RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux lgw01-38 3.19.0-37-generic #42~14.04.1-Ubuntu SMP Mon Nov 23 15:13:51 UTC 2015 x86_64 Buildd toolchain package versions: launchpad-buildd_135 python-lpbuildd_135 sbuild_0.65.2-1ubuntu2~ubuntu14.04.1~ppa6 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.04.1 bzr_2.6.0+bzr6593-1ubuntu1.1 dpkg-dev_1.17.5ubuntu5.5 python-debian_0.1.27ubuntu1~ubuntu14.04.1~ppa1. Syncing the system clock with the buildd NTP service... 4 Dec 11:48:50 ntpdate[1646]: adjust time server 10.211.37.1 offset 0.170325 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-8391953', '/home/buildd/filecache-default/8204889cda79fca0b488b979ea0c52fb9d6dbd17'] Unpacking chroot for build PACKAGEBUILD-8391953 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-8391953'] Mounting chroot for build PACKAGEBUILD-8391953 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-8391953', 'deb http://ftpmaster.internal/ubuntu xenial main universe', 'deb http://ftpmaster.internal/ubuntu xenial-security main universe', 'deb http://ftpmaster.internal/ubuntu xenial-updates main universe', 'deb http://ftpmaster.internal/ubuntu xenial-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-8391953 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-8391953', 'amd64'] Updating debian chroot for build PACKAGEBUILD-8391953 Get:1 http://ftpmaster.internal xenial InRelease [227 kB] Get:2 http://ftpmaster.internal xenial-security InRelease [73.5 kB] Get:3 http://ftpmaster.internal xenial-updates InRelease [73.5 kB] Get:4 http://ftpmaster.internal xenial-proposed InRelease [227 kB] Get:5 http://ftpmaster.internal xenial/main amd64 Packages [1452 kB] Get:6 http://ftpmaster.internal xenial/universe amd64 Packages [7040 kB] Get:7 http://ftpmaster.internal xenial/main Translation-en [845 kB] Get:8 http://ftpmaster.internal xenial/universe Translation-en [4726 kB] Get:9 http://ftpmaster.internal xenial-security/main amd64 Packages [28 B] Get:10 http://ftpmaster.internal xenial-security/universe amd64 Packages [28 B] Get:11 http://ftpmaster.internal xenial-security/main Translation-en [28 B] Get:12 http://ftpmaster.internal xenial-security/universe Translation-en [28 B] Get:13 http://ftpmaster.internal xenial-updates/main amd64 Packages [28 B] Get:14 http://ftpmaster.internal xenial-updates/universe amd64 Packages [28 B] Get:15 http://ftpmaster.internal xenial-updates/main Translation-en [28 B] Get:16 http://ftpmaster.internal xenial-updates/universe Translation-en [28 B] Get:17 http://ftpmaster.internal xenial-proposed/main amd64 Packages [93.2 kB] Get:18 http://ftpmaster.internal xenial-proposed/universe amd64 Packages [307 kB] Get:19 http://ftpmaster.internal xenial-proposed/main Translation-en [46.2 kB] Get:20 http://ftpmaster.internal xenial-proposed/universe Translation-en [154 kB] Fetched 15.3 MB in 6s (2261 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libapt-pkg4.16 libisl13 udev Use 'apt-get autoremove' to remove them. The following NEW packages will be installed: libapt-pkg5.0 libisl15 The following packages will be upgraded: advancecomp apt apt-transport-https base-files binutils bsdutils cpp cpp-5 debconf diffutils dpkg dpkg-dev e2fslibs e2fsprogs findutils g++ g++-5 gcc gcc-5 gcc-5-base gnupg gpgv grep hostname init initscripts libapparmor1 libasan2 libatomic1 libaudit-common libaudit1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap2 libcap2-bin libcc1-0 libcilkrts5 libcomerr2 libcurl3-gnutls libdbus-1-3 libdebconfclient0 libdpkg-perl libfdisk1 libgcc-5-dev libgcc1 libgcrypt20 libgmp10 libgnutls-deb0-28 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn11 libitm1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblsan0 libmount1 libmpx0 libpng12-0 libquadmath0 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-5-dev libstdc++6 libsystemd0 libtasn1-6 libtsan0 libubsan0 libudev1 libuuid1 linux-libc-dev lsb-base mount multiarch-support openssl pkg-create-dbgsym pkgbinarymangler systemd systemd-sysv sysv-rc sysvinit-utils tar udev util-linux 95 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 116 MB of archives. After this operation, 322 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ xenial/main base-files amd64 9.4ubuntu3 [62.0 kB] Get:2 http://ftpmaster.internal/ubuntu/ xenial/main bsdutils amd64 1:2.27.1-1ubuntu3 [51.5 kB] Get:3 http://ftpmaster.internal/ubuntu/ xenial/main diffutils amd64 1:3.3-2 [156 kB] Get:4 http://ftpmaster.internal/ubuntu/ xenial/main dpkg amd64 1.18.3ubuntu1 [2081 kB] Get:5 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libc6-dev amd64 2.21-0ubuntu5 [1951 kB] Get:6 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libc-dev-bin amd64 2.21-0ubuntu5 [68.7 kB] Get:7 http://ftpmaster.internal/ubuntu/ xenial-proposed/main linux-libc-dev amd64 4.3.0-1.10 [814 kB] Get:8 http://ftpmaster.internal/ubuntu/ xenial/main libcap2 amd64 1:2.24-12 [12.9 kB] Get:9 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libc-bin amd64 2.21-0ubuntu5 [1172 kB] Get:10 http://ftpmaster.internal/ubuntu/ xenial/main libgomp1 amd64 5.2.1-27ubuntu1 [55.0 kB] Get:11 http://ftpmaster.internal/ubuntu/ xenial/main libitm1 amd64 5.2.1-27ubuntu1 [27.4 kB] Get:12 http://ftpmaster.internal/ubuntu/ xenial/main libatomic1 amd64 5.2.1-27ubuntu1 [8906 B] Get:13 http://ftpmaster.internal/ubuntu/ xenial/main libasan2 amd64 5.2.1-27ubuntu1 [269 kB] Get:14 http://ftpmaster.internal/ubuntu/ xenial/main liblsan0 amd64 5.2.1-27ubuntu1 [109 kB] Get:15 http://ftpmaster.internal/ubuntu/ xenial/main libtsan0 amd64 5.2.1-27ubuntu1 [249 kB] Get:16 http://ftpmaster.internal/ubuntu/ xenial/main gcc-5-base amd64 5.2.1-27ubuntu1 [17.0 kB] Get:17 http://ftpmaster.internal/ubuntu/ xenial/main libgcc1 amd64 1:5.2.1-27ubuntu1 [38.8 kB] Get:18 http://ftpmaster.internal/ubuntu/ xenial/main libubsan0 amd64 5.2.1-27ubuntu1 [100 kB] Get:19 http://ftpmaster.internal/ubuntu/ xenial/main libcilkrts5 amd64 5.2.1-27ubuntu1 [40.1 kB] Get:20 http://ftpmaster.internal/ubuntu/ xenial/main libmpx0 amd64 5.2.1-27ubuntu1 [9738 B] Get:21 http://ftpmaster.internal/ubuntu/ xenial/main libquadmath0 amd64 5.2.1-27ubuntu1 [131 kB] Get:22 http://ftpmaster.internal/ubuntu/ xenial/main libisl15 amd64 0.15-3 [514 kB] Get:23 http://ftpmaster.internal/ubuntu/ xenial/main cpp-5 amd64 5.2.1-27ubuntu1 [26.4 MB] Get:24 http://ftpmaster.internal/ubuntu/ xenial/main libcc1-0 amd64 5.2.1-27ubuntu1 [30.9 kB] Get:25 http://ftpmaster.internal/ubuntu/ xenial/main binutils amd64 2.25.90.20151125-2ubuntu1 [2310 kB] Get:26 http://ftpmaster.internal/ubuntu/ xenial/main g++-5 amd64 5.2.1-27ubuntu1 [28.1 MB] Get:27 http://ftpmaster.internal/ubuntu/ xenial/main gcc-5 amd64 5.2.1-27ubuntu1 [26.6 MB] Get:28 http://ftpmaster.internal/ubuntu/ xenial/main libgcc-5-dev amd64 5.2.1-27ubuntu1 [2230 kB] Get:29 http://ftpmaster.internal/ubuntu/ xenial/main libstdc++-5-dev amd64 5.2.1-27ubuntu1 [1423 kB] Get:30 http://ftpmaster.internal/ubuntu/ xenial/main libstdc++6 amd64 5.2.1-27ubuntu1 [393 kB] Get:31 http://ftpmaster.internal/ubuntu/ xenial/main libgmp10 amd64 2:6.1.0+dfsg-2 [240 kB] Get:32 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libc6 amd64 2.21-0ubuntu5 [4789 kB] Get:33 http://ftpmaster.internal/ubuntu/ xenial/main e2fslibs amd64 1.42.13-1ubuntu1 [188 kB] Get:34 http://ftpmaster.internal/ubuntu/ xenial/main e2fsprogs amd64 1.42.13-1ubuntu1 [771 kB] Get:35 http://ftpmaster.internal/ubuntu/ xenial/main findutils amd64 4.4.2-10 [281 kB] Get:36 http://ftpmaster.internal/ubuntu/ xenial-proposed/main grep amd64 2.22-1 [149 kB] Get:37 http://ftpmaster.internal/ubuntu/ xenial/main hostname amd64 3.16ubuntu2 [11.5 kB] Get:38 http://ftpmaster.internal/ubuntu/ xenial/main init amd64 1.24ubuntu2 [3966 B] Get:39 http://ftpmaster.internal/ubuntu/ xenial/main libsmartcols1 amd64 2.27.1-1ubuntu3 [62.3 kB] Get:40 http://ftpmaster.internal/ubuntu/ xenial/main libuuid1 amd64 2.27.1-1ubuntu3 [14.7 kB] Get:41 http://ftpmaster.internal/ubuntu/ xenial/main libblkid1 amd64 2.27.1-1ubuntu3 [107 kB] Get:42 http://ftpmaster.internal/ubuntu/ xenial/main libfdisk1 amd64 2.27.1-1ubuntu3 [139 kB] Get:43 http://ftpmaster.internal/ubuntu/ xenial/main debconf all 1.5.58ubuntu1 [136 kB] Get:44 http://ftpmaster.internal/ubuntu/ xenial/main sysvinit-utils amd64 2.88dsf-59.2ubuntu3 [25.7 kB] Get:45 http://ftpmaster.internal/ubuntu/ xenial/main sysv-rc all 2.88dsf-59.2ubuntu3 [36.1 kB] Get:46 http://ftpmaster.internal/ubuntu/ xenial/main initscripts amd64 2.88dsf-59.2ubuntu3 [24.8 kB] Get:47 http://ftpmaster.internal/ubuntu/ xenial/main util-linux amd64 2.27.1-1ubuntu3 [847 kB] Get:48 http://ftpmaster.internal/ubuntu/ xenial/main libudev1 amd64 228-2ubuntu1 [56.4 kB] Get:49 http://ftpmaster.internal/ubuntu/ xenial/main udev amd64 228-2ubuntu1 [980 kB] Get:50 http://ftpmaster.internal/ubuntu/ xenial/main libsystemd0 amd64 228-2ubuntu1 [203 kB] Get:51 http://ftpmaster.internal/ubuntu/ xenial/main systemd amd64 228-2ubuntu1 [3491 kB] Get:52 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libselinux1 amd64 2.4-3 [56.0 kB] Get:53 http://ftpmaster.internal/ubuntu/ xenial/main libapparmor1 amd64 2.10-0ubuntu8 [29.1 kB] Get:54 http://ftpmaster.internal/ubuntu/ xenial/main libaudit-common all 1:2.4.4-4ubuntu1 [3892 B] Get:55 http://ftpmaster.internal/ubuntu/ xenial/main libaudit1 amd64 1:2.4.4-4ubuntu1 [36.3 kB] Get:56 http://ftpmaster.internal/ubuntu/ xenial/main libmount1 amd64 2.27.1-1ubuntu3 [114 kB] Get:57 http://ftpmaster.internal/ubuntu/ xenial/main libcap2-bin amd64 1:2.24-12 [20.2 kB] Get:58 http://ftpmaster.internal/ubuntu/ xenial/main lsb-base all 9.20150917ubuntu1 [13.4 kB] Get:59 http://ftpmaster.internal/ubuntu/ xenial/main mount amd64 2.27.1-1ubuntu3 [121 kB] Get:60 http://ftpmaster.internal/ubuntu/ xenial/main tar amd64 1.28-2.1 [209 kB] Get:61 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libapt-pkg5.0 amd64 1.1.3 [676 kB] Get:62 http://ftpmaster.internal/ubuntu/ xenial-proposed/main apt amd64 1.1.3 [961 kB] Get:63 http://ftpmaster.internal/ubuntu/ xenial/main gpgv amd64 1.4.19-6ubuntu1 [165 kB] Get:64 http://ftpmaster.internal/ubuntu/ xenial/main gnupg amd64 1.4.19-6ubuntu1 [626 kB] Get:65 http://ftpmaster.internal/ubuntu/ xenial/main systemd-sysv amd64 228-2ubuntu1 [14.9 kB] Get:66 http://ftpmaster.internal/ubuntu/ xenial/main libcomerr2 amd64 1.42.13-1ubuntu1 [65.7 kB] Get:67 http://ftpmaster.internal/ubuntu/ xenial/main libdebconfclient0 amd64 0.198ubuntu1 [6368 B] Get:68 http://ftpmaster.internal/ubuntu/ xenial/main libgpg-error0 amd64 1.20-1 [32.8 kB] Get:69 http://ftpmaster.internal/ubuntu/ xenial/main libgcrypt20 amd64 1.6.4-3 [336 kB] Get:70 http://ftpmaster.internal/ubuntu/ xenial/main libsepol1 amd64 2.4-2 [186 kB] Get:71 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsemanage-common all 2.4-3 [6744 B] Get:72 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsemanage1 amd64 2.4-3 [79.3 kB] Get:73 http://ftpmaster.internal/ubuntu/ xenial/main libss2 amd64 1.42.13-1ubuntu1 [70.0 kB] Get:74 http://ftpmaster.internal/ubuntu/ xenial-proposed/main multiarch-support amd64 2.21-0ubuntu5 [7174 B] Get:75 http://ftpmaster.internal/ubuntu/ xenial/main libtasn1-6 amd64 4.7-2 [43.1 kB] Get:76 http://ftpmaster.internal/ubuntu/ xenial/main libgnutls-deb0-28 amd64 3.3.18-1ubuntu1 [520 kB] Get:77 http://ftpmaster.internal/ubuntu/ xenial/main libpng12-0 amd64 1.2.54-1 [116 kB] Get:78 http://ftpmaster.internal/ubuntu/ xenial/main libsqlite3-0 amd64 3.9.2-1 [395 kB] Get:79 http://ftpmaster.internal/ubuntu/ xenial/main libssl1.0.0 amd64 1.0.2d-0ubuntu2 [1079 kB] Get:80 http://ftpmaster.internal/ubuntu/ xenial/main libgssapi-krb5-2 amd64 1.13.2+dfsg-4 [120 kB] Get:81 http://ftpmaster.internal/ubuntu/ xenial/main libkrb5-3 amd64 1.13.2+dfsg-4 [274 kB] Get:82 http://ftpmaster.internal/ubuntu/ xenial/main libkrb5support0 amd64 1.13.2+dfsg-4 [30.4 kB] Get:83 http://ftpmaster.internal/ubuntu/ xenial/main libk5crypto3 amd64 1.13.2+dfsg-4 [81.3 kB] Get:84 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libkeyutils1 amd64 1.5.9-8 [9824 B] Get:85 http://ftpmaster.internal/ubuntu/ xenial/main libidn11 amd64 1.32-3ubuntu1 [45.5 kB] Get:86 http://ftpmaster.internal/ubuntu/ xenial/main libcurl3-gnutls amd64 7.45.0-1ubuntu1 [183 kB] Get:87 http://ftpmaster.internal/ubuntu/ xenial-proposed/main apt-transport-https amd64 1.1.3 [25.3 kB] Get:88 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libdbus-1-3 amd64 1.10.6-1ubuntu1 [161 kB] Get:89 http://ftpmaster.internal/ubuntu/ xenial/main openssl amd64 1.0.2d-0ubuntu2 [511 kB] Get:90 http://ftpmaster.internal/ubuntu/ xenial/main advancecomp amd64 1.20-1 [160 kB] Get:91 http://ftpmaster.internal/ubuntu/ xenial/main cpp amd64 4:5.2.1-16ubuntu2 [27.6 kB] Get:92 http://ftpmaster.internal/ubuntu/ xenial/main dpkg-dev all 1.18.3ubuntu1 [583 kB] Get:93 http://ftpmaster.internal/ubuntu/ xenial/main libdpkg-perl all 1.18.3ubuntu1 [195 kB] Get:94 http://ftpmaster.internal/ubuntu/ xenial/main gcc amd64 4:5.2.1-16ubuntu2 [5208 B] Get:95 http://ftpmaster.internal/ubuntu/ xenial/main g++ amd64 4:5.2.1-16ubuntu2 [1506 B] Get:96 http://ftpmaster.internal/ubuntu/ xenial/main pkg-create-dbgsym all 0.70 [9046 B] Get:97 http://ftpmaster.internal/ubuntu/ xenial/main pkgbinarymangler all 123 [28.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 116 MB in 12s (9053 kB/s) (Reading database ... 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Updating /etc/profile to current default. Updating /etc/nsswitch.conf to current default. Updating /root/.profile to current default. (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 ... 11692 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.27.1-1ubuntu3_amd64.deb ... Unpacking bsdutils (1:2.27.1-1ubuntu3) over (1:2.26.2-6ubuntu3) ... Setting up bsdutils (1:2.27.1-1ubuntu3) ... (Reading database ... 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Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/system.conf ... addgroup: The group `systemd-journal' already exists as a system group. Exiting. (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 ... 11701 files and directories currently installed.) Preparing to unpack .../libselinux1_2.4-3_amd64.deb ... Unpacking libselinux1:amd64 (2.4-3) over (2.3-2build1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... 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(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 ... 11701 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a2.4.4-4ubuntu1_all.deb ... Unpacking libaudit-common (1:2.4.4-4ubuntu1) over (1:2.4.2-1ubuntu1) ... Setting up libaudit-common (1:2.4.4-4ubuntu1) ... (Reading database ... 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Setting up libasan2:amd64 (5.2.1-27ubuntu1) ... Setting up liblsan0:amd64 (5.2.1-27ubuntu1) ... Setting up libtsan0:amd64 (5.2.1-27ubuntu1) ... Setting up libubsan0:amd64 (5.2.1-27ubuntu1) ... Setting up libcilkrts5:amd64 (5.2.1-27ubuntu1) ... Setting up libmpx0:amd64 (5.2.1-27ubuntu1) ... Setting up libquadmath0:amd64 (5.2.1-27ubuntu1) ... Setting up libgmp10:amd64 (2:6.1.0+dfsg-2) ... Setting up libisl15:amd64 (0.15-3) ... Setting up cpp-5 (5.2.1-27ubuntu1) ... Setting up libcc1-0:amd64 (5.2.1-27ubuntu1) ... Setting up binutils (2.25.90.20151125-2ubuntu1) ... Setting up libgcc-5-dev:amd64 (5.2.1-27ubuntu1) ... Setting up gcc-5 (5.2.1-27ubuntu1) ... Setting up libstdc++-5-dev:amd64 (5.2.1-27ubuntu1) ... Setting up g++-5 (5.2.1-27ubuntu1) ... Setting up udev (228-2ubuntu1) ... Installing new version of config file /etc/init.d/udev ... addgroup: The group `input' already exists as a system group. Exiting. virtio network devices detected, disabling predictable interface names in /etc/systemd/network/50-virtio-kernel-names.link Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Setting up apt (1.1.3) ... Installing new version of config file /etc/apt/apt.conf.d/01-vendor-ubuntu ... Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... Installing new version of config file /etc/cron.daily/apt ... Installing new version of config file /etc/kernel/postinst.d/apt-auto-removal ... usermod: no changes Setting up libtasn1-6:amd64 (4.7-2) ... Setting up libgnutls-deb0-28:amd64 (3.3.18-1ubuntu1) ... Setting up libpng12-0:amd64 (1.2.54-1) ... Setting up libsqlite3-0:amd64 (3.9.2-1) ... Setting up libssl1.0.0:amd64 (1.0.2d-0ubuntu2) ... Setting up libkrb5support0:amd64 (1.13.2+dfsg-4) ... Setting up libk5crypto3:amd64 (1.13.2+dfsg-4) ... Setting up libkeyutils1:amd64 (1.5.9-8) ... Setting up libkrb5-3:amd64 (1.13.2+dfsg-4) ... Setting up libgssapi-krb5-2:amd64 (1.13.2+dfsg-4) ... Setting up libidn11:amd64 (1.32-3ubuntu1) ... Setting up libcurl3-gnutls:amd64 (7.45.0-1ubuntu1) ... Setting up apt-transport-https (1.1.3) ... Setting up libdbus-1-3:amd64 (1.10.6-1ubuntu1) ... Setting up openssl (1.0.2d-0ubuntu2) ... Setting up advancecomp (1.20-1) ... Setting up cpp (4:5.2.1-16ubuntu2) ... Setting up libdpkg-perl (1.18.3ubuntu1) ... Setting up dpkg-dev (1.18.3ubuntu1) ... Setting up gcc (4:5.2.1-16ubuntu2) ... Setting up g++ (4:5.2.1-16ubuntu2) ... Setting up pkg-create-dbgsym (0.70) ... Setting up pkgbinarymangler (123) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Processing triggers for systemd (228-2ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-8391953', 'amd64', 'xenial-proposed', '-c', 'chroot:autobuild', '--arch=amd64', '--dist=xenial-proposed', '--purge=never', '--nolog', '-A', 'r-base_3.2.2.20151203-1.dsc'] Initiating build PACKAGEBUILD-8391953 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 3.19.0-37-generic #42~14.04.1-Ubuntu SMP Mon Nov 23 15:13:51 UTC 2015 x86_64 sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on lgw01-38.buildd ╔══════════════════════════════════════════════════════════════════════════════╗ ║ r-base 3.2.2.20151203-1 (amd64) 04 Dec 2015 11:50 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: r-base Version: 3.2.2.20151203-1 Source Version: 3.2.2.20151203-1 Distribution: xenial-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/r-base-F7xAyH/r-base-3.2.2.20151203' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/r-base-F7xAyH' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-8391953/chroot-autobuild' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Local sources ───────────── r-base_3.2.2.20151203-1.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-c86U88/apt_archive/sbuild-build-depends-core-dummy.deb'. Get:1 file:/«BUILDDIR»/resolver-c86U88/apt_archive ./ InRelease Ign:1 file:/«BUILDDIR»/resolver-c86U88/apt_archive ./ InRelease Get:2 file:/«BUILDDIR»/resolver-c86U88/apt_archive ./ Release [2119 B] Get:2 file:/«BUILDDIR»/resolver-c86U88/apt_archive ./ Release [2119 B] Get:3 file:/«BUILDDIR»/resolver-c86U88/apt_archive ./ Release.gpg Ign:3 file:/«BUILDDIR»/resolver-c86U88/apt_archive ./ Release.gpg Get:4 file:/«BUILDDIR»/resolver-c86U88/apt_archive ./ Sources [208 B] Ign:4 file:/«BUILDDIR»/resolver-c86U88/apt_archive ./ Sources Get:5 file:/«BUILDDIR»/resolver-c86U88/apt_archive ./ Packages [526 B] Ign:5 file:/«BUILDDIR»/resolver-c86U88/apt_archive ./ Packages Get:4 file:/«BUILDDIR»/resolver-c86U88/apt_archive ./ Sources [208 B] Get:5 file:/«BUILDDIR»/resolver-c86U88/apt_archive ./ Packages [526 B] Reading package lists... W: The repository 'file:/«BUILDDIR»/resolver-c86U88/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 packages were automatically installed and are no longer required: libapt-pkg4.16 libisl13 udev Use 'sudo apt autoremove' to remove them. 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 0 B/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 file:/«BUILDDIR»/resolver-c86U88/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B] debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sbuild-build-depends-core-dummy. (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 ... 11722 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... 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-Pccvc3/apt_archive/sbuild-build-depends-r-base-dummy.deb'. Get:1 file:/«BUILDDIR»/resolver-Pccvc3/apt_archive ./ InRelease Ign:1 file:/«BUILDDIR»/resolver-Pccvc3/apt_archive ./ InRelease Get:2 file:/«BUILDDIR»/resolver-Pccvc3/apt_archive ./ Release [2119 B] Get:2 file:/«BUILDDIR»/resolver-Pccvc3/apt_archive ./ Release [2119 B] Get:3 file:/«BUILDDIR»/resolver-Pccvc3/apt_archive ./ Release.gpg Ign:3 file:/«BUILDDIR»/resolver-Pccvc3/apt_archive ./ Release.gpg Get:4 file:/«BUILDDIR»/resolver-Pccvc3/apt_archive ./ Sources [685 B] Get:5 file:/«BUILDDIR»/resolver-Pccvc3/apt_archive ./ Packages [936 B] Ign:4 file:/«BUILDDIR»/resolver-Pccvc3/apt_archive ./ Sources Ign:5 file:/«BUILDDIR»/resolver-Pccvc3/apt_archive ./ Packages Get:4 file:/«BUILDDIR»/resolver-Pccvc3/apt_archive ./ Sources [685 B] Get:5 file:/«BUILDDIR»/resolver-Pccvc3/apt_archive ./ Packages [936 B] Reading package lists... W: The repository 'file:/«BUILDDIR»/resolver-Pccvc3/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 packages were automatically installed and are no longer required: libapt-pkg4.16 libisl13 udev Use 'sudo apt autoremove' to remove them. The following additional packages will be installed: bash-completion bison bsdmainutils ca-certificates-java debhelper default-jdk default-jre default-jre-headless 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-inconsolata fonts-junicode fonts-lato fonts-linuxlibertine fonts-lobster fonts-lobstertwo fonts-oflb-asana-math fonts-roboto 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 intltool-debian java-common libarchive-zip-perl libasound2 libasound2-data libasprintf0v5 libasyncns0 libatk-bridge2.0-0 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 libatk1.0-data libatspi2.0-0 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 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 libgs9 libgs9-common libgtk2.0-0 libgtk2.0-common libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libice-dev libice6 libicu55 libijs-0.35 libintl-perl libjbig-dev libjbig0 libjbig2dec0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjson-c2 libkpathsea6 liblapack-dev liblapack3 liblcms2-2 libllvm3.6v5 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 libpng12-dev libpoppler57 libpotrace0 libptexenc1 libpthread-stubs0-dev libpulse0 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline-dev libreadline6-dev libsctp1 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 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-shape0 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 libxv1 libxxf86dga1 libxxf86vm1 libzzip-0-13 m4 man-db mime-support mpack openjdk-7-jdk openjdk-7-jre openjdk-7-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 tzdata-java ucf x11-common x11-utils 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: bison-doc wamerican | wordlist whois vacation dh-make fontforge gettext-doc gfortran-multilib gfortran-doc gfortran-5-multilib gfortran-5-doc libgfortran3-dbg groff equivs libasound2-plugins alsa-utils 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 libintl-xs-perl liblcms2-utils liblzma-doc ncurses-doc imagemagick libpango1.0-doc pciutils pcscd pulseaudio readline-doc lksctp-tools libsm-doc libxcb-doc libxext-doc libxt-doc less www-browser mail-transport-agent inews openjdk-7-demo openjdk-7-source visualvm icedtea-7-plugin icedtea-7-jre-jamvm libnss-mdns sun-java6-fonts 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 gv | postscript-viewer xpdf-reader | pdf-viewer perl-tk xindy latexmk purifyeps chktex fragmaster latexdiff dvidvi lacheck dvipng cm-super python-pygments libspreadsheet-parseexcel-perl libfile-which-perl texlive-pstricks dot2tex libtcltk-ruby prerex tk8.6-doc mesa-utils gvfs-bin Recommended packages: curl | wget | lynx-cur libasprintf-dev libgettextpo-dev at-spi2-core bzip2-doc libtxc-dxtn-s2tc0 | libtxc-dxtn0 xdg-user-dirs hicolor-icon-theme libgtk2.0-bin tcpd libx11-doc libxml-sax-expat-perl xml-core libgnome-2-0 libgnomevfs2-0 libgconf-2-4 libmail-sendmail-perl lmodern ruby wish ruby | ruby-interpreter ghostscript libfile-homedir-perl libyaml-tiny-perl texlive-fonts-extra-doc tex-gyre texlive-fonts-recommended-doc tipa texlive-latex-base-doc texlive-latex-extra-doc prosper texlive-latex-recommended-doc tk texlive-pictures-doc xterm | x-terminal-emulator libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-xserver-utils The following NEW packages will be installed: bash-completion bison bsdmainutils ca-certificates-java debhelper default-jdk default-jre default-jre-headless 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-inconsolata fonts-junicode fonts-lato fonts-linuxlibertine fonts-lobster fonts-lobstertwo fonts-oflb-asana-math fonts-roboto 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 intltool-debian java-common libarchive-zip-perl libasound2 libasound2-data libasprintf0v5 libasyncns0 libatk-bridge2.0-0 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 libatk1.0-data libatspi2.0-0 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 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 libgs9 libgs9-common libgtk2.0-0 libgtk2.0-common libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libice-dev libice6 libicu55 libijs-0.35 libintl-perl libjbig-dev libjbig0 libjbig2dec0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjson-c2 libkpathsea6 liblapack-dev liblapack3 liblcms2-2 libllvm3.6v5 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 libpng12-dev libpoppler57 libpotrace0 libptexenc1 libpthread-stubs0-dev libpulse0 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline-dev libreadline6-dev libsctp1 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 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-shape0 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 libxv1 libxxf86dga1 libxxf86vm1 libzzip-0-13 m4 man-db mime-support mpack openjdk-7-jdk openjdk-7-jre openjdk-7-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 tzdata-java ucf x11-common x11-utils 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 482 MB/482 MB of archives. After this operation, 1552 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 file:/«BUILDDIR»/resolver-Pccvc3/apt_archive ./ sbuild-build-depends-r-base-dummy 0.invalid.0 [1180 B] Get:2 http://ftpmaster.internal/ubuntu xenial/main amd64 libjson-c2 amd64 0.11-4ubuntu2 [22.3 kB] Get:3 http://ftpmaster.internal/ubuntu xenial/main amd64 bash-completion all 1:2.1-4.2ubuntu1 [153 kB] Get:4 http://ftpmaster.internal/ubuntu xenial/main amd64 libasprintf0v5 amd64 0.19.4-1ubuntu3 [6676 B] Get:5 http://ftpmaster.internal/ubuntu xenial/main amd64 libxau6 amd64 1:1.0.8-1 [8376 B] Get:6 http://ftpmaster.internal/ubuntu xenial-proposed/main amd64 libxdmcp6 amd64 1:1.1.2-1.1 [11.0 kB] Get:7 http://ftpmaster.internal/ubuntu xenial/main amd64 libxcb1 amd64 1.11.1-1ubuntu1 [40.0 kB] Get:8 http://ftpmaster.internal/ubuntu xenial/main amd64 libx11-data all 2:1.6.3-1ubuntu2 [113 kB] Get:9 http://ftpmaster.internal/ubuntu xenial/main amd64 libx11-6 amd64 2:1.6.3-1ubuntu2 [571 kB] Get:10 http://ftpmaster.internal/ubuntu xenial/main amd64 libxext6 amd64 2:1.3.3-1 [29.4 kB] Get:11 http://ftpmaster.internal/ubuntu xenial/main amd64 groff-base amd64 1.22.3-4 [1143 kB] Get:12 http://ftpmaster.internal/ubuntu xenial/main amd64 bsdmainutils amd64 9.0.6ubuntu1 [175 kB] Get:13 http://ftpmaster.internal/ubuntu xenial/main amd64 libpipeline1 amd64 1.4.1-1 [24.9 kB] Get:14 http://ftpmaster.internal/ubuntu xenial/main amd64 man-db amd64 2.7.5-1 [854 kB] Get:15 http://ftpmaster.internal/ubuntu xenial/main amd64 fonts-dejavu-core all 2.35-1 [1039 kB] Get:16 http://ftpmaster.internal/ubuntu xenial/main amd64 fonts-freefont-ttf all 20120503-4 [4140 kB] Get:17 http://ftpmaster.internal/ubuntu xenial/main amd64 ucf all 3.0031 [52.7 kB] Get:18 http://ftpmaster.internal/ubuntu xenial/main amd64 fontconfig-config all 2.11.1-0ubuntu6 [48.7 kB] Get:19 http://ftpmaster.internal/ubuntu xenial/main amd64 libexpat1 amd64 2.1.0-7 [71.4 kB] Get:20 http://ftpmaster.internal/ubuntu xenial/main amd64 libfreetype6 amd64 2.5.2-4ubuntu2 [312 kB] Get:21 http://ftpmaster.internal/ubuntu xenial/main amd64 libfontconfig1 amd64 2.11.1-0ubuntu6 [127 kB] Get:22 http://ftpmaster.internal/ubuntu xenial/main amd64 fontconfig amd64 2.11.1-0ubuntu6 [176 kB] Get:23 http://ftpmaster.internal/ubuntu xenial/main amd64 fonts-lato all 2.0-1 [2693 kB] Get:24 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-roboto all 1:4.4.4r2-6ubuntu1 [368 kB] Get:25 http://ftpmaster.internal/ubuntu xenial/main amd64 libasyncns0 amd64 0.8-5build1 [12.3 kB] Get:26 http://ftpmaster.internal/ubuntu xenial/main amd64 libgraphite2-3 amd64 1.2.4-3ubuntu1 [54.6 kB] Get:27 http://ftpmaster.internal/ubuntu xenial/main amd64 x11-common all 1:7.7+12ubuntu1 [22.4 kB] Get:28 http://ftpmaster.internal/ubuntu xenial/main amd64 libice6 amd64 2:1.0.9-1 [39.2 kB] Get:29 http://ftpmaster.internal/ubuntu xenial/main amd64 libjpeg-turbo8 amd64 1.3.0-0ubuntu2 [104 kB] Get:30 http://ftpmaster.internal/ubuntu xenial/main amd64 liblcms2-2 amd64 2.6-3ubuntu2 [137 kB] Get:31 http://ftpmaster.internal/ubuntu xenial/main amd64 liblzo2-2 amd64 2.08-1.2 [48.7 kB] Get:32 http://ftpmaster.internal/ubuntu xenial/main amd64 libogg0 amd64 1.3.2-1 [17.2 kB] Get:33 http://ftpmaster.internal/ubuntu xenial/main amd64 libpcrecpp0v5 amd64 2:8.35-7.1ubuntu1 [15.4 kB] Get:34 http://ftpmaster.internal/ubuntu xenial/main amd64 libsigsegv2 amd64 2.10-4 [14.1 kB] Get:35 http://ftpmaster.internal/ubuntu xenial/main amd64 libsm6 amd64 2:1.2.2-1 [15.8 kB] Get:36 http://ftpmaster.internal/ubuntu xenial/main amd64 libtcl8.6 amd64 8.6.4+dfsg-2ubuntu1 [878 kB] Get:37 http://ftpmaster.internal/ubuntu xenial/main amd64 libxrender1 amd64 1:0.9.9-0ubuntu1 [18.5 kB] Get:38 http://ftpmaster.internal/ubuntu xenial/main amd64 libxft2 amd64 2.3.2-1 [36.1 kB] Get:39 http://ftpmaster.internal/ubuntu xenial/main amd64 libxss1 amd64 1:1.2.2-1 [8582 B] Get:40 http://ftpmaster.internal/ubuntu xenial/main amd64 libtk8.6 amd64 8.6.4+dfsg-2ubuntu1 [699 kB] Get:41 http://ftpmaster.internal/ubuntu xenial/main amd64 libunistring0 amd64 0.9.3-5.2ubuntu1 [279 kB] Get:42 http://ftpmaster.internal/ubuntu xenial/main amd64 libwrap0 amd64 7.6.q-25 [46.2 kB] Get:43 http://ftpmaster.internal/ubuntu xenial/main amd64 libxcomposite1 amd64 1:0.4.4-1 [7714 B] Get:44 http://ftpmaster.internal/ubuntu xenial/main amd64 libxfixes3 amd64 1:5.0.1-2 [11.1 kB] Get:45 http://ftpmaster.internal/ubuntu xenial/main amd64 libxcursor1 amd64 1:1.1.14-1 [22.8 kB] Get:46 http://ftpmaster.internal/ubuntu xenial/main amd64 libxdamage1 amd64 1:1.1.4-2 [6946 B] Get:47 http://ftpmaster.internal/ubuntu