ‘/«PKGBUILDDIR»/tests/KernSmooth.Rcheck/00check.log’ for details. checking package 'rpart' * using log directory ‘/«PKGBUILDDIR»/tests/rpart.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * checking for file ‘rpart/DESCRIPTION’ ... OK * this is package ‘rpart’ version ‘4.1-10’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib: cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib: cannot download all files NOTE Package suggested but not available for checking: ‘survival’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * skipping installation test * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... ERROR Loading this package had a fatal error status code 1 Loading log: Error in library(rpart) : there is no package called ‘rpart’ Execution halted * DONE Status: 1 ERROR, 1 NOTE See ‘/«PKGBUILDDIR»/tests/rpart.Rcheck/00check.log’ for details. checking package 'class' * using log directory ‘/«PKGBUILDDIR»/tests/class.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * checking for file ‘class/DESCRIPTION’ ... OK * this is package ‘class’ version ‘7.3-14’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib: cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib: cannot download all files ERROR Package required but not available: ‘MASS’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. * DONE Status: 1 ERROR See ‘/«PKGBUILDDIR»/tests/class.Rcheck/00check.log’ for details. checking package 'nnet' * using log directory ‘/«PKGBUILDDIR»/tests/nnet.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * checking for file ‘nnet/DESCRIPTION’ ... OK * this is package ‘nnet’ version ‘7.3-12’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib: cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib: cannot download all files NOTE Package suggested but not available for checking: ‘MASS’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... WARNING Invalid citation information in ‘inst/CITATION’: Warning message: In utils::packageDescription(basename(dir), dirname(dir)) : no package 'nnet' was found * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... ERROR Loading this package had a fatal error status code 1 Loading log: Error in library(nnet) : there is no package called ‘nnet’ Execution halted * DONE Status: 1 ERROR, 1 WARNING, 1 NOTE See ‘/«PKGBUILDDIR»/tests/nnet.Rcheck/00check.log’ for details. checking package 'spatial' * using log directory ‘/«PKGBUILDDIR»/tests/spatial.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * checking for file ‘spatial/DESCRIPTION’ ... OK * this is package ‘spatial’ version ‘7.3-11’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib: cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib: cannot download all files NOTE Package suggested but not available for checking: ‘MASS’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * skipping installation test * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... WARNING Invalid citation information in ‘inst/CITATION’: Warning message: In utils::packageDescription(basename(dir), dirname(dir)) : no package 'spatial' was found * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... ERROR Loading this package had a fatal error status code 1 Loading log: Error in library(spatial) : there is no package called ‘spatial’ Execution halted * DONE Status: 1 ERROR, 1 WARNING, 1 NOTE See ‘/«PKGBUILDDIR»/tests/spatial.Rcheck/00check.log’ for details. checking package 'mgcv' * using log directory ‘/«PKGBUILDDIR»/tests/mgcv.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: i686-pc-linux-gnu (32-bit) * using session charset: UTF-8 * checking for file ‘mgcv/DESCRIPTION’ ... OK * this is package ‘mgcv’ version ‘1.8-12’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository http://CRAN.R-project.org/src/contrib: cannot open URL 'http://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/annotation/src/contrib: cannot download all files Warning: unable to access index for repository https://bioconductor.org/packages/3.3/data/experiment/src/contrib: cannot download all files ERROR Packages required but not available: ‘nlme’ ‘Matrix’ Packages suggested but not available for checking: ‘survival’ ‘MASS’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. * DONE Status: 1 ERROR See ‘/«PKGBUILDDIR»/tests/mgcv.Rcheck/00check.log’ for details. make[3]: Leaving directory '/«PKGBUILDDIR»/tests' make[2]: Leaving directory '/«PKGBUILDDIR»/tests' make[1]: Leaving directory '/«PKGBUILDDIR»' touch check-stamp fakeroot debian/rules binary-arch *** install-arch *** dh_testdir dh_testroot dh_prep -a dh_installdirs -A /«PKGBUILDDIR»/debian/r-base-core /usr/bin/make DESTDIR=/«PKGBUILDDIR»/debian/r-base-core install make[1]: Entering directory '/«PKGBUILDDIR»' make[2]: Entering directory '/«PKGBUILDDIR»/m4' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/«PKGBUILDDIR»/m4' make[2]: Entering directory '/«PKGBUILDDIR»/tools' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/«PKGBUILDDIR»/tools' make[2]: Entering directory '/«PKGBUILDDIR»/doc' installing doc ... mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/doc mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/man/man1 make[3]: Entering directory '/«PKGBUILDDIR»/doc/html' installing doc/html ... mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/doc/html make[3]: Leaving directory '/«PKGBUILDDIR»/doc/html' make[3]: Entering directory '/«PKGBUILDDIR»/doc/manual' installing doc/manual ... mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/doc/manual mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/doc/manual/images make[3]: Leaving directory '/«PKGBUILDDIR»/doc/manual' make[2]: Leaving directory '/«PKGBUILDDIR»/doc' make[2]: Entering directory '/«PKGBUILDDIR»/etc' mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/etc installing etc ... make[2]: Leaving directory '/«PKGBUILDDIR»/etc' make[2]: Entering directory '/«PKGBUILDDIR»/share' installing share ... mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/R mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/dictionaries mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/encodings mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/java mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/licenses mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/make mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/Rd mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/Rd/macros mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/sh mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/texmf mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/texmf/bibtex/bib mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/texmf/bibtex/bst mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/texmf/tex/latex make[2]: Leaving directory '/«PKGBUILDDIR»/share' make[2]: Entering directory '/«PKGBUILDDIR»/src' make[3]: Entering directory '/«PKGBUILDDIR»/src/scripts' mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/bin make[3]: Leaving directory '/«PKGBUILDDIR»/src/scripts' make[3]: Entering directory '/«PKGBUILDDIR»/src/include' make[4]: Entering directory '/«PKGBUILDDIR»/src/include/R_ext' mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/include/R_ext make[4]: Leaving directory '/«PKGBUILDDIR»/src/include/R_ext' make[3]: Leaving directory '/«PKGBUILDDIR»/src/include' make[3]: Entering directory '/«PKGBUILDDIR»/src/extra' make[4]: Entering directory '/«PKGBUILDDIR»/src/extra/blas' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/«PKGBUILDDIR»/src/extra/blas' make[4]: Entering directory '/«PKGBUILDDIR»/src/extra/tre' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/«PKGBUILDDIR»/src/extra/tre' make[4]: Entering directory '/«PKGBUILDDIR»/src/extra/xdr' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/«PKGBUILDDIR»/src/extra/xdr' make[4]: Entering directory '/«PKGBUILDDIR»/src/extra/intl' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/«PKGBUILDDIR»/src/extra/intl' make[3]: Leaving directory '/«PKGBUILDDIR»/src/extra' make[3]: Entering directory '/«PKGBUILDDIR»/src/appl' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/«PKGBUILDDIR»/src/appl' make[3]: Entering directory '/«PKGBUILDDIR»/src/nmath' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/«PKGBUILDDIR»/src/nmath' make[3]: Entering directory '/«PKGBUILDDIR»/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/usr/lib/R"' \ -o Rscript ./Rscript.c mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/lib/pkgconfig make[3]: Leaving directory '/«PKGBUILDDIR»/src/unix' make[3]: Entering directory '/«PKGBUILDDIR»/src/main' mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/bin/exec make[4]: Entering directory '/«PKGBUILDDIR»/src/main' make[4]: Leaving directory '/«PKGBUILDDIR»/src/main' make[4]: Entering directory '/«PKGBUILDDIR»/src/main' mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/lib make[4]: Leaving directory '/«PKGBUILDDIR»/src/main' make[3]: Leaving directory '/«PKGBUILDDIR»/src/main' make[3]: Entering directory '/«PKGBUILDDIR»/src/modules' make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/internet' mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/modules make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/internet' make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/lapack' make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/lapack' make[4]: Entering directory '/«PKGBUILDDIR»/src/modules/X11' make[4]: Leaving directory '/«PKGBUILDDIR»/src/modules/X11' make[3]: Leaving directory '/«PKGBUILDDIR»/src/modules' make[3]: Entering directory '/«PKGBUILDDIR»/src/library' mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/library installing packages ... building HTML index ... make[3]: Leaving directory '/«PKGBUILDDIR»/src/library' make[2]: Leaving directory '/«PKGBUILDDIR»/src' make[2]: Entering directory '/«PKGBUILDDIR»/tests' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/«PKGBUILDDIR»/tests' make[1]: Leaving directory '/«PKGBUILDDIR»' (cd src/unix; \ rm -vf Rscript /«PKGBUILDDIR»/debian/r-base-core/usr/bin/Rscript; \ /usr/bin/make CFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ FFLAGS="-g -O2 -fstack-protector-strong -D_REENTRANT" \ CC="gcc -std=gnu99" \ CXX=g++ \ F77=gfortran \ RHOME=/usr/lib/R \ DESTDIR=/«PKGBUILDDIR»/debian/r-base-core \ install-Rscript ) removed 'Rscript' removed '/«PKGBUILDDIR»/debian/r-base-core/usr/bin/Rscript' make[1]: Entering directory '/«PKGBUILDDIR»/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/usr/lib/R"' \ -o Rscript ./Rscript.c make[1]: Leaving directory '/«PKGBUILDDIR»/src/unix' #ls -ltr /«PKGBUILDDIR»/debian/r-base-core/usr/bin/ #strings src/unix/Rscript cp -vax src/unix/Rscript /«PKGBUILDDIR»/debian/r-base-core/usr/bin/ 'src/unix/Rscript' -> '/«PKGBUILDDIR»/debian/r-base-core/usr/bin/Rscript' #ls -ltr /«PKGBUILDDIR»/debian/r-base-core/usr/bin/ #strings /«PKGBUILDDIR»/debian/r-base-core/usr/bin/Rscript (cd src/nmath/standalone; \ /usr/bin/make DESTDIR=/«PKGBUILDDIR»/debian/r-base-core install ) make[1]: Entering directory '/«PKGBUILDDIR»/src/nmath/standalone' make[2]: Entering directory '/«PKGBUILDDIR»/src/include' make[2]: 'Rmath.h' is up to date. make[2]: Leaving directory '/«PKGBUILDDIR»/src/include' /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/include/Rmath.h is unchanged make[1]: Leaving directory '/«PKGBUILDDIR»/src/nmath/standalone' chmod a+x /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/share/sh/echo.sh rm -v /«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/COPYING removed '/«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/COPYING' (cd /«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/; \ ln -s ../../share/common-licenses/GPL-2 COPYING) rm -v /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/doc/COPYING removed '/«PKGBUILDDIR»/debian/r-base-core/usr/share/R/doc/COPYING' (cd /«PKGBUILDDIR»/debian/r-base-core/usr/share/R/doc; \ ln -s ../../../share/common-licenses/GPL-2 COPYING) # edd 03 Oct 2006 use link into /usr/share/, not /usr/lib/ (cd /«PKGBUILDDIR»/debian/r-base-core/usr/share/texmf/tex/latex && \ ln -s ../../../R/share/texmf R) dh_movefiles --sourcedir=debian/r-base-core -pr-doc-html dh_movefiles --sourcedir=debian/r-base-core -pr-base-html dh_movefiles --sourcedir=debian/r-base-core -pr-base-latex make prefix=/«PKGBUILDDIR»/debian/r-base-core/usr \ rdocdir=/«PKGBUILDDIR»/debian/r-base-core/usr/share/R/doc \ install-pdf make[1]: Entering directory '/«PKGBUILDDIR»' make[2]: Entering directory '/«PKGBUILDDIR»/doc/manual' installing R manuals in PDF format ... make[2]: Leaving directory '/«PKGBUILDDIR»/doc/manual' make[1]: Leaving directory '/«PKGBUILDDIR»' make prefix=/«PKGBUILDDIR»/debian/r-base-core/usr \ infodir=/«PKGBUILDDIR»/debian/r-base-core/usr/share/info install-info make[1]: Entering directory '/«PKGBUILDDIR»' make[2]: Entering directory '/«PKGBUILDDIR»/doc/manual' mkdir -p -- /«PKGBUILDDIR»/debian/r-base-core/usr/share/info /usr/bin/install -c -m 644 "./dir" "/«PKGBUILDDIR»/debian/r-base-core/usr/share/info" installing R info pages ... updating '/«PKGBUILDDIR»/debian/r-base-core/usr/share/info/dir' ... you need to adjust /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/dir manually you need to adjust /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/dir manually you need to adjust /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/dir manually you need to adjust /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/dir manually you need to adjust /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/dir manually you need to adjust /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/dir manually you need to adjust /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/dir manually make[2]: Leaving directory '/«PKGBUILDDIR»/doc/manual' make[1]: Leaving directory '/«PKGBUILDDIR»' dh_movefiles --sourcedir=debian/r-base-core -pr-doc-pdf dh_movefiles --sourcedir=debian/r-base-core -pr-doc-html touch install-indep-stamp gunzip -9v /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/*.gz /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-FAQ.info.gz: 67.1% -- replaced with /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-FAQ.info /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-admin.info.gz: 68.2% -- replaced with /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-admin.info /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-data.info.gz: 70.6% -- replaced with /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-data.info /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-exts.info-1.gz: 66.8% -- replaced with /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-exts.info-1 /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-exts.info-2.gz: 70.8% -- replaced with /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-exts.info-2 /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-exts.info.gz: 68.4% -- replaced with /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-exts.info /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-intro.info.gz: 70.0% -- replaced with /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-intro.info /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-ints.info.gz: 67.8% -- replaced with /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-ints.info /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-lang.info.gz: 71.7% -- replaced with /«PKGBUILDDIR»/debian/r-base-core/usr/share/info/R-lang.info dh_movefiles --sourcedir=debian/r-base-core -pr-doc-info rm -vf /«PKGBUILDDIR»/debian/r-doc-info/usr/share/info/dir \ /«PKGBUILDDIR»/debian/r-doc-info/usr/share/info/dir.old removed '/«PKGBUILDDIR»/debian/r-doc-info/usr/share/info/dir' dh_installdirs -pr-mathlib usr/include usr/lib \ usr/share/lintian/overrides \ usr/lib/pkgconfig dh_movefiles --sourcedir=debian/r-base-core -pr-mathlib (cd /«PKGBUILDDIR»/debian/r-mathlib/usr/lib; \ ls -l ; \ mv -v libRmath.so libRmath.so.1.0.0; \ ln -sv libRmath.so.1.0.0 libRmath.so.1; \ ln -sv libRmath.so.1 libRmath.so) total 1732 -rw-rw-r-- 1 root root 1116894 May 3 23:46 libRmath.a -rwxrwxr-x 1 root root 651084 May 3 23:46 libRmath.so drwxr-xr-x 2 root root 4096 May 3 23:46 pkgconfig 'libRmath.so' -> 'libRmath.so.1.0.0' 'libRmath.so.1' -> 'libRmath.so.1.0.0' 'libRmath.so' -> 'libRmath.so.1' install -m 0644 src/include/Rmath.h \ /«PKGBUILDDIR»/debian/r-mathlib/usr/include install -m 0644 debian/Rprofile.site /«PKGBUILDDIR»/debian/r-base-core/etc/R install -m 0644 debian/Renviron.site /«PKGBUILDDIR»/debian/r-base-core/etc/R (cd /«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/etc; \ cat /«PKGBUILDDIR»/debian/Renviron-R_LIBS.patch | patch --verbose; \ mv Makeconf repositories ldpaths ../../../../etc/R/; \ mv Renviron Renviron.ucf; \ ln -s /etc/R/Makeconf .; \ ln -s /etc/R/Renviron .; \ ln -s /etc/R/Renviron.site .; \ ln -s /etc/R/Rprofile.site .; \ ln -s /etc/R/ldpaths .; \ ln -s /etc/R/repositories . ) Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |--- Renviron.orig 2003-04-04 06:52:22.000000000 -0500 |+++ Renviron 2003-04-04 06:49:05.000000000 -0500 -------------------------- patching file Renviron Using Plan A... Hunk #1 succeeded at 43 with fuzz 2 (offset 10 lines). done dh_bash-completion # edd 12 Jan 2016 new location #install -m 0644 debian/R.bash-completion \ # debian/r-base-core/usr/share/bash-completion/completions/R (cd /«PKGBUILDDIR»/debian/r-base-core/usr/lib/; \ ln -sv R/lib/libR.so . ) './libR.so' -> 'R/lib/libR.so' (cd debian/icon-class-patch && munpack rlogo_icon.png.mpack) rlogo_icon.png (application/octet-stream) install -m 0644 debian/icon-class-patch/rlogo_icon.png \ debian/r-base-core/usr/share/icons/hicolor/48x48/apps install -m 0644 debian/icon-class-patch/R.desktop \ debian/r-base-core/usr/share/applications rm debian/icon-class-patch/rlogo_icon.png touch install-arch-stamp *** binary-arch *** dh_testdir -a dh_testroot -a dh_installdocs -pr-base-core doc/NEWS.* README \ debian/README.Atlas \ debian/README.mathlib dh_installdocs -pr-mathlib doc/NEWS.* README \ debian/README.mathlib dh_installdocs -pr-base-core-dbg dh_installexamples -pr-mathlib src/nmath/standalone/test.c #dh_installmenu -a # (cd /«PKGBUILDDIR»/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../../lib/R/doc .) (cd /«PKGBUILDDIR»/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../R/doc .) (cd /«PKGBUILDDIR»/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../../lib/R/library .) install -p -m 0644 debian/r-base-core.lintian \ /«PKGBUILDDIR»/debian/r-base-core/usr/share/lintian/overrides/r-base-core install -p -m 0644 debian/r-recommended.lintian \ /«PKGBUILDDIR»/debian/r-recommended/usr/share/lintian/overrides/r-recommended install -p -m 0644 debian/r-mathlib.lintian \ /«PKGBUILDDIR»/debian/r-mathlib/usr/share/lintian/overrides/r-mathlib dh_installchangelogs -a -k doc/NEWS dh_strip --sourcedir=/«PKGBUILDDIR»/debian/r-base-core --dbg-package=r-base-core-dbg dh_strip debug symbol extraction: enabling -a due to Build-Debug-Symbols: yes in /CurrentlyBuilding dh_strip debug symbol extraction: all non-arch-all packages for this build platform i386: r-base-core r-mathlib r-base-core-dbg dh_strip debug symbol extraction: not adding gnu debuglinks since --dbg-package is given dh_strip debug symbol extraction: packages to act on: r-base-core r-mathlib r-base-core-dbg dh_strip debug symbol extraction: ignored