xenial/main amd64 libfontenc1 amd64 1:1.1.3-1 [13.9 kB] Get:48 http://ftpmaster.internal/ubuntu xenial/main amd64 libxfont1 amd64 1:1.5.1-1 [94.7 kB] Get:49 http://ftpmaster.internal/ubuntu xenial/main amd64 libxinerama1 amd64 2:1.1.3-1 [7908 B] Get:50 http://ftpmaster.internal/ubuntu xenial/main amd64 libxpm4 amd64 1:3.5.11-1 [33.1 kB] Get:51 http://ftpmaster.internal/ubuntu xenial/main amd64 libxshmfence1 amd64 1.2-1 [5042 B] Get:52 http://ftpmaster.internal/ubuntu xenial/main amd64 libxtst6 amd64 2:1.2.2-1 [14.1 kB] Get:53 http://ftpmaster.internal/ubuntu xenial/main amd64 libxv1 amd64 2:1.0.10-1 [10.3 kB] Get:54 http://ftpmaster.internal/ubuntu xenial/main amd64 libxxf86dga1 amd64 2:1.1.4-1 [13.7 kB] Get:55 http://ftpmaster.internal/ubuntu xenial/main amd64 libxxf86vm1 amd64 1:1.1.4-1 [10.6 kB] Get:56 http://ftpmaster.internal/ubuntu xenial/main amd64 libzzip-0-13 amd64 0.13.62-3 [26.1 kB] Get:57 http://ftpmaster.internal/ubuntu xenial/main amd64 java-common all 0.52.1 [131 kB] Get:58 http://ftpmaster.internal/ubuntu xenial/main amd64 default-jre-headless amd64 2:1.7-52.1 [4000 B] Get:59 http://ftpmaster.internal/ubuntu xenial/main amd64 libnspr4 amd64 2:4.11-1ubuntu1 [112 kB] Get:60 http://ftpmaster.internal/ubuntu xenial/main amd64 libnss3-nssdb all 2:3.21-1ubuntu2 [10.6 kB] Get:61 http://ftpmaster.internal/ubuntu xenial/main amd64 libnss3 amd64 2:3.21-1ubuntu2 [1130 kB] Get:62 http://ftpmaster.internal/ubuntu xenial/main amd64 ca-certificates-java all 20140324 [12.3 kB] Get:63 http://ftpmaster.internal/ubuntu xenial/main amd64 tzdata-java all 2015g-1 [69.1 kB] Get:64 http://ftpmaster.internal/ubuntu xenial/main amd64 libavahi-common-data amd64 0.6.32~rc+dfsg-1ubuntu2 [21.7 kB] Get:65 http://ftpmaster.internal/ubuntu xenial/main amd64 libavahi-common3 amd64 0.6.32~rc+dfsg-1ubuntu2 [21.6 kB] Get:66 http://ftpmaster.internal/ubuntu xenial/main amd64 libavahi-client3 amd64 0.6.32~rc+dfsg-1ubuntu2 [25.1 kB] Get:67 http://ftpmaster.internal/ubuntu xenial/main amd64 libcups2 amd64 2.1.0-7 [196 kB] Get:68 http://ftpmaster.internal/ubuntu xenial/main amd64 libjpeg8 amd64 8c-2ubuntu8 [2194 B] Get:69 http://ftpmaster.internal/ubuntu xenial/main amd64 libglib2.0-0 amd64 2.47.3-3 [1114 kB] Get:70 http://ftpmaster.internal/ubuntu xenial/main amd64 libpcsclite1 amd64 1.8.14-1ubuntu1 [21.4 kB] Get:71 http://ftpmaster.internal/ubuntu xenial/main amd64 libflac8 amd64 1.3.1-4 [210 kB] Get:72 http://ftpmaster.internal/ubuntu xenial/main amd64 libvorbis0a amd64 1.3.4-3 [86.9 kB] Get:73 http://ftpmaster.internal/ubuntu xenial/main amd64 libvorbisenc2 amd64 1.3.4-3 [70.8 kB] Get:74 http://ftpmaster.internal/ubuntu xenial/main amd64 libsndfile1 amd64 1.0.25-10 [137 kB] Get:75 http://ftpmaster.internal/ubuntu xenial/main amd64 libpulse0 amd64 1:7.1-1ubuntu2 [247 kB] Get:76 http://ftpmaster.internal/ubuntu xenial/main amd64 libsctp1 amd64 1.0.16+dfsg-3 [8088 B] Get:77 http://ftpmaster.internal/ubuntu xenial-proposed/main amd64 openjdk-7-jre-headless amd64 7u91-2.6.3-2 [39.8 MB] Get:78 http://ftpmaster.internal/ubuntu xenial/main amd64 poppler-data all 0.4.7-5 [1493 kB] Get:79 http://ftpmaster.internal/ubuntu xenial/main amd64 libpython2.7-minimal amd64 2.7.10-4ubuntu2 [337 kB] Get:80 http://ftpmaster.internal/ubuntu xenial/main amd64 python2.7-minimal amd64 2.7.10-4ubuntu2 [1262 kB] Get:81 http://ftpmaster.internal/ubuntu xenial/main amd64 python-minimal amd64 2.7.9-1 [28.2 kB] Get:82 http://ftpmaster.internal/ubuntu xenial/main amd64 mime-support all 3.59ubuntu1 [31.0 kB] Get:83 http://ftpmaster.internal/ubuntu xenial/main amd64 libpython2.7-stdlib amd64 2.7.10-4ubuntu2 [1794 kB] Get:84 http://ftpmaster.internal/ubuntu xenial/main amd64 python2.7 amd64 2.7.10-4ubuntu2 [210 kB] Get:85 http://ftpmaster.internal/ubuntu xenial/main amd64 libpython-stdlib amd64 2.7.9-1 [7754 B] Get:86 http://ftpmaster.internal/ubuntu xenial/main amd64 python amd64 2.7.9-1 [137 kB] Get:87 http://ftpmaster.internal/ubuntu xenial/main amd64 libjbig0 amd64 2.1-3.1 [26.6 kB] Get:88 http://ftpmaster.internal/ubuntu xenial/main amd64 libmagic1 amd64 1:5.25-2ubuntu1 [216 kB] Get:89 http://ftpmaster.internal/ubuntu xenial/main amd64 file amd64 1:5.25-2ubuntu1 [21.2 kB] Get:90 http://ftpmaster.internal/ubuntu xenial/main amd64 libbsd0 amd64 0.8.0-2 [42.1 kB] Get:91 http://ftpmaster.internal/ubuntu xenial/main amd64 xkb-data all 2.12-1ubuntu1 [297 kB] Get:92 http://ftpmaster.internal/ubuntu xenial/main amd64 gettext-base amd64 0.19.4-1ubuntu3 [48.3 kB] Get:93 http://ftpmaster.internal/ubuntu xenial/main amd64 libgirepository-1.0-1 amd64 1.46.0-3ubuntu1 [88.3 kB] Get:94 http://ftpmaster.internal/ubuntu xenial/main amd64 gir1.2-glib-2.0 amd64 1.46.0-3ubuntu1 [127 kB] Get:95 http://ftpmaster.internal/ubuntu xenial/main amd64 libdrm2 amd64 2.4.65-3 [27.6 kB] Get:96 http://ftpmaster.internal/ubuntu xenial/main amd64 libedit2 amd64 3.1-20150325-1ubuntu1 [76.6 kB] Get:97 http://ftpmaster.internal/ubuntu xenial/main amd64 libelf1 amd64 0.163-5.1 [39.3 kB] Get:98 http://ftpmaster.internal/ubuntu xenial/main amd64 libglib2.0-data all 2.47.3-3 [129 kB] Get:99 http://ftpmaster.internal/ubuntu xenial/main amd64 libicu55 amd64 55.1-6ubuntu1 [7643 kB] Get:100 http://ftpmaster.internal/ubuntu xenial/main amd64 libxml2 amd64 2.9.2+zdfsg1-4ubuntu1 [695 kB] Get:101 http://ftpmaster.internal/ubuntu xenial/main amd64 libxmuu1 amd64 2:1.1.2-1ubuntu1 [9668 B] Get:102 http://ftpmaster.internal/ubuntu xenial/main amd64 shared-mime-info amd64 1.5-2 [405 kB] Get:103 http://ftpmaster.internal/ubuntu xenial/main amd64 xauth amd64 1:1.0.9-1ubuntu2 [22.7 kB] Get:104 http://ftpmaster.internal/ubuntu xenial/main amd64 m4 amd64 1.4.17-4 [193 kB] Get:105 http://ftpmaster.internal/ubuntu xenial/main amd64 libbison-dev amd64 2:3.0.4.dfsg-1 [338 kB] Get:106 http://ftpmaster.internal/ubuntu xenial/main amd64 bison amd64 2:3.0.4.dfsg-1 [259 kB] Get:107 http://ftpmaster.internal/ubuntu xenial/main amd64 libcroco3 amd64 0.6.9-1 [82.0 kB] Get:108 http://ftpmaster.internal/ubuntu xenial/main amd64 gettext amd64 0.19.4-1ubuntu3 [857 kB] Get:109 http://ftpmaster.internal/ubuntu xenial/main amd64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:110 http://ftpmaster.internal/ubuntu xenial/main amd64 po-debconf all 1.0.18 [234 kB] Get:111 http://ftpmaster.internal/ubuntu xenial/main amd64 libarchive-zip-perl all 1.53-1 [87.0 kB] Get:112 http://ftpmaster.internal/ubuntu xenial/main amd64 libfile-stripnondeterminism-perl all 0.014-1 [10.1 kB] Get:113 http://ftpmaster.internal/ubuntu xenial/main amd64 libtimedate-perl all 2.3000-2 [37.5 kB] Get:114 http://ftpmaster.internal/ubuntu xenial/main amd64 dh-strip-nondeterminism all 0.014-1 [5596 B] Get:115 http://ftpmaster.internal/ubuntu xenial/main amd64 debhelper all 9.20151126ubuntu1 [741 kB] Get:116 http://ftpmaster.internal/ubuntu xenial/main amd64 libasound2-data all 1.0.29-0ubuntu1 [28.4 kB] Get:117 http://ftpmaster.internal/ubuntu xenial/main amd64 libasound2 amd64 1.0.29-0ubuntu1 [337 kB] Get:118 http://ftpmaster.internal/ubuntu xenial/main amd64 libtiff5 amd64 4.0.5-1 [144 kB] Get:119 http://ftpmaster.internal/ubuntu xenial/main amd64 libgdk-pixbuf2.0-common all 2.32.2-1ubuntu1 [9996 B] Get:120 http://ftpmaster.internal/ubuntu xenial/main amd64 libgdk-pixbuf2.0-0 amd64 2.32.2-1ubuntu1 [158 kB] Get:121 http://ftpmaster.internal/ubuntu xenial/main amd64 libgif7 amd64 5.1.1-0.1 [29.9 kB] Get:122 http://ftpmaster.internal/ubuntu xenial/main amd64 libgtk2.0-common all 2.24.28-1ubuntu1 [123 kB] Get:123 http://ftpmaster.internal/ubuntu xenial/main amd64 libatk1.0-data all 2.18.0-1 [17.1 kB] Get:124 http://ftpmaster.internal/ubuntu xenial/main amd64 libatk1.0-0 amd64 2.18.0-1 [56.9 kB] Get:125 http://ftpmaster.internal/ubuntu xenial/main amd64 libpixman-1-0 amd64 0.33.4-1 [231 kB] Get:126 http://ftpmaster.internal/ubuntu xenial/main amd64 libxcb-render0 amd64 1.11.1-1ubuntu1 [11.4 kB] Get:127 http://ftpmaster.internal/ubuntu xenial/main amd64 libxcb-shm0 amd64 1.11.1-1ubuntu1 [5588 B] Get:128 http://ftpmaster.internal/ubuntu xenial/main amd64 libcairo2 amd64 1.14.4-1 [556 kB] Get:129 http://ftpmaster.internal/ubuntu xenial/main amd64 libthai-data all 0.1.24-1 [131 kB] Get:130 http://ftpmaster.internal/ubuntu xenial/main amd64 libdatrie1 amd64 0.2.10-1 [17.0 kB] Get:131 http://ftpmaster.internal/ubuntu xenial/main amd64 libthai0 amd64 0.1.24-1 [16.7 kB] Get:132 http://ftpmaster.internal/ubuntu xenial/main amd64 libpango-1.0-0 amd64 1.38.1-1 [148 kB] Get:133 http://ftpmaster.internal/ubuntu xenial/main amd64 libharfbuzz0b amd64 1.0.1-1build2 [140 kB] Get:134 http://ftpmaster.internal/ubuntu xenial/main amd64 libpangoft2-1.0-0 amd64 1.38.1-1 [33.3 kB] Get:135 http://ftpmaster.internal/ubuntu xenial/main amd64 libpangocairo-1.0-0 amd64 1.38.1-1 [20.5 kB] Get:136 http://ftpmaster.internal/ubuntu xenial/main amd64 libxi6 amd64 2:1.7.5-1 [28.6 kB] Get:137 http://ftpmaster.internal/ubuntu xenial/main amd64 libxrandr2 amd64 2:1.5.0-1 [17.6 kB] Get:138 http://ftpmaster.internal/ubuntu xenial/main amd64 libgtk2.0-0 amd64 2.24.28-1ubuntu1 [1775 kB] Get:139 http://ftpmaster.internal/ubuntu xenial/main amd64 libglapi-mesa amd64 11.0.6-1ubuntu1 [23.2 kB] Get:140 http://ftpmaster.internal/ubuntu xenial/main amd64 libx11-xcb1 amd64 2:1.6.3-1ubuntu2 [8956 B] Get:141 http://ftpmaster.internal/ubuntu xenial/main amd64 libxcb-dri2-0 amd64 1.11.1-1ubuntu1 [6882 B] Get:142 http://ftpmaster.internal/ubuntu xenial/main amd64 libxcb-dri3-0 amd64 1.11.1-1ubuntu1 [5218 B] Get:143 http://ftpmaster.internal/ubuntu xenial/main amd64 libxcb-glx0 amd64 1.11.1-1ubuntu1 [20.9 kB] Get:144 http://ftpmaster.internal/ubuntu xenial/main amd64 libxcb-present0 amd64 1.11.1-1ubuntu1 [5218 B] Get:145 http://ftpmaster.internal/ubuntu xenial/main amd64 libxcb-sync1 amd64 1.11.1-1ubuntu1 [8324 B] Get:146 http://ftpmaster.internal/ubuntu xenial/main amd64 libdrm-amdgpu1 amd64 2.4.65-3 [15.4 kB] Get:147 http://ftpmaster.internal/ubuntu xenial/main amd64 libpciaccess0 amd64 0.13.4-1 [18.1 kB] Get:148 http://ftpmaster.internal/ubuntu xenial/main amd64 libdrm-intel1 amd64 2.4.65-3 [55.4 kB] Get:149 http://ftpmaster.internal/ubuntu xenial/main amd64 libdrm-nouveau2 amd64 2.4.65-3 [14.2 kB] Get:150 http://ftpmaster.internal/ubuntu xenial/main amd64 libdrm-radeon1 amd64 2.4.65-3 [21.6 kB] Get:151 http://ftpmaster.internal/ubuntu xenial/main amd64 libllvm3.6v5 amd64 1:3.6.2-3build1 [8086 kB] Get:152 http://ftpmaster.internal/ubuntu xenial/main amd64 libgl1-mesa-dri amd64 11.0.6-1ubuntu1 [4303 kB] Get:153 http://ftpmaster.internal/ubuntu xenial/main amd64 libgl1-mesa-glx amd64 11.0.6-1ubuntu1 [145 kB] Get:154 http://ftpmaster.internal/ubuntu xenial/main amd64 libatspi2.0-0 amd64 2.18.3-1ubuntu1 [57.3 kB] Get:155 http://ftpmaster.internal/ubuntu xenial/main amd64 libatk-bridge2.0-0 amd64 2.18.1-1ubuntu1 [52.6 kB] Get:156 http://ftpmaster.internal/ubuntu xenial/main amd64 libxt6 amd64 1:1.1.5-0ubuntu1 [160 kB] Get:157 http://ftpmaster.internal/ubuntu xenial/main amd64 libxmu6 amd64 2:1.1.2-1ubuntu1 [46.0 kB] Get:158 http://ftpmaster.internal/ubuntu xenial/main amd64 libxaw7 amd64 2:1.0.13-1 [173 kB] Get:159 http://ftpmaster.internal/ubuntu xenial/main amd64 libxcb-shape0 amd64 1.11.1-1ubuntu1 [5756 B] Get:160 http://ftpmaster.internal/ubuntu xenial/main amd64 x11-utils amd64 7.7+3 [189 kB] Get:161 http://ftpmaster.internal/ubuntu xenial/main amd64 libatk-wrapper-java all 0.33.3-5 [33.7 kB] Get:162 http://ftpmaster.internal/ubuntu xenial/main amd64 libatk-wrapper-java-jni amd64 0.33.3-5 [27.0 kB] Get:163 http://ftpmaster.internal/ubuntu xenial-proposed/main amd64 openjdk-7-jre amd64 7u91-2.6.3-2 [173 kB] Get:164 http://ftpmaster.internal/ubuntu xenial/main amd64 default-jre amd64 2:1.7-52.1 [966 B] Get:165 http://ftpmaster.internal/ubuntu xenial-proposed/main amd64 openjdk-7-jdk amd64 7u91-2.6.3-2 [16.3 MB] Get:166 http://ftpmaster.internal/ubuntu xenial/main amd64 default-jdk amd64 2:1.7-52.1 [958 B] Get:167 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-cabin all 1.5-2 [140 kB] Get:168 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-comfortaa all 2.003-1 [131 kB] Get:169 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-crosextra-caladea all 20130214-1 [82.3 kB] Get:170 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-crosextra-carlito all 20130920-1 [742 kB] Get:171 http://ftpmaster.internal/ubuntu xenial/main amd64 fonts-dejavu-extra all 2.35-1 [1749 kB] Get:172 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-ebgaramond all 0.015+git20130628-3 [651 kB] Get:173 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-ebgaramond-extra all 0.015+git20130628-3 [933 kB] Get:174 http://ftpmaster.internal/ubuntu xenial/main amd64 fonts-font-awesome all 4.4.0~dfsg-1 [491 kB] Get:175 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-freefont-otf all 20120503-4 [3068 kB] Get:176 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-gfs-artemisia all 1.1-5 [260 kB] Get:177 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-gfs-complutum all 1.1-6 [41.6 kB] Get:178 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-gfs-didot all 1.1-6 [278 kB] Get:179 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-gfs-neohellenic all 1.1-6 [215 kB] Get:180 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-gfs-olga all 1.1-5 [33.4 kB] Get:181 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-gfs-solomos all 1.1-5 [40.7 kB] Get:182 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-inconsolata all 001.010-5 [61.8 kB] Get:183 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-junicode all 0.7.8-2 [642 kB] Get:184 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-linuxlibertine all 5.3.0-2 [1688 kB] Get:185 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-lobster all 2.0-2 [38.7 kB] Get:186 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-lobstertwo all 2.0-2 [92.7 kB] Get:187 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-oflb-asana-math all 000.907-6 [246 kB] Get:188 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-sil-gentium all 20081126:1.03-1 [247 kB] Get:189 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-sil-gentium-basic all 1.1-7 [379 kB] Get:190 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-sil-gentiumplus all 5.000-1 [2805 kB] Get:191 http://ftpmaster.internal/ubuntu xenial/main amd64 libgfortran3 amd64 5.2.1-27ubuntu1 [258 kB] Get:192 http://ftpmaster.internal/ubuntu xenial/main amd64 libgfortran-5-dev amd64 5.2.1-27ubuntu1 [289 kB] Get:193 http://ftpmaster.internal/ubuntu xenial/main amd64 gfortran-5 amd64 5.2.1-27ubuntu1 [27.3 MB] Get:194 http://ftpmaster.internal/ubuntu xenial/main amd64 gfortran amd64 4:5.2.1-16ubuntu2 [1288 B] Get:195 http://ftpmaster.internal/ubuntu xenial/main amd64 gir1.2-freedesktop amd64 1.46.0-3ubuntu1 [5742 B] Get:196 http://ftpmaster.internal/ubuntu xenial/main amd64 libpangoxft-1.0-0 amd64 1.38.1-1 [15.1 kB] Get:197 http://ftpmaster.internal/ubuntu xenial/main amd64 gir1.2-pango-1.0 amd64 1.38.1-1 [21.0 kB] Get:198 http://ftpmaster.internal/ubuntu xenial/main amd64 libblas-common amd64 1.2.20110419-11 [3036 B] Get:199 http://ftpmaster.internal/ubuntu xenial/main amd64 libblas3 amd64 1.2.20110419-11 [158 kB] Get:200 http://ftpmaster.internal/ubuntu xenial/main amd64 libblas-dev amd64 1.2.20110419-11 [154 kB] Get:201 