packages: we have -dbg package(s), not installing anything into ddeb find: ‘/«PKGBUILDDIR»/debian/r-base-core-dbgsym’: No such file or directory dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe /usr/bin/pkg_create_dbgsym: deferring build of .ddeb to dh_gencontrol we have -dbg package(s), not installing anything into ddeb find: ‘/«PKGBUILDDIR»/debian/r-mathlib-dbgsym’: No such file or directory dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe /usr/bin/pkg_create_dbgsym: deferring build of .ddeb to dh_gencontrol Unknown option: sourcedir dh_strip --sourcedir=/«PKGBUILDDIR»/debian/r-mathlib dh_strip debug symbol extraction: enabling -a due to Build-Debug-Symbols: yes in /CurrentlyBuilding dh_strip debug symbol extraction: all non-arch-all packages for this build platform i386: r-base-core r-mathlib r-base-core-dbg dh_strip debug symbol extraction: packages to act on: r-base-core r-mathlib r-base-core-dbg dh_strip debug symbol extraction: ignored packages: pkg_create_dbgsym: /«PKGBUILDDIR»/debian/r-base-core-dbgsym already exists, ignoring pkg_create_dbgsym: /«PKGBUILDDIR»/debian/r-mathlib-dbgsym already exists, ignoring Unknown option: sourcedir dh_compress -a dh_fixperms -a dh_link -a dh_makeshlibs -a dh_installdeb -a dh_perl -a dh_shlibdeps -a -l /«PKGBUILDDIR»/debian/r-base-core/usr/lib/R/lib dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libtk8.6.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libtcl8.6.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package r-base-core: unknown substitution variable ${perl:Depends} dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform i386: r-base-core r-mathlib r-base-core-dbg dh_gencontrol debug symbol wrapper: packages to act on: r-base-core r-mathlib r-base-core-dbg dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: processing package r-base-core (pkgdir debian/r-base-core, ddeb package dir debian/r-base-core-dbgsym) dh_gencontrol debug symbol wrapper: building r-base-core-dbgsym_3.3.0-1_i386.ddeb dpkg-deb: building package 'r-base-core-dbgsym' in '../r-base-core-dbgsym_3.3.0-1_i386.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile r-base-core-dbgsym_3.3.0-1_i386.ddeb gnu-r extra dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_gencontrol debug symbol wrapper: processing package r-mathlib (pkgdir debian/r-mathlib, ddeb package dir debian/r-mathlib-dbgsym) dh_gencontrol debug symbol wrapper: building r-mathlib-dbgsym_3.3.0-1_i386.ddeb dpkg-deb: building package 'r-mathlib-dbgsym' in '../r-mathlib-dbgsym_3.3.0-1_i386.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile r-mathlib-dbgsym_3.3.0-1_i386.ddeb gnu-r extra dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 129 INFO: pkgstriptranslations version 129 INFO: pkgstriptranslations version 129 pkgstriptranslations: processing r-base-core-dbg (in debian/r-base-core-dbg); do_strip: , oemstrip: pkgstriptranslations: processing r-base-core (in debian/r-base-core); do_strip: , oemstrip: pkgstriptranslations: processing r-mathlib (in debian/r-mathlib); do_strip: , oemstrip: debian/r-base-core/usr/share/applications/R.desktop: does not have gettext domain, not stripping pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>" pkgstripfiles: processing control file: debian/r-base-core/DEBIAN/control, package r-base-core, directory debian/r-base-core .. removing usr/share/doc/r-base-core/changelog.gz pkgstripfiles: Truncating usr/share/doc/r-base-core/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-base-core ... WARNING: optipng failed on usr/lib/R/library/graphics/help/figures/pch.png, ignoring WARNING: optipng failed on usr/lib/R/library/graphics/help/figures/mai.png, ignoring WARNING: optipng failed on usr/lib/R/library/graphics/help/figures/oma.png, ignoring ..ooooopkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>" pkgstripfiles: processing control file: debian/r-base-core-dbg/DEBIAN/control, package r-base-core-dbg, directory debian/r-base-core-dbg .. removing usr/share/doc/r-base-core-dbg/changelog.gz INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... oINFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... oINFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... o pkgstripfiles: PNG optimization (8/0) for package r-base-core took 7 s dpkg-deb: building package 'r-base-core' in '../r-base-core_3.3.0-1_i386.deb'. INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>" pkgstripfiles: processing control file: debian/r-mathlib/DEBIAN/control, package r-mathlib, directory debian/r-mathlib .. removing usr/share/doc/r-mathlib/changelog.gz pkgstripfiles: Truncating usr/share/doc/r-mathlib/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-mathlib ... pkgstripfiles: No PNG files. dpkg-deb: building package 'r-mathlib' in '../r-mathlib_3.3.0-1_i386.deb'. Searching for duplicated docs in dependency r-base-core... symlinking changelog.Debian.gz in r-base-core-dbg to file in r-base-core pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-base-core-dbg ... pkgstripfiles: No PNG files. dpkg-deb: building package 'r-base-core-dbg' in '../r-base-core-dbg_3.3.0-1_i386.deb'. dpkg-genchanges -B -mLaunchpad Build Daemon <buildd@lgw01-48.buildd> >../r-base_3.3.0-1_i386.changes dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build r-base-3.3.0 dpkg-buildpackage: binary-only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20160503-2347 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build Chroot │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ r-base_3.3.0-1_i386.changes: ──────────────────────────── Format: 1.8 Date: Tue, 03 May 2016 06:05:36 -0500 Source: r-base Binary: r-base r-base-core r-base-dev r-mathlib r-base-html r-doc-pdf r-doc-html r-doc-info r-recommended r-base-core-dbg Architecture: i386 Version: 3.3.0-1 Distribution: yakkety-proposed Urgency: medium Maintainer: Launchpad Build Daemon <buildd@lgw01-48.buildd> Changed-By: Dirk Eddelbuettel <edd@debian.org> Description: r-base - GNU R statistical computation and graphics system r-base-core - GNU R core of statistical computation and graphics system r-base-core-dbg - GNU R debug symbols for statistical comp. language and environmen r-base-dev - GNU R installation of auxiliary GNU R packages r-base-html - GNU R html docs for statistical computing system functions r-doc-html - GNU R html manuals for statistical computing system r-doc-info - GNU R info manuals statistical computing system r-doc-pdf - GNU R pdf manuals for statistical computing system r-mathlib - GNU R standalone mathematics library r-recommended - GNU R collection of recommended packages [metapackage] Changes: r-base (3.3.0-1) unstable; urgency=medium . * New upstream version released this morning Checksums-Sha1: b9f59d91fb476bf68c327eba2ba1a92bae0b0c74 2670494 r-base-core-dbg_3.3.0-1_i386.deb c74d03a890ea66e79d2a51f37fc87a29b94cb9b4 1506 r-base-core-dbgsym_3.3.0-1_i386.ddeb 72e8f553bcf8af42bd95701235aef11aa0dcb3e0 20832082 r-base-core_3.3.0-1_i386.deb 7416471dc2a3ef08c537c7ec37bc7a9fc7a925f1 1474 r-mathlib-dbgsym_3.3.0-1_i386.ddeb d6103707170d977c14731da6b72ac871bd8f4826 1436606 r-mathlib_3.3.0-1_i386.deb Checksums-Sha256: ac292d4b2b796cac87cda38271fec1a2d8fca0d937f89068ce6d7b43a85d7bda 2670494 r-base-core-dbg_3.3.0-1_i386.deb f9122362e6484249c99975a988079be971e72bbbba32841bdcbaf03c5b17ede6 1506 r-base-core-dbgsym_3.3.0-1_i386.ddeb 86a53923c11dcff4b27384c377bf8314280473c22a2063bc49c571c0ba5e5aab 20832082 r-base-core_3.3.0-1_i386.deb 671f45d5030f7125a8164ea0e7b98f7538a05c1708c037eef93a3cc50d2786fd 1474 r-mathlib-dbgsym_3.3.0-1_i386.ddeb e965351dc3c3455e7b3b6439d94b74d77f15e7262f10d82ed990294dd0cc5f2c 1436606 r-mathlib_3.3.0-1_i386.deb Files: 6df0a6a806d2712541450b0edf62ab28 2670494 debug extra r-base-core-dbg_3.3.0-1_i386.deb c66fc864b4f84c250aab29157644e49a 1506 gnu-r extra r-base-core-dbgsym_3.3.0-1_i386.ddeb 7c953c5608553be0c239e8c71b6ae1b2 20832082 gnu-r optional r-base-core_3.3.0-1_i386.deb 824c2bdc6e29943ca4b8bbc5e19dc805 1474 gnu-r extra r-mathlib-dbgsym_3.3.0-1_i386.ddeb 06a7f9dc207adfa1db3f9115da2134d5 1436606 gnu-r optional r-mathlib_3.3.0-1_i386.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ r-base-core-dbg_3.3.0-1_i386.deb ──────────────────────────────── new debian package, version 2.0. size 2670494 bytes: control archive=1845 bytes. 1842 bytes, 39 lines control 1700 bytes, 21 lines md5sums Package: r-base-core-dbg Source: r-base Version: 3.3.0-1 Architecture: i386 Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com> Original-Maintainer: Dirk Eddelbuettel <edd@debian.org> Installed-Size: 8649 Depends: r-base-core (= 3.3.0-1), r-base-dev (= 3.3.0-1) Section: debug Priority: extra Homepage: http://www.r-project.org/ Description: GNU R debug symbols for statistical comp. language and environment R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files. . The design of R has been heavily influenced by two existing languages: Becker, Chambers & Wilks' S and Sussman's Scheme. Whereas the resulting language is very similar in appearance to S, the underlying implementation and semantics are derived from Scheme. . The core of R is an interpreted computer language which allows branching and looping as well as modular programming using functions. Most of the user-visible functions in R are written in R. It is possible for the user to interface to procedures written in the C, C++, or FORTRAN languages for efficiency, and many of R's core functions do so. The R distribution contains functionality for a large number of statistical procedures and underlying applied math computations. There is also a large set of functions which provide a flexible graphical environment for creating various kinds of data