http://ftpmaster.internal/ubuntu xenial/main amd64 libbz2-dev amd64 1.0.6-8 [29.1 kB] Get:202 http://ftpmaster.internal/ubuntu xenial/main amd64 libcairo-gobject2 amd64 1.14.4-1 [17.2 kB] Get:203 http://ftpmaster.internal/ubuntu xenial/main amd64 libcairo-script-interpreter2 amd64 1.14.4-1 [54.4 kB] Get:204 http://ftpmaster.internal/ubuntu xenial/main amd64 libexpat1-dev amd64 2.1.0-7 [115 kB] Get:205 http://ftpmaster.internal/ubuntu xenial/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-2ubuntu4 [168 kB] Get:206 http://ftpmaster.internal/ubuntu xenial/main amd64 libpng12-dev amd64 1.2.54-1 [183 kB] Get:207 http://ftpmaster.internal/ubuntu xenial/main amd64 libfreetype6-dev amd64 2.5.2-4ubuntu2 [630 kB] Get:208 http://ftpmaster.internal/ubuntu xenial/main amd64 pkg-config amd64 0.29-2ubuntu1 [44.2 kB] Get:209 http://ftpmaster.internal/ubuntu xenial/main amd64 libfontconfig1-dev amd64 2.11.1-0ubuntu6 [641 kB] Get:210 http://ftpmaster.internal/ubuntu xenial/main amd64 xorg-sgml-doctools all 1:1.11-1 [12.9 kB] Get:211 http://ftpmaster.internal/ubuntu xenial/main amd64 x11proto-core-dev all 7.0.28-0ubuntu1 [699 kB] Get:212 http://ftpmaster.internal/ubuntu xenial/main amd64 libxau-dev amd64 1:1.0.8-1 [11.1 kB] Get:213 http://ftpmaster.internal/ubuntu xenial-proposed/main amd64 libxdmcp-dev amd64 1:1.1.2-1.1 [25.1 kB] Get:214 http://ftpmaster.internal/ubuntu xenial/main amd64 x11proto-input-dev all 2.3.1-1 [118 kB] Get:215 http://ftpmaster.internal/ubuntu xenial/main amd64 x11proto-kb-dev all 1.0.7-0ubuntu1 [224 kB] Get:216 http://ftpmaster.internal/ubuntu xenial/main amd64 xtrans-dev all 1.3.5-1 [70.5 kB] Get:217 http://ftpmaster.internal/ubuntu xenial/main amd64 libpthread-stubs0-dev amd64 0.3-4 [4068 B] Get:218 http://ftpmaster.internal/ubuntu xenial/main amd64 libxcb1-dev amd64 1.11.1-1ubuntu1 [74.2 kB] Get:219 http://ftpmaster.internal/ubuntu xenial/main amd64 libx11-dev amd64 2:1.6.3-1ubuntu2 [642 kB] Get:220 http://ftpmaster.internal/ubuntu xenial/main amd64 x11proto-render-dev all 2:0.11.1-2 [20.1 kB] Get:221 http://ftpmaster.internal/ubuntu xenial/main amd64 libxrender-dev amd64 1:0.9.9-0ubuntu1 [24.5 kB] Get:222 http://ftpmaster.internal/ubuntu xenial/main amd64 x11proto-xext-dev all 7.3.0-1 [212 kB] Get:223 http://ftpmaster.internal/ubuntu xenial/main amd64 libxext-dev amd64 2:1.3.3-1 [82.1 kB] Get:224 http://ftpmaster.internal/ubuntu xenial/main amd64 libice-dev amd64 2:1.0.9-1 [44.9 kB] Get:225 http://ftpmaster.internal/ubuntu xenial/main amd64 libsm-dev amd64 2:1.2.2-1 [16.2 kB] Get:226 http://ftpmaster.internal/ubuntu xenial/main amd64 libpixman-1-dev amd64 0.33.4-1 [248 kB] Get:227 http://ftpmaster.internal/ubuntu xenial/main amd64 libxcb-render0-dev amd64 1.11.1-1ubuntu1 [15.3 kB] Get:228 http://ftpmaster.internal/ubuntu xenial/main amd64 libxcb-shm0-dev amd64 1.11.1-1ubuntu1 [6604 B] Get:229 http://ftpmaster.internal/ubuntu xenial/main amd64 libglib2.0-bin amd64 2.47.3-3 [39.5 kB] Get:230 http://ftpmaster.internal/ubuntu xenial/main amd64 libpcre16-3 amd64 2:8.35-7.1ubuntu1 [141 kB] Get:231 http://ftpmaster.internal/ubuntu xenial/main amd64 libpcre32-3 amd64 2:8.35-7.1ubuntu1 [133 kB] Get:232 http://ftpmaster.internal/ubuntu xenial/main amd64 libpcre3-dev amd64 2:8.35-7.1ubuntu1 [520 kB] Get:233 http://ftpmaster.internal/ubuntu xenial/main amd64 libglib2.0-dev amd64 2.47.3-3 [1373 kB] Get:234 http://ftpmaster.internal/ubuntu xenial/main amd64 libcairo2-dev amd64 1.14.4-1 [590 kB] Get:235 http://ftpmaster.internal/ubuntu xenial-proposed/main amd64 libcupsfilters1 amd64 1.2.0-1 [76.6 kB] Get:236 http://ftpmaster.internal/ubuntu xenial/main amd64 libcupsimage2 amd64 2.1.0-7 [16.0 kB] Get:237 http://ftpmaster.internal/ubuntu xenial/main amd64 libcurl3 amd64 7.45.0-1ubuntu1 [184 kB] Get:238 http://ftpmaster.internal/ubuntu xenial/main amd64 libcurl4-openssl-dev amd64 7.45.0-1ubuntu1 [262 kB] Get:239 http://ftpmaster.internal/ubuntu xenial/main amd64 libijs-0.35 amd64 0.35-11 [15.5 kB] Get:240 http://ftpmaster.internal/ubuntu xenial/main amd64 libjbig2dec0 amd64 0.12+20150918-1 [55.1 kB] Get:241 http://ftpmaster.internal/ubuntu xenial/main amd64 libpaper1 amd64 1.1.24+nmu4ubuntu1 [13.7 kB] Get:242 http://ftpmaster.internal/ubuntu xenial/main amd64 libgs9-common all 9.16~dfsg~0-0ubuntu3 [2938 kB] Get:243 http://ftpmaster.internal/ubuntu xenial/main amd64 libgs9 amd64 9.16~dfsg~0-0ubuntu3 [2062 kB] Get:244 http://ftpmaster.internal/ubuntu xenial/main amd64 libharfbuzz-icu0 amd64 1.0.1-1build2 [5282 B] Get:245 http://ftpmaster.internal/ubuntu xenial/main amd64 libharfbuzz-gobject0 amd64 1.0.1-1build2 [11.0 kB] Get:246 http://ftpmaster.internal/ubuntu xenial/main amd64 libharfbuzz-dev amd64 1.0.1-1build2 [189 kB] Get:247 http://ftpmaster.internal/ubuntu xenial/main amd64 libintl-perl all 1.24-1 [805 kB] Get:248 http://ftpmaster.internal/ubuntu xenial/main amd64 libjpeg-turbo8-dev amd64 1.3.0-0ubuntu2 [242 kB] Get:249 http://ftpmaster.internal/ubuntu xenial/main amd64 libjpeg8-dev amd64 8c-2ubuntu8 [1552 B] Get:250 http://ftpmaster.internal/ubuntu xenial/main amd64 libjpeg-dev amd64 8c-2ubuntu8 [1546 B] Get:251 http://ftpmaster.internal/ubuntu xenial-proposed/main amd64 libkpathsea6 amd64 2015.20150524.37493-7build2 [54.8 kB] Get:252 http://ftpmaster.internal/ubuntu xenial/main amd64 liblapack3 amd64 3.5.0-5 [1816 kB] Get:253 http://ftpmaster.internal/ubuntu xenial/main amd64 liblapack-dev amd64 3.5.0-5 [1820 kB] Get:254 http://ftpmaster.internal/ubuntu xenial/main amd64 libtinfo-dev amd64 5.9+20150516-2ubuntu1 [77.2 kB] Get:255 http://ftpmaster.internal/ubuntu xenial/main amd64 libncurses5-dev amd64 5.9+20150516-2ubuntu1 [176 kB] Get:256 http://ftpmaster.internal/ubuntu xenial/main amd64 libxft-dev amd64 2.3.2-1 [45.7 kB] Get:257 http://ftpmaster.internal/ubuntu xenial/main amd64 libpango1.0-dev amd64 1.38.1-1 [277 kB] Get:258 http://ftpmaster.internal/ubuntu xenial/main amd64 libpaper-utils amd64 1.1.24+nmu4ubuntu1 [8276 B] Get:259 http://ftpmaster.internal/ubuntu xenial-proposed/main amd64 libpoppler57 amd64 0.38.0-0ubuntu1 [753 kB] Get:260 http://ftpmaster.internal/ubuntu xenial/main amd64 libpotrace0 amd64 1.12-1 [17.8 kB] Get:261 http://ftpmaster.internal/ubuntu xenial-proposed/main amd64 libptexenc1 amd64 2015.20150524.37493-7build2 [34.5 kB] Get:262 http://ftpmaster.internal/ubuntu xenial/main amd64 libreadline6-dev amd64 6.3-8ubuntu1 [123 kB] Get:263 http://ftpmaster.internal/ubuntu xenial/main amd64 libreadline-dev amd64 6.3-8ubuntu1 [1040 B] Get:264 http://ftpmaster.internal/ubuntu xenial-proposed/main amd64 libsynctex1 amd64 2015.20150524.37493-7build2 [41.4 kB] Get:265 http://ftpmaster.internal/ubuntu xenial-proposed/main amd64 libtexlua52 amd64 2015.20150524.37493-7build2 [90.5 kB] Get:266 http://ftpmaster.internal/ubuntu xenial-proposed/main amd64 libtexluajit2 amd64 2015.20150524.37493-7build2 [213 kB] Get:267 http://ftpmaster.internal/ubuntu xenial/main amd64 libtext-unidecode-perl all 1.27-1 [103 kB] Get:268 http://ftpmaster.internal/ubuntu xenial/main amd64 libjbig-dev amd64 2.1-3.1 [24.8 kB] Get:269 http://ftpmaster.internal/ubuntu xenial/main amd64 liblzma-dev amd64 5.1.1alpha+20120614-2ubuntu2 [137 kB] Get:270 http://ftpmaster.internal/ubuntu xenial/main amd64 libtiffxx5 amd64 4.0.5-1 [5582 B] Get:271 http://ftpmaster.internal/ubuntu xenial/main amd64 libtiff5-dev amd64 4.0.5-1 [266 kB] Get:272 http://ftpmaster.internal/ubuntu xenial/main amd64 libxkbfile1 amd64 1:1.0.9-0ubuntu1 [65.1 kB] Get:273 http://ftpmaster.internal/ubuntu xenial/main amd64 libxml-namespacesupport-perl all 1.11-1 [13.2 kB] Get:274 http://ftpmaster.internal/ubuntu xenial/main amd64 libxml-sax-base-perl all 1.07-1 [21.5 kB] Get:275 http://ftpmaster.internal/ubuntu xenial/main amd64 libxml-sax-perl all 0.99+dfsg-2ubuntu1 [64.6 kB] Get:276 http://ftpmaster.internal/ubuntu xenial/main amd64 libxml-libxml-perl amd64 2.0116+dfsg-5 [340 kB] Get:277 http://ftpmaster.internal/ubuntu xenial/main amd64 x11proto-scrnsaver-dev all 1.2.2-1 [25.0 kB] Get:278 http://ftpmaster.internal/ubuntu xenial/main amd64 libxss-dev amd64 1:1.2.2-1 [12.7 kB] Get:279 http://ftpmaster.internal/ubuntu xenial/main amd64 libxt-dev amd64 1:1.1.5-0ubuntu1 [394 kB] Get:280 http://ftpmaster.internal/ubuntu xenial/universe amd64 mpack amd64 1.6-8 [40.7 kB] Get:281 http://ftpmaster.internal/ubuntu xenial/main amd64 tex-common all 6.04 [545 kB] Get:282 http://ftpmaster.internal/ubuntu xenial/main amd64 preview-latex-style all 11.88-1.1ubuntu1 [184 kB] Get:283 http://ftpmaster.internal/ubuntu xenial/main amd64 t1utils amd64 1.38-4 [52.5 kB] Get:284 http://ftpmaster.internal/ubuntu xenial/main amd64 tcl8.6 amd64 8.6.4+dfsg-2ubuntu1 [14.3 kB] Get:285 http://ftpmaster.internal/ubuntu xenial/main amd64 tcl8.6-dev amd64 8.6.4+dfsg-2ubuntu1 [887 kB] Get:286 http://ftpmaster.internal/ubuntu xenial/main amd64 texinfo amd64 6.0.0.dfsg.1-3 [573 kB] Get:287 http://ftpmaster.internal/ubuntu xenial-proposed/main amd64 texlive-binaries amd64 2015.20150524.37493-7build2 [9483 kB] Get:288 http://ftpmaster.internal/ubuntu xenial/main amd64 xdg-utils all 1.1.0~rc3+git20150907-1ubuntu3 [58.1 kB] Get:289 http://ftpmaster.internal/ubuntu xenial/main amd64 texlive-base all 2015.20150625-1ubuntu1 [18.1 MB] Get:290 http://ftpmaster.internal/ubuntu xenial/main amd64 texlive-latex-base all 2015.20150625-1ubuntu1 [968 kB] Get:291 http://ftpmaster.internal/ubuntu xenial/main amd64 texlive-extra-utils all 2015.20151116-1 [11.9 MB] Get:292 http://ftpmaster.internal/ubuntu xenial/universe amd64 ttf-adf-universalis all 0.20090423-2 [221 kB] Get:293 http://ftpmaster.internal/ubuntu xenial/universe amd64 fonts-stix all 1.1.1-4 [591 kB] Get:294 http://ftpmaster.internal/ubuntu xenial/universe amd64 ttf-adf-gillius all 0.20090423-2 [400 kB] Get:295 http://ftpmaster.internal/ubuntu xenial/universe amd64 ttf-adf-accanthis all 0.20090423-2 [401 kB] Get:296 http://ftpmaster.internal/ubuntu xenial/universe amd64 texlive-fonts-extra all 2015.20151116-1 [223 MB] Get:297 http://ftpmaster.internal/ubuntu xenial/main amd64 texlive-fonts-recommended all 2015.20150625-1ubuntu1 [5704 kB] Get:298 http://ftpmaster.internal/ubuntu xenial/main amd64 texlive-generic-recommended all 2015.20150625-1ubuntu1 [2624 kB] Get:299 http://ftpmaster.internal/ubuntu xenial/main amd64 texlive-latex-recommended all 2015.20150625-1ubuntu1 [10.2 MB] Get:300 http://ftpmaster.internal/ubuntu xenial/main amd64 texlive-pictures all 2015.20150625-1ubuntu1 [3089 kB] Get:301 http://ftpmaster.internal/ubuntu xenial/main amd64 texlive-latex-extra all 2015.20151116-1 [10.8 MB] Get:302 http://ftpmaster.internal/ubuntu xenial/main amd64 tk8.6 amd64 8.6.4+dfsg-2ubuntu1 [12.3 kB] Get:303 http://ftpmaster.internal/ubuntu xenial/main amd64 tk8.6-dev amd64 8.6.4+dfsg-2ubuntu1 [682 kB] Get:304 http://ftpmaster.internal/ubuntu xenial/main amd64 x11-xkb-utils amd64 7.7+2 [153 kB] Get:305 http://ftpmaster.internal/ubuntu xenial/main amd64 xfonts-encodings all 1:1.0.4-2 [573 kB] Get:306 http://ftpmaster.internal/ubuntu xenial/main amd64 xfonts-utils amd64 1:7.7+3 [75.3 kB] Get:307 http://ftpmaster.internal/ubuntu xenial/main amd64 xfonts-base all 1:1.0.4+nmu1 [5914 kB] Get:308 http://ftpmaster.internal/ubuntu xenial/main amd64 xserver-common all 2:1.17.3-2ubuntu2 [27.1 kB] Get:309 http://ftpmaster.internal/ubuntu xenial/main amd64 xvfb amd64 2:1.17.3-2ubuntu2 [769 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 482 MB in 1min 48s (4454 kB/s) Selecting previously unselected package libjson-c2:amd64. (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 ... 11722 files and directories currently installed.) Preparing to unpack .../libjson-c2_0.11-4ubuntu2_amd64.deb ... Unpacking libjson-c2:amd64 (0.11-4ubuntu2) ... Selecting previously unselected package bash-completion. Preparing to unpack .../bash-completion_1%3a2.1-4.2ubuntu1_all.deb ... Unpacking bash-completion (1:2.1-4.2ubuntu1) ... Selecting previously unselected package libasprintf0v5:amd64. 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Unpacking fonts-freefont-ttf (20120503-4) ... Selecting previously unselected package ucf. Preparing to unpack .../archives/ucf_3.0031_all.deb ... Moving old data out of the way Unpacking ucf (3.0031) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../fontconfig-config_2.11.1-0ubuntu6_all.deb ... Unpacking fontconfig-config (2.11.1-0ubuntu6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.1.0-7_amd64.deb ... Unpacking libexpat1:amd64 (2.1.0-7) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../libfreetype6_2.5.2-4ubuntu2_amd64.deb ... Unpacking libfreetype6:amd64 (2.5.2-4ubuntu2) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../libfontconfig1_2.11.1-0ubuntu6_amd64.deb ... Unpacking libfontconfig1:amd64 (2.11.1-0ubuntu6) ... Selecting previously unselected package fontconfig. Preparing to unpack .../fontconfig_2.11.1-0ubuntu6_amd64.deb ... Unpacking fontconfig (2.11.1-0ubuntu6) ... 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 fonts-roboto. Preparing to unpack .../fonts-roboto_1%3a4.4.4r2-6ubuntu1_all.deb ... Unpacking fonts-roboto (1:4.4.4r2-6ubuntu1) ... Selecting previously unselected package libasyncns0:amd64. Preparing to unpack .../libasyncns0_0.8-5build1_amd64.deb ... Unpacking libasyncns0:amd64 (0.8-5build1) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../libgraphite2-3_1.2.4-3ubuntu1_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.2.4-3ubuntu1) ... Selecting previously unselected package x11-common. Preparing to unpack .../x11-common_1%3a7.7+12ubuntu1_all.deb ... Unpacking x11-common (1:7.7+12ubuntu1) ... Selecting previously unselected package libice6:amd64. Preparing to unpack .../libice6_2%3a1.0.9-1_amd64.deb ... Unpacking libice6:amd64 (2:1.0.9-1) ... Selecting previously unselected package libjpeg-turbo8:amd64. Preparing to unpack .../libjpeg-turbo8_1.3.0-0ubuntu2_amd64.deb ... Unpacking libjpeg-turbo8:amd64 (1.3.0-0ubuntu2) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../liblcms2-2_2.6-3ubuntu2_amd64.deb ... Unpacking liblcms2-2:amd64 (2.6-3ubuntu2) ... Selecting previously unselected package liblzo2-2:amd64. Preparing to unpack .../liblzo2-2_2.08-1.2_amd64.deb ... Unpacking liblzo2-2:amd64 (2.08-1.2) ... Selecting previously unselected package libogg0:amd64. Preparing to unpack .../libogg0_1.3.2-1_amd64.deb ... Unpacking libogg0:amd64 (1.3.2-1) ... Selecting previously unselected package libpcrecpp0v5:amd64. Preparing to unpack .../libpcrecpp0v5_2%3a8.35-7.1ubuntu1_amd64.deb ... Unpacking libpcrecpp0v5:amd64 (2:8.35-7.1ubuntu1) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../libsigsegv2_2.10-4_amd64.deb ... Unpacking libsigsegv2:amd64 (2.10-4) ... Selecting previously unselected package libsm6:amd64. Preparing to unpack .../libsm6_2%3a1.2.2-1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.2-1) ... Selecting previously unselected package libtcl8.6:amd64. Preparing to unpack .../libtcl8.6_8.6.4+dfsg-2ubuntu1_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.4+dfsg-2ubuntu1) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../libxrender1_1%3a0.9.9-0ubuntu1_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.9-0ubuntu1) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../libxft2_2.3.2-1_amd64.deb ... Unpacking libxft2:amd64 (2.3.2-1) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../libxss1_1%3a1.2.2-1_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.2-1) ... Selecting previously unselected package libtk8.6:amd64. 