presentations. . Additionally, several thousand extension "packages" are available from CRAN, the Comprehensive R Archive Network, many also as Debian packages, named 'r-cran-<name>'. . This package contains debugging symbol tables for the binaries and dynamic libraries in the r-base-core package. drwxr-xr-x root/root 0 2016-05-03 23:46 ./ drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/ drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/lib/ drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/lib/debug/ drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/lib/debug/usr/ drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/lib/debug/usr/bin/ -rw-r--r-- root/root 14192 2016-05-03 23:46 ./usr/lib/debug/usr/bin/Rscript drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/lib/debug/usr/lib/ drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/lib/debug/usr/lib/R/ drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/lib/debug/usr/lib/R/bin/ -rw-r--r-- root/root 14192 2016-05-03 23:46 ./usr/lib/debug/usr/lib/R/bin/Rscript drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/lib/debug/usr/lib/R/bin/exec/ -rw-r--r-- root/root 6380 2016-05-03 23:46 ./usr/lib/debug/usr/lib/R/bin/exec/R drwxr-xr-x root/root 0 2016-05-03 23:46 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20761 2016-05-03 23:26 ./usr/share/doc/r-base-core-dbg/copyright drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/share/lintian/ drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/share/lintian/overrides/ r-base-core_3.3.0-1_i386.deb ──────────────────────────── new debian package, version 2.0. size 20832082 bytes: control archive=27806 bytes. 93 bytes, 5 lines conffiles 2778 bytes, 45 lines control 72275 bytes, 917 lines md5sums 2236 bytes, 65 lines * postinst #!/bin/sh 667 bytes, 34 lines * preinst #!/bin/sh 689 bytes, 26 lines * prerm #!/bin/sh Package: r-base-core Source: r-base Version: 3.3.0-1 Architecture: i386 Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com> Original-Maintainer: Dirk Eddelbuettel <edd@debian.org> Installed-Size: 33725 Depends: zip, unzip, libpaper-utils, xdg-utils, libblas3 | libblas.so.3, libbz2-1.0, libc6 (>= 2.23), libcairo2 (>= 1.6.0), libcurl3 (>= 7.28.0), libglib2.0-0 (>= 2.12.0), libgomp1 (>= 4.9), libicu57 (>= 57.1-1~), libjpeg8 (>= 8c), liblapack3 | liblapack.so.3, liblzma5 (>= 5.1.1alpha+20120614), libpango-1.0-0 (>= 1.14.0), libpangocairo-1.0-0 (>= 1.14.0), libpcre3, libpng16-16 (>= 1.6.2-1), libreadline6 (>= 6.0), libtcl8.6 (>= 8.6.0), libtiff5 (>= 4.0.3), libtk8.6 (>= 8.6.0), libx11-6, libxt6, zlib1g (>= 1:1.1.4), ucf (>= 3.0), ca-certificates Recommends: r-recommended, r-base-dev, r-doc-html Suggests: ess, r-doc-info | r-doc-pdf, r-mathlib, r-base-html Conflicts: r-base-latex, r-cran-rcompgen, r-gnome Replaces: r-base (<= 1.4.1-1), r-base-latex (<= 2.9.2-4), r-cran-rcompgen (<= 0.1-17-1), r-gnome (<= 2.3.1), r-recommended (<< 1.9.0) Provides: r-api-3, r-base-latex, r-cran-rcompgen, r-gnome Section: gnu-r Priority: optional Homepage: http://www.r-project.org/ Description: GNU R core of statistical computation and graphics system R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files. . The design of R has been heavily influenced by two existing languages: Becker, Chambers & Wilks' S and Sussman's Scheme. Whereas the resulting language is very similar in appearance to S, the underlying implementation and semantics are derived from Scheme. . The core of R is an interpreted computer language which allows branching and looping as well as modular programming using functions. Most of the user-visible functions in R are written in R. It is possible for the user to interface to procedures written in the C, C++, or FORTRAN languages for efficiency, and many of R's core functions do so. The R distribution contains functionality for a large number of statistical procedures and underlying applied math computations. There is also a large set of functions which provide a flexible graphical environment for creating various kinds of data presentations. . Additionally, several thousand extension "packages" are available from CRAN, the Comprehensive R Archive Network, many also as Debian packages, named 'r-cran-<name>'. . This package provides the core GNU R system from which only the optional documentation packages r-base-html, r-doc-html, r-doc-pdf and r-doc-info have been split off to somewhat reduce the size of this package. drwxr-xr-x root/root 0 2016-05-03 23:46 ./ drwxr-xr-x root/root 0 2016-05-03 23:46 ./etc/ drwxr-xr-x root/root 0 2016-05-03 23:46 ./etc/R/ -rw-r--r-- root/root 6312 2016-05-03 23:46 ./etc/R/Makeconf -rw-r--r-- root/root 608 2016-05-03 23:46 ./etc/R/Renviron.site -rw-r--r-- root/root 792 2016-05-03 23:46 ./etc/R/Rprofile.site -rw-r--r-- root/root 784 2016-05-03 23:46 ./etc/R/ldpaths -rw-r--r-- root/root 