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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 (4.4.0~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-inconsolata (001.010-5) ... 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-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:amd64 (5.2.1-27ubuntu1) ... Setting up libgfortran-5-dev:amd64 (5.2.1-27ubuntu1) ... Setting up gfortran-5 (5.2.1-27ubuntu1) ... Setting up gfortran (4:5.2.1-16ubuntu2) ... 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:amd64 (1.46.0-3ubuntu1) ... Setting up libpangoxft-1.0-0:amd64 (1.38.1-1) ... Setting up gir1.2-pango-1.0:amd64 (1.38.1-1) ... Setting up libblas-common (1.2.20110419-11) ... Setting up libblas3 (1.2.20110419-11) ... 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 (1.2.20110419-11) ... update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode Setting up libbz2-dev:amd64 (1.0.6-8) ... Setting up libcairo-gobject2:amd64 (1.14.4-1) ... Setting up libcairo-script-interpreter2:amd64 (1.14.4-1) ... Setting up libexpat1-dev:amd64 (2.1.0-7) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2ubuntu4) ... Setting up libpng12-dev:amd64 (1.2.54-1) ... Setting up libfreetype6-dev:amd64 (2.5.2-4ubuntu2) ... Setting up pkg-config (0.29-2ubuntu1) ... Setting up libfontconfig1-dev:amd64 (2.11.1-0ubuntu6) ... Setting up xorg-sgml-doctools (1:1.11-1) ... Setting up x11proto-core-dev (7.0.28-0ubuntu1) ... Setting up libxau-dev:amd64 (1:1.0.8-1) ... Setting up libxdmcp-dev:amd64 (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:amd64 (0.3-4) ... Setting up libxcb1-dev:amd64 (1.11.1-1ubuntu1) ... Setting up libx11-dev:amd64 (2:1.6.3-1ubuntu2) ... Setting up x11proto-render-dev (2:0.11.1-2) ... Setting up libxrender-dev:amd64 (1:0.9.9-0ubuntu1) ... Setting up x11proto-xext-dev (7.3.0-1) ... Setting up libxext-dev:amd64 (2:1.3.3-1) ... Setting up libice-dev:amd64 (2:1.0.9-1) ... Setting up libsm-dev:amd64 (2:1.2.2-1) ... Setting up libpixman-1-dev (0.33.4-1) ... Setting up libxcb-render0-dev:amd64 (1.11.1-1ubuntu1) ... Setting up libxcb-shm0-dev:amd64 (1.11.1-1ubuntu1) ... Setting up libglib2.0-bin (2.47.3-3) ... Setting up libpcre16-3:amd64 (2:8.35-7.1ubuntu1) ... Setting up libpcre32-3:amd64 (2:8.35-7.1ubuntu1) ... Setting up libpcre3-dev:amd64 (2:8.35-7.1ubuntu1) ... Setting up libglib2.0-dev (2.47.3-3) ... Setting up libcairo2-dev (1.14.4-1) ... Setting up libcupsfilters1:amd64 (1.2.0-1) ... Setting up libcupsimage2:amd64 (2.1.0-7) ... Setting up libcurl3:amd64 (7.45.0-1ubuntu1) ... Setting up libcurl4-openssl-dev:amd64 (7.45.0-1ubuntu1) ... Setting up libijs-0.35:amd64 (0.35-11) ... Setting up libjbig2dec0 (0.12+20150918-1) ... Setting up libpaper1:amd64 (1.1.24+nmu4ubuntu1) ... Creating config file /etc/papersize with new version Setting up libgs9-common (9.16~dfsg~0-0ubuntu3) ... update-alternatives: using /usr/share/ghostscript/9.16 to provide /usr/share/ghostscript/current (ghostscript-current) in auto mode Setting up libgs9 (9.16~dfsg~0-0ubuntu3) ... Setting up libharfbuzz-icu0:amd64 (1.0.1-1build2) ... Setting up libharfbuzz-gobject0:amd64 (1.0.1-1build2) ... Setting up libharfbuzz-dev (1.0.1-1build2) ... Setting up libintl-perl (1.24-1) ... Setting up libjpeg-turbo8-dev:amd64 (1.3.0-0ubuntu2) ... Setting up libjpeg8-dev:amd64 (8c-2ubuntu8) ... Setting up libjpeg-dev:amd64 (8c-2ubuntu8) ... Setting up libkpathsea6:amd64 (2015.20150524.37493-7build2) ... Setting up liblapack3 (3.5.0-5) ... 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 (3.5.0-5) ... update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode Setting up libtinfo-dev:amd64 (5.9+20150516-2ubuntu1) ... Setting up libncurses5-dev:amd64 (5.9+20150516-2ubuntu1) ... Setting up libxft-dev (2.3.2-1) ... Setting up libpango1.0-dev (1.38.1-1) ... Setting up libpaper-utils (1.1.24+nmu4ubuntu1) ... Setting up libpoppler57:amd64 (0.38.0-0ubuntu1) ... Setting up libpotrace0 (1.12-1) ... Setting up libptexenc1:amd64 (2015.20150524.37493-7build2) ... Setting up libreadline6-dev:amd64 (6.3-8ubuntu1) ... Setting up libreadline-dev:amd64 (6.3-8ubuntu1) ... Setting up libsynctex1:amd64 (2015.20150524.37493-7build2) ... Setting up libtexlua52:amd64 (2015.20150524.37493-7build2) ... Setting up libtexluajit2:amd64 (2015.20150524.37493-7build2) ... Setting up libtext-unidecode-perl (1.27-1) ... Setting up libjbig-dev:amd64 (2.1-3.1) ... Setting up liblzma-dev:amd64 (5.1.1alpha+20120614-2ubuntu2) ... Setting up libtiffxx5:amd64 (4.0.5-1) ... Setting up libtiff5-dev:amd64 (4.0.5-1) ... Setting up libxkbfile1:amd64 (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 (2.0116+dfsg-5) ... 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:amd64 (1:1.2.2-1) ... Setting up libxt-dev:amd64 (1:1.1.5-0ubuntu1) ... Setting up mpack (1.6-8) ... Setting up tex-common (6.04) ... update-language: texlive-base not installed and configured, doing nothing! Setting up preview-latex-style (11.88-1.1ubuntu1) ... Setting up t1utils (1.38-4) ... Setting up tcl8.6 (8.6.4+dfsg-2ubuntu1) ... Setting up tcl8.6-dev:amd64 (8.6.4+dfsg-2ubuntu1) ... Setting up texinfo (6.0.0.dfsg.1-3) ... Running mktexlsr. This may take some time. ... done. Setting up texlive-binaries (2015.20150524.37493-7build2) ... 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 (1.1.0~rc3+git20150907-1ubuntu3) ... Setting up ttf-adf-universalis (0.20090423-2) ... Setting up fonts-stix (1.1.1-4) ... Setting up ttf-adf-gillius (0.20090423-2) ... Setting up ttf-adf-accanthis (0.20090423-2) ... Setting up tk8.6 (8.6.4+dfsg-2ubuntu1) ... Setting up tk8.6-dev:amd64 (8.6.4+dfsg-2ubuntu1) ... 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 (2:1.17.3-2ubuntu2) ... Setting up xvfb (2:1.17.3-2ubuntu2) ... Processing triggers for tex-common (6.04) ... update-language: texlive-base not installed and configured, doing nothing! texlive-base is not ready, skipping fmtutil-sys --all call Setting up texlive-base (2015.20150625-1ubuntu1) ... /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 (6.04) ... 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 (2015.20151116-1) ... Setting up texlive-fonts-recommended (2015.20150625-1ubuntu1) ... Setting up texlive-generic-recommended (2015.20150625-1ubuntu1) ... Setting up texlive-latex-base (2015.20150625-1ubuntu1) ... Processing triggers for tex-common (6.04) ... 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 (2015.20150625-1ubuntu1) ... Setting up texlive-pictures (2015.20150625-1ubuntu1) ... Setting up texlive-extra-utils (2015.20151116-1) ... Processing triggers for tex-common (6.04) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Setting up texlive-latex-extra (2015.20151116-1) ... Processing triggers for tex-common (6.04) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Setting up libnss3-nssdb (2:3.21-1ubuntu2) ... Setting up debhelper (9.20151126ubuntu1) ... Setting up libnss3:amd64 (2:3.21-1ubuntu2) ... Setting up openjdk-7-jre-headless:amd64 (7u91-2.6.3-2) ... update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up ca-certificates-java (20140324) ... Adding debian:SwissSign_Platinum_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Certinomis_-_Autorité_Racine.pem Adding debian:AddTrust_External_Root.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G3.pem Adding debian:ValiCert_Class_1_VA.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:Camerfirma_Global_Chambersign_Root.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:StartCom_Certification_Authority.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:ComSign_Secured_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:UTN_USERFirst_Hardware_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:ACEDICOM_Root.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:Izenpe.com.pem Adding debian:StartCom_Certification_Authority_G2.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Certum_Root_CA.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:PSCProcert.pem Adding debian:AddTrust_Qualified_Certificates_Root.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:TURKTRUST_Certificate_Services_Provider_Root_1.pem Adding debian:A-Trust-nQual-03.pem Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G2.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:S-TRUST_Authentication_and_Encryption_Root_CA_2005_PN.pem Adding debian:Swisscom_Root_CA_1.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Swisscom_Root_CA_2.pem Adding debian:SG_TRUST_SERVICES_RACINE.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:RSA_Root_Certificate_1.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:Entrust.net_Secure_Server_CA.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Equifax_Secure_eBusiness_CA_1.pem Adding debian:NetLock_Qualified_=Class_QA=_Root.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:UTN_USERFirst_Email_Root_CA.pem Adding debian:TC_TrustCenter_Class_2_CA_II.pem Adding debian:NetLock_Notary_=Class_A=_Root.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DST_ACES_CA_X6.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Thawte_Premium_Server_CA.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:Sonera_Class_1_Root_CA.pem Adding debian:AffirmTrust_Networking.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_2.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Digital_Signature_Trust_Co._Global_CA_3.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:Camerfirma_Chambers_of_Commerce_Root.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:RSA_Security_2048_v3.pem Adding debian:SecureTrust_CA.pem Adding debian:EC-ACC.pem Adding debian:Staat_der_Nederlanden_Root_CA.pem Adding debian:UTN_DATACorp_SGC_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Thawte_Server_CA.pem Adding debian:NetLock_Express_=Class_C=_Root.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:ValiCert_Class_2_VA.pem Adding debian:DST_Root_CA_X3.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority.pem Adding debian:AC_Raíz_Certicámara_S.A..pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:StartCom_Certification_Authority_2.pem Adding debian:WoSign.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:AffirmTrust_Premium.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:Comodo_Trusted_Services_root.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:Certigna.pem Adding debian:Buypass_Class_2_CA_1.pem Adding debian:Juur-SK.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:NetLock_Business_=Class_B=_Root.pem Adding debian:GeoTrust_Global_CA_2.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:Verisign_Class_4_Public_Primary_Certification_Authority_-_G3.pem Adding debian:TC_TrustCenter_Class_3_CA_II.pem Adding debian:WoSign_China.pem Adding debian:Equifax_Secure_Global_eBusiness_CA.pem Adding debian:CA_Disig_Root_R1.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:TÜBİTAK_UEKAE_Kök_Sertifika_Hizmet_Sağlayıcısı_-_Sürüm_3.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Swisscom_Root_EV_CA_2.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:AddTrust_Low-Value_Services_Root.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2.pem Adding debian:Root_CA_Generalitat_Valenciana.pem Adding debian:GTE_CyberTrust_Global_Root.pem Adding debian:Taiwan_GRCA.pem Adding debian:CA_Disig.pem Adding debian:Comodo_Secure_Services_root.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Equifax_Secure_CA.pem Adding debian:spi-cacert-2008.pem Adding debian:ApplicationCA_-_Japanese_Government.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:China_Internet_Network_Information_Center_EV_Certificates_Root.pem Adding debian:IGC_A.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Buypass_Class_3_CA_1.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G3.pem Adding debian:Visa_eCommerce_Root.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:ComSign_CA.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:Digital_Signature_Trust_Co._Global_CA_1.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:CNNIC_ROOT.pem Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2007.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:WellsSecure_Public_Root_Certificate_Authority.pem Adding debian:ACCVRAIZ1.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:AddTrust_Public_Services_Root.pem Adding debian:Security_Communication_EV_RootCA1.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G2.pem Adding debian:SecureSign_RootCA11.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:S-TRUST_Universal_Root_CA.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:EBG_Elektronik_Sertifika_Hizmet_Sağlayıcısı.pem Adding debian:TC_TrustCenter_Universal_CA_I.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:Microsec_e-Szigno_Root_CA.pem done. Setting up default-jre-headless (2:1.7-52.1) ... Setting up dh-strip-nondeterminism (0.014-1) ... Setting up openjdk-7-jre:amd64 (7u91-2.6.3-2) ... update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/policytool to provide /usr/bin/policytool (policytool) in auto mode Setting up default-jre (2:1.7-52.1) ... Setting up openjdk-7-jdk:amd64 (7u91-2.6.3-2) ... update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/wsimport to provide /usr/bin/wsimport (wsimport) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jsadebugd to provide /usr/bin/jsadebugd (jsadebugd) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/native2ascii to provide /usr/bin/native2ascii (native2ascii) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/javah to provide /usr/bin/javah (javah) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/idlj to provide /usr/bin/idlj (idlj) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/extcheck to provide /usr/bin/extcheck (extcheck) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/schemagen to provide /usr/bin/schemagen (schemagen) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/xjc to provide /usr/bin/xjc (xjc) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/appletviewer to provide /usr/bin/appletviewer (appletviewer) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jhat to provide /usr/bin/jhat (jhat) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/wsgen to provide /usr/bin/wsgen (wsgen) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode Setting up default-jdk (2:1.7-52.1) ... Setting up sbuild-build-depends-r-base-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Processing triggers for systemd (228-2ubuntu1) ... Processing triggers for ca-certificates (20150426ubuntu1) ... Updating certificates in /etc/ssl/certs... 7 added, 7 removed; done. Running hooks in /etc/ca-certificates/update.d... Replacing debian:Entrust.net_Secure_Server_CA.pem Replacing debian:GTE_CyberTrust_Global_Root.pem Replacing debian:RSA_Root_Certificate_1.pem Replacing debian:Thawte_Premium_Server_CA.pem Replacing debian:Thawte_Server_CA.pem Replacing debian:ValiCert_Class_1_VA.pem Replacing debian:ValiCert_Class_2_VA.pem Removing debian:Entrust.net_Secure_Server_CA.pem Removing debian:GTE_CyberTrust_Global_Root.pem Removing debian:RSA_Root_Certificate_1.pem Removing debian:Thawte_Premium_Server_CA.pem Removing debian:Thawte_Server_CA.pem Removing debian:ValiCert_Class_1_VA.pem Removing debian:ValiCert_Class_2_VA.pem done. done. ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.19.0-37-generic amd64 (x86_64) Toolchain package versions: binutils_2.25.90.20151125-2ubuntu1 dpkg-dev_1.18.3ubuntu1 g++-5_5.2.1-27ubuntu1 gcc-5_5.2.1-27ubuntu1 libc6-dev_2.21-0ubuntu5 libstdc++-5-dev_5.2.1-27ubuntu1 libstdc++6_5.2.1-27ubuntu1 linux-libc-dev_4.3.0-1.10 Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.1.3 apt-transport-https_1.1.3 base-files_9.4ubuntu3 base-passwd_3.5.38 bash_4.3-14ubuntu1 bash-completion_1:2.1-4.2ubuntu1 binutils_2.25.90.20151125-2ubuntu1 bison_2:3.0.4.dfsg-1 bsdmainutils_9.0.6ubuntu1 bsdutils_1:2.27.1-1ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8 ca-certificates_20150426ubuntu1 ca-certificates-java_20140324 coreutils_8.23-4ubuntu2 cpp_4:5.2.1-16ubuntu2 cpp-5_5.2.1-27ubuntu1 dash_0.5.7-4ubuntu2 debconf_1.5.58ubuntu1 debhelper_9.20151126ubuntu1 debianutils_4.5.1 default-jdk_2:1.7-52.1 default-jre_2:1.7-52.1 default-jre-headless_2:1.7-52.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dmsetup_2:1.02.99-1ubuntu1 dpkg_1.18.3ubuntu1 dpkg-dev_1.18.3ubuntu1 e2fslibs_1.42.13-1ubuntu1 e2fsprogs_1.42.13-1ubuntu1 fakeroot_1.20.2-1ubuntu1 file_1:5.25-2ubuntu1 findutils_4.4.2-10 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openjdk-7-jdk_7u91-2.6.3-2 openjdk-7-jre_7u91-2.6.3-2 openjdk-7-jre-headless_7u91-2.6.3-2 openssl_1.0.2d-0ubuntu2 optipng_0.7.5-1 passwd_1:4.1.5.1-1.1ubuntu7 patch_2.7.5-1 perl_5.20.2-6 perl-base_5.20.2-6 perl-modules_5.20.2-6 pkg-config_0.29-2ubuntu1 pkg-create-dbgsym_0.70 pkgbinarymangler_123 po-debconf_1.0.18 policyrcd-script-zg2_0.1-2 poppler-data_0.4.7-5 preview-latex-style_11.88-1.1ubuntu1 procps_1:3.3.9-1ubuntu8 python_2.7.9-1 python-minimal_2.7.9-1 python2.7_2.7.10-4ubuntu2 python2.7-minimal_2.7.10-4ubuntu2 readline-common_6.3-8ubuntu1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-base-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 shared-mime-info_1.5-2 systemd_228-2ubuntu1 systemd-sysv_228-2ubuntu1 sysv-rc_2.88dsf-59.2ubuntu3 sysvinit-utils_2.88dsf-59.2ubuntu3 t1utils_1.38-4 tar_1.28-2.1 tcl8.6_8.6.4+dfsg-2ubuntu1 tcl8.6-dev_8.6.4+dfsg-2ubuntu1 tex-common_6.04 texinfo_6.0.0.dfsg.1-3 texlive-base_2015.20150625-1ubuntu1 texlive-binaries_2015.20150524.37493-7build2 texlive-extra-utils_2015.20151116-1 texlive-fonts-extra_2015.20151116-1 texlive-fonts-recommended_2015.20150625-1ubuntu1 texlive-generic-recommended_2015.20150625-1ubuntu1 texlive-latex-base_2015.20150625-1ubuntu1 texlive-latex-extra_2015.20151116-1 texlive-latex-recommended_2015.20150625-1ubuntu1 texlive-pictures_2015.20150625-1ubuntu1 tk8.6_8.6.4+dfsg-2ubuntu1 tk8.6-dev_8.6.4+dfsg-2ubuntu1 ttf-adf-accanthis_0.20090423-2 ttf-adf-gillius_0.20090423-2 ttf-adf-universalis_0.20090423-2 tzdata_2015g-1 tzdata-java_2015g-1 ubuntu-keyring_2012.05.19 ucf_3.0031 udev_228-2ubuntu1 util-linux_2.27.1-1ubuntu3 x11-common_1:7.7+12ubuntu1 x11-utils_7.7+3 x11-xkb-utils_7.7+2 x11proto-core-dev_7.0.28-0ubuntu1 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_1.1.0~rc3+git20150907-1ubuntu3 xfonts-base_1:1.0.4+nmu1 xfonts-encodings_1:1.0.4-2 xfonts-utils_1:7.7+3 xkb-data_2.12-1ubuntu1 xorg-sgml-doctools_1:1.11-1 xserver-common_2:1.17.3-2ubuntu2 xtrans-dev_1.3.5-1 xvfb_2:1.17.3-2ubuntu2 xz-utils_5.1.1alpha+20120614-2ubuntu2 zlib1g_1:1.2.8.dfsg-2ubuntu4 zlib1g-dev_1:1.2.8.dfsg-2ubuntu4 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: Signature made Fri Dec 4 04:45:21 2015 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_3.2.2.20151203-1.dsc dpkg-source: info: extracting r-base in r-base-3.2.2.20151203 dpkg-source: info: unpacking r-base_3.2.2.20151203.orig.tar.gz dpkg-source: info: applying r-base_3.2.2.20151203-1.diff.gz dpkg-source: info: upstream files that have been modified: r-base-3.2.2.20151203/src/modules/X11/devX11.c r-base-3.2.2.20151203/src/modules/X11/rlogo_icon.h Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C 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 3.2.2.20151203-1 dpkg-buildpackage: source distribution unstable dpkg-source --before-build r-base-3.2.2.20151203 dpkg-buildpackage: host architecture amd64 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 *** configure *** #automake #autoconf dh_testdir R_PAPERSIZE=letter \ R_BROWSER=xdg-open \ 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 -D_FORTIFY_SOURCE=2 -g" \ CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -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 x86_64-linux-gnu checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu loading site script './config.site' loading build-specific script './config.site' checking for pwd... /bin/pwd checking whether builddir is srcdir... yes checking for working aclocal... missing checking for working autoconf... missing checking for working automake... missing checking for working autoheader... missing checking for gawk... 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(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/bzip2/Makefile config.status: creating src/extra/intl/Makefile config.status: creating src/extra/pcre/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/extra/xz/Makefile config.status: creating src/extra/zlib/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 R is now configured for x86_64-pc-linux-gnu Source directory: . Installation directory: /usr C compiler: gcc -std=gnu99 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -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 -D_FORTIFY_SOURCE=2 -g C++ 11 compiler: g++ -std=c++11 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -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), zlib, bzlib, lzma, PCRE, curl Additional capabilities: PNG, JPEG, TIFF, NLS, cairo Options enabled: shared R library, R profiling, memory profiling Capabilities skipped: ICU 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 -D_FORTIFY_SOURCE=2 -g" \ CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -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 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c xmalloc.c -o xmalloc.o rm -f libtre.a 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 -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 -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 -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 -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 -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 -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 rm -f libappl.a 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -D_FORTIFY_SOURCE=2 -g -c signrank.c -o signrank.o rm -rf libnmath.a 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 -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 -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 -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 -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 -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 -D_FORTIFY_SOURCE=2 -g -c X11.c -o X11.o rm -rf libunix.a 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 -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 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -D_FORTIFY_SOURCE=2 -g -c main.c -o main.o main.c: In function 'dummy_ii': main.c:1606:12: 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 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 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 -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 -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 -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 -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 -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 -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 -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 -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 -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/x86_64-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 -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. -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/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c devX11.c -o devX11.o 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/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rotated.c -o rotated.o 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/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -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 -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng12 -lz -lcairo -lX11 -lXext -lX11 -lXt -ltiff -ljpeg -lpng -lz -lR -lm 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/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -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 -lpng12 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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' 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I../../../../../src/modules/X11 -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -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 -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng12 -lz -lcairo -ltiff -ljpeg -lpng -lz -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 -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 -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 -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 -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 -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 -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 -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 -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c kmeans.c -o kmeans.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ansari.c -o ansari.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c bandwidths.c -o bandwidths.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c chisqsim.c -o chisqsim.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c d2x2xk.c -o d2x2xk.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fexact.c -o fexact.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c kendall.c -o kendall.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ks.c -o ks.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c line.c -o line.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c smooth.c -o smooth.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c prho.c -o prho.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c swilk.c -o swilk.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ksmooth.c -o ksmooth.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c loessc.c -o loessc.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c monoSpl.c -o monoSpl.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c isoreg.c -o isoreg.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Srunmed.c -o Srunmed.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c dblcen.c -o dblcen.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c distance.c -o distance.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c hclust-utils.c -o hclust-utils.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c nls.c -o nls.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rWishart.c -o rWishart.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c HoltWinters.c -o HoltWinters.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c PPsum.c -o PPsum.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c arima.c -o arima.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c burg.c -o burg.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c filter.c -o filter.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c mAR.c -o mAR.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c pacf.c -o pacf.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c starma.c -o starma.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c port.c -o port.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c family.c -o family.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c sbart.c -o sbart.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c approx.c -o approx.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c loglin.c -o loglin.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c lowess.c -o lowess.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c massdist.c -o massdist.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c splines.c -o splines.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c lm.c -o lm.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c complete_cases.c -o complete_cases.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c cov.c -o cov.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c deriv.c -o deriv.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fft.c -o fft.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fourier.c -o fourier.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c model.c -o model.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c optim.c -o optim.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c optimize.c -o optimize.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c integrate.c -o integrate.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c random.c -o random.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c distn.c -o distn.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c zeroin.c -o zeroin.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rcont.c -o rcont.o gcc -std=gnu99 -I -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -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 -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 -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 -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/x86_64-linux-gnu -ltcl8.6 -L/usr/lib/x86_64-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 -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 -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 -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 -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ FFLAGS="-g -O2 -fstack-protector-strong -D_REENTRANT" \ CC="gcc -std=gnu99" \ CXX=g++ \ F77=gfortran \ 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_i.c -o bessel_i.lo In file included from bessel_i.c:26:0: bessel_i.c: In function 'bessel_i': bessel_i.c:77:25: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_i(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_i.c:77:23: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_i(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_i.c:77:25: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_i(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_i.c:77:23: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_i(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_i.c: In function 'bessel_i_ex': bessel_i.c:122:25: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_i(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_i.c:122:23: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_i(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_i.c:122:25: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_i(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_i.c:122:23: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_i(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ 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 -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_j.c -o bessel_j.lo In file included from bessel_j.c:27:0: bessel_j.c: In function 'bessel_j': bessel_j.c:79:21: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_j(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_j.c:79:19: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_j(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_j.c:79:21: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_j(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_j.c:79:19: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_j(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_j.c: In function 'bessel_j_ex': bessel_j.c:125:21: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_j(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_j.c:125:19: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_j(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_j.c:125:21: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_j(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_j.c:125:19: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_j(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ 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 -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_k.c -o bessel_k.lo In file included from bessel_k.c:27:0: bessel_k.c: In function 'bessel_k': bessel_k.c:71:21: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_k(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_k.c:71:19: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_k(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_k.c:71:21: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_k(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_k.c:71:19: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_k(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_k.c: In function 'bessel_k_ex': bessel_k.c:108:21: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_k(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_k.c:108:19: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_k(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_k.c:108:21: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_k(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_k.c:108:19: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_k(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ 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 -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_y.c -o bessel_y.lo In file included from bessel_y.c:26:0: bessel_y.c: In function 'bessel_y': bessel_y.c:86:25: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_y(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_y.c:86:23: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_y(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_y.c:86:25: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_y(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_y.c:86:23: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_y(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_y.c: In function 'bessel_y_ex': bessel_y.c:134:25: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_y(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_y.c:134:23: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_y(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_y.c:134:25: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_y(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_y.c:134:23: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_y(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbeta.c -o qbeta.lo In file included from qbeta.c:33:0: ../../../src/include/R_ext/Arith.h:89:0: warning: "R_FINITE" redefined # define R_FINITE(x) isfinite(x) ^ In file included from qbeta.c:31:0: ./../nmath.h:107:0: note: this is the location of the previous definition #define R_FINITE(x) R_finite(x) ^ 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_i.c -o bessel_i.o In file included from bessel_i.c:26:0: bessel_i.c: In function 'bessel_i': bessel_i.c:77:25: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_i(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_i.c:77:23: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_i(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_i.c:77:25: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_i(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_i.c:77:23: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_i(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_i.c: In function 'bessel_i_ex': bessel_i.c:122:25: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_i(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_i.c:122:23: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_i(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_i.c:122:25: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_i(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_i.c:122:23: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_i(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ 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 -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_j.c -o bessel_j.o In file included from bessel_j.c:27:0: bessel_j.c: In function 'bessel_j': bessel_j.c:79:21: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_j(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_j.c:79:19: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_j(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_j.c:79:21: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_j(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_j.c:79:19: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_j(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_j.c: In function 'bessel_j_ex': bessel_j.c:125:21: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_j(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_j.c:125:19: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_j(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_j.c:125:21: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_j(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_j.c:125:19: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_j(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ 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 -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_k.c -o bessel_k.o In file included from bessel_k.c:27:0: bessel_k.c: In function 'bessel_k': bessel_k.c:71:21: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_k(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_k.c:71:19: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_k(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_k.c:71:21: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_k(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_k.c:71:19: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_k(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_k.c: In function 'bessel_k_ex': bessel_k.c:108:21: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_k(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_k.c:108:19: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_k(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_k.c:108:21: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_k(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_k.c:108:19: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_k(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ 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 -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_y.c -o bessel_y.o In file included from bessel_y.c:26:0: bessel_y.c: In function 'bessel_y': bessel_y.c:86:25: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_y(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_y.c:86:23: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_y(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_y.c:86:25: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_y(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_y.c:86:23: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_y(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_y.c: In function 'bessel_y_ex': bessel_y.c:134:25: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_y(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_y.c:134:23: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_y(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ bessel_y.c:134:25: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] MATHLIB_WARNING4(_("bessel_y(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ ./../nmath.h:103:49: note: in definition of macro 'MATHLIB_WARNING4' #define MATHLIB_WARNING4(fmt,x,x2,x3,x4) printf(fmt,x,x2,x3,x4) ^ bessel_y.c:134:23: note: in expansion of macro '_' MATHLIB_WARNING4(_("bessel_y(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range?\n"), ^ 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbeta.c -o qbeta.o In file included from qbeta.c:33:0: ../../../src/include/R_ext/Arith.h:89:0: warning: "R_FINITE" redefined # define R_FINITE(x) isfinite(x) ^ In file included from qbeta.c:31:0: ./../nmath.h:107:0: note: this is the location of the previous definition #define R_FINITE(x) R_finite(x) ^ 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 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-fstack-protector-strong -Wformat -Werror=format-security -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 -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 -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 -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 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-I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -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 -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' /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 -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' 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 -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' 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 : 1.7.0_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$(JAVA_HOME)/include detected JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm make[3]: Entering directory '/tmp/Rjavareconf.de2xFL' gcc -std=gnu99 -I/«PKGBUILDDIR»/include -DNDEBUG -I/usr/lib/jvm/default-java/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -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/amd64/server -ljvm -L/«PKGBUILDDIR»/lib -lR make[3]: Leaving directory '/tmp/Rjavareconf.de2xFL' JAVA_HOME : /usr/lib/jvm/default-java Java library path: $(JAVA_HOME)/jre/lib/amd64/server JNI cpp flags : -I$(JAVA_HOME)/include JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm Updating Java configuration in /«PKGBUILDDIR» Done. make[2]: Leaving directory '/«PKGBUILDDIR»' make[1]: Leaving directory '/«PKGBUILDDIR»' touch make-arch-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' ... OK Testing examples for package 'datasets' comparing 'datasets-Ex.Rout' to 'datasets-Ex.Rout.save' ... OK Testing examples for package 'methods' Testing examples for package 'grid' comparing 'grid-Ex.Rout' to 'grid-Ex.Rout.save' ... OK Testing examples for package 'splines' comparing 'splines-Ex.Rout' to 'splines-Ex.Rout.save' ... OK Testing examples for package 'stats4' comparing 'stats4-Ex.Rout' to 'stats4-Ex.Rout.save' ... OK Testing examples for package 'tcltk' Testing examples for package 'compiler' Testing examples for package 'parallel' make[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 'array-subset.R' ... OK comparing 'array-subset.Rout' to './array-subset.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' ... 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 '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 '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' ...Makefile.common:93: recipe for target 'reg-BLAS.Rout' failed make[4]: *** [reg-BLAS.Rout] Error 1 make[4]: Leaving directory '/«PKGBUILDDIR»/tests' Makefile.common:260: recipe for target 'test-Reg' failed make[3]: *** [test-Reg] Error 2 make[3]: Leaving directory '/«PKGBUILDDIR»/tests' Makefile.common:159: recipe for target 'test-all-basics' failed make[2]: *** [test-all-basics] Error 1 make[2]: Leaving directory '/«PKGBUILDDIR»/tests' Makefile:239: recipe for target 'check-all' failed make[1]: *** [check-all] Error 2 make[1]: Leaving directory '/«PKGBUILDDIR»' debian/rules:360: recipe for target 'check-stamp' failed make: [check-stamp] Error 2 (ignored) touch check-stamp fakeroot debian/rules binary *** make-indep *** /usr/bin/make 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 -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' 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 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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 <2015/01/01> Babel <3.9l> and hyphenation patterns for 2 languages 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 511--517 []\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 1122--1125 []\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 1339--1345 []\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] Overfull \hbox (26.88089pt too wide) in paragraph at lines 1849--1849 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [30] [31] [32] Underfull \hbox (badness 10000) in paragraph at lines 2034--2036 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] Underfull \hbox (badness 10000) in paragraph at lines 3532--3534 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [56] [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 4728--4730 []\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] [93] Underfull \hbox (badness 2096) in paragraph at lines 5945--5958 []\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 [94] [95] [96] Overfull \hbox (58.35893pt too wide) in paragraph at lines 6146--6149 []\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 : [97] [98] Underfull \hbox (badness 10000) in paragraph at lines 6290--6293 []\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 [99] [100] Underfull \hbox (badness 1442) in paragraph at lines 6451--6457 []\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 6451--6457 \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 6451--6457 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). 