1161 2016-05-03 23:46 ./etc/R/repositories drwxr-xr-x root/root 0 2016-05-03 23:46 ./etc/ld.so.conf.d/ drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/ drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/bin/ -rwxr-xr-x root/root 8712 2016-05-03 23:46 ./usr/bin/R -rwxr-xr-x root/root 9708 2016-05-03 23:46 ./usr/bin/Rscript drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/lib/ drwxr-xr-x 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It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files. . The design of R has been heavily influenced by two existing languages: Becker, Chambers & Wilks' S and Sussman's Scheme. Whereas the resulting language is very similar in appearance to S, the underlying implementation and semantics are derived from Scheme. . The core of R is an interpreted computer language which allows branching and looping as well as modular programming using functions. Most of the user-visible functions in R are written in R. It is possible for the user to interface to procedures written in the C, C++, or FORTRAN languages for efficiency, and many of R's core functions do so. The R distribution contains functionality for a large number of statistical procedures and underlying applied math computations. There is also a large set of functions which provide a flexible graphical environment for creating various kinds of data presentations. . Additionally, several thousand extension "packages" are available from CRAN, the Comprehensive R Archive Network, many also as Debian packages, named 'r-cran-<name>'. . This package provides the libRmath shared and static libraries which can be called from standalone C or C++ code. drwxr-xr-x root/root 0 2016-05-03 23:46 ./ drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/ drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/include/ -rw-r--r-- root/root 17995 2016-05-03 23:46 ./usr/include/Rmath.h drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/lib/ -rw-r--r-- root/root 372078 2016-05-03 23:46 ./usr/lib/libRmath.a lrwxrwxrwx root/root 0 2016-05-03 23:46 ./usr/lib/libRmath.so -> libRmath.so.1 lrwxrwxrwx root/root 0 2016-05-03 23:46 ./usr/lib/libRmath.so.1 -> libRmath.so.1.0.0 -rw-r--r-- root/root 214560 2016-05-03 23:46 ./usr/lib/libRmath.so.1.0.0 drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/lib/pkgconfig/ -rw-r--r-- root/root 173 2016-05-03 23:46 ./usr/lib/pkgconfig/libRmath.pc drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/share/ drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-05-03 23:47 ./usr/share/doc/r-mathlib/ -rw-r--r-- root/root 35933 2014-03-12 23:03 ./usr/share/doc/r-mathlib/NEWS.0.gz -rw-r--r-- root/root 108753 2014-03-12 23:03 ./usr/share/doc/r-mathlib/NEWS.1.gz -rw-r--r-- root/root 96628 2016-03-16 23:04 ./usr/share/doc/r-mathlib/NEWS.2.Rd.gz -rw-r--r-- root/root 229656 2014-03-12 23:03 ./usr/share/doc/r-mathlib/NEWS.2.gz -rw-r--r-- root/root 72506 2016-04-25 22:02 ./usr/share/doc/r-mathlib/NEWS.Rd.gz lrwxrwxrwx root/root 0 2016-05-03 23:46 ./usr/share/doc/r-mathlib/NEWS.gz -> changelog.gz -rw-r--r-- root/root 411521 2016-05-03 23:33 ./usr/share/doc/r-mathlib/NEWS.pdf.gz -rw-r--r-- root/root 306501 2016-05-03 23:33 ./usr/share/doc/r-mathlib/NEWS.rds.gz -rw-r--r-- root/root 2107 2014-07-07 22:15 ./usr/share/doc/r-mathlib/README.gz -rw-r--r-- root/root 3026 2016-05-03 23:26 ./usr/share/doc/r-mathlib/README.mathlib -rw-r--r-- root/root 794 2016-05-03 23:47 ./usr/share/doc/r-mathlib/changelog.Debian.gz -rw-r--r-- root/root 20761 2016-05-03 23:26 ./usr/share/doc/r-mathlib/copyright drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/share/doc/r-mathlib/examples/ -rw-r--r-- root/root 1371 2015-08-25 22:18 ./usr/share/doc/r-mathlib/examples/test.c drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/share/lintian/ drwxr-xr-x root/root 0 2016-05-03 23:46 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 231 2016-05-03 23:26 ./usr/share/lintian/overrides/r-mathlib ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Not removing build depends: as requested Keeping session: ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: i386 Build-Space: 365532 Build-Time: 1271 Distribution: yakkety-proposed Host Architecture: i386 Install-Time: 195 Job: r-base_3.3.0-1.dsc Machine Architecture: amd64 Package: r-base Package-Time: 1469 Source-Version: 3.3.0-1 Space: 365532 Status: successful Version: 3.3.0-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20160503-2347 Build needed 00:24:29, 365532k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-9686715'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-9686715/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-9686715'] Unmounting chroot for build PACKAGEBUILD-9686715... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-9686715'] Removing build PACKAGEBUILD-9686715