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[112] Underfull \hbox (badness 4595) in paragraph at lines 7206--7209 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [113] Underfull \hbox (badness 3000) in paragraph at lines 7242--7244 []\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 7267--7270 [][][]\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 , [114] [115] [116] [117] Underfull \hbox (badness 10000) in paragraph at lines 7517--7528 []\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 [118] Underfull \hbox (badness 4479) in paragraph at lines 7589--7598 [][][]\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 7589--7598 [][]\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 [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] Underfull \hbox (badness 1394) in paragraph at lines 9200--9205 []\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 [144] [145] [146] [147] [148] Underfull \hbox (badness 1052) in paragraph at lines 9537--9542 []\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 9537--9542 \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 [149] [150] Underfull \hbox (badness 1735) in paragraph at lines 9675--9679 \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 . [151] [152] [153] [154] [155] [156] Underfull \hbox (badness 2150) in paragraph at lines 10079--10082 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse [157] Underfull \hbox (badness 6396) in paragraph at lines 10093--10101 []\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 10134--10141 []\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 [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] Underfull \hbox (badness 4569) in paragraph at lines 11178--11182 []\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 11178--11182 \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 [174] [175] [176] [177] [178] [179] [180] [181] Underfull \hbox (badness 2698) in paragraph at lines 11754--11763 []\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 11754--11763 \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 [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] Underfull \hbox (badness 6236) in paragraph at lines 12398--12401 []\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 [192] [193] [194] [195] [196] [197] Underfull \hbox (badness 2253) in paragraph at lines 12776--12778 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [198] Underfull \hbox (badness 1565) in paragraph at lines 12847--12851 [][][]\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 [199] Underfull \hbox (badness 10000) in paragraph at lines 12891--12893 []\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 [200] [201] Underfull \hbox (badness 1466) in paragraph at lines 13032--13035 []\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 [202] [203] Underfull \hbox (badness 10000) in paragraph at lines 13140--13144 [][][]\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 13151--13154 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [204] [205] [206] [207] Underfull \hbox (badness 3965) in paragraph at lines 13403--13407 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] Underfull \hbox (badness 4429) in paragraph at lines 14133--14136 []\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 [219] Underfull \hbox (badness 10000) in paragraph at lines 14225--14227 []\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 14231--14235 []\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 [220] Underfull \hbox (badness 10000) in paragraph at lines 14273--14277 []\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 14273--14277 \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 [221] Underfull \vbox (badness 3803) has occurred while \output is active [222] [223] [224] [225] [226] [227] [228] [229] Underfull \hbox (badness 2452) in paragraph at lines 14853--14857 []\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 14853--14857 \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 [230] [231] [232] Underfull \hbox (badness 1092) in paragraph at lines 15026--15031 [][]\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 [233] [234] [235] [236] Underfull \hbox (badness 6741) in paragraph at lines 15274--15278 \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 , [237] [238] [239] [240] Underfull \hbox (badness 1867) in paragraph at lines 15580--15587 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [241] [242] [243] [244] Underfull \vbox (badness 10000) has occurred while \output is active [245] [246] Underfull \hbox (badness 3679) in paragraph at lines 15960--15962 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [247] [248] [249] [250] [251] [252] [253] Underfull \hbox (badness 1478) in paragraph at lines 16440--16443 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [254] [255] [256] [257] Underfull \hbox (badness 10000) in paragraph at lines 16693--16695 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [258] [259] [260] [261] [262] [263] [264] [265] [266] Underfull \hbox (badness 1442) in paragraph at lines 17256--17258 []\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 [267] Underfull \hbox (badness 2452) in paragraph at lines 17348--17364 [][][]\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 , [268] [269] [270] [271] [272] [273] [274] Underfull \hbox (badness 1248) in paragraph at lines 17756--17759 []\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 , [275] [276] [277] [278] Underfull \hbox (badness 4739) in paragraph at lines 18012--18014 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [279] [280] [281] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] Underfull \hbox (badness 1360) in paragraph at lines 18960--18965 \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 18983--18989 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / Underfull \hbox (badness 1127) in paragraph at lines 18983--18989 \T1/zi4/m/n/10 ssl-[]compared . html$[][] \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 [295] Underfull \hbox (badness 10000) in paragraph at lines 19056--19060 []\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 19056--19060 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [296] [297] Underfull \hbox (badness 1509) in paragraph at lines 19191--19198 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1354) in paragraph at lines 19191--19198 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19207--19212 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] [309] Underfull \hbox (badness 1264) in paragraph at lines 19938--19943 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] Underfull \hbox (badness 10000) in paragraph at lines 20692--20694 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] Underfull \hbox (badness 1077) in paragraph at lines 21690--21696 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [337] [338] [339] Underfull \hbox (badness 1484) in paragraph at lines 21851--21859 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [340] [341] [342] [343] Underfull \hbox (badness 2790) in paragraph at lines 22122--22125 []\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 22122--22125 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [344] [345] [346] [347] Underfull \hbox (badness 1194) in paragraph at lines 22403--22406 []\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 [348] [349] [350] [351] Underfull \hbox (badness 10000) in paragraph at lines 22609--22615 []\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 22609--22615 \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 22619--22622 []\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 22619--22622 \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 [352] [353] [354] [355] [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] Underfull \hbox (badness 10000) in paragraph at lines 23544--23546 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [366] [367] [368] [369] Underfull \hbox (badness 1199) in paragraph at lines 23771--23777 []\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 23771--23777 \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, [370] [371] [372] [373] [374] [375] [376] [377] Underfull \hbox (badness 1038) in paragraph at lines 24336--24344 []\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 24345--24348 []\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 24364--24366 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [378] Underfull \hbox (badness 10000) in paragraph at lines 24436--24446 []\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 24447--24453 []\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 24460--24465 []\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 24470--24472 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [379] [380] [381] Underfull \hbox (badness 10000) in paragraph at lines 24721--24727 []\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 24721--24727 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "http://bioconductor.org"\T1/p tm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 24721--24727 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "http://bioconductor.statistik.tu-dortmund.de"\T 1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 24734--24737 []\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 [382] Underfull \hbox (badness 2689) in paragraph at lines 24758--24760 []\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 24790--24795 []\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 24796--24807 \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 24808--24811 []\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 Underfull \hbox (badness 4084) in paragraph at lines 24818--24830 \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 24818--24830 \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 24818--24830 \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 24832--24839 []\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 24832--24839 \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 24832--24839 \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 24832--24839 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [383] [384] [385] [386] [387] Underfull \hbox (badness 10000) in paragraph at lines 25153--25157 []\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 25153--25157 \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)] [388] [389] [390] [391] [392] Underfull \hbox (badness 1735) in paragraph at lines 25471--25475 []\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 [393] [394] [395] [396] [397] [398] [399] [400] [401] [402] Underfull \hbox (badness 2726) in paragraph at lines 26030--26033 []\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 [403] [404] [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] [415] Underfull \hbox (badness 1052) in paragraph at lines 26849--26854 []\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 [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] Underfull \hbox (badness 1533) in paragraph at lines 27577--27580 []\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 [427] [428] Underfull \hbox (badness 1163) in paragraph at lines 27739--27749 []\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 [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] Underfull \hbox (badness 10000) in paragraph at lines 29241--29245 []\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 29241--29245 \T1/zi4/m/n/10 "(?[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 29263--29265 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [453] [454] [455] [456] [457] [458] [459] [460] [461] Underfull \hbox (badness 1655) in paragraph at lines 29808--29810 []\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 [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] Underfull \hbox (badness 10000) in paragraph at lines 30476--30480 []\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., [473] [474] [475] Underfull \hbox (badness 2302) in paragraph at lines 30716--30723 []\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 30716--30723 \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 30716--30723 \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 30716--30723 \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 [476] [477] [478] Underfull \hbox (badness 2261) in paragraph at lines 30870--30875 []\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 30897--30903 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [479] Underfull \hbox (badness 10000) in paragraph at lines 30973--30978 []\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 [480] [481] [482] [483] [484] [485] [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] Underfull \hbox (badness 1072) in paragraph at lines 33757--33761 []\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 33762--33766 []\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 ', [523] Underfull \hbox (badness 10000) in paragraph at lines 33790--33796 []\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 33790--33796 \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 33790--33796 \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 33803--33810 \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 33803--33810 \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 33803--33810 \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 [524] [525] [526] [527] [528] Underfull \hbox (badness 10000) in paragraph at lines 34094--34100 []\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 34094--34100 \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 [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] Underfull \hbox (badness 3333) in paragraph at lines 35877--35882 []\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 [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] Underfull \hbox (badness 1472) in paragraph at lines 36497--36500 []\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 [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] Underfull \hbox (badness 2671) in paragraph at lines 37159--37162 []\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 [578] [579] [580] [581] [582] [583] Underfull \hbox (badness 10000) in paragraph at lines 37563--37566 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$http : / / developer . r-[]project . org / [584] [585] Underfull \hbox (badness 10000) in paragraph at lines 37684--37688 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 http : / / developer . [586] Underfull \hbox (badness 10000) in paragraph at lines 37746--37750 [][][]\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 http : / / developer . [587] [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] Underfull \hbox (badness 1990) in paragraph at lines 39041--39049 []\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 39041--39049 \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 [606] [607] [608] [609] [610] Underfull \hbox (badness 1515) in paragraph at lines 39313--39318 []\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 [611] [612] [613] Underfull \hbox (badness 1917) in paragraph at lines 39543--39550 []\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 [614] [615] [616] [617] [618] [619] [620] [621] [622] Underfull \hbox (badness 3668) in paragraph at lines 40128--40130 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [623] [624] Underfull \hbox (badness 2401) in paragraph at lines 40233--40237 []\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 [625] [626] [627] Underfull \hbox (badness 2111) in paragraph at lines 40402--40407 \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. Underfull \hbox (badness 6542) in paragraph at lines 40418--40423 []\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 [628] [629] [630] [631] [632] [633] [634] Underfull \hbox (badness 10000) in paragraph at lines 40863--40868 []\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 40863--40868 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to [635] [636] Underfull \hbox (badness 5417) in paragraph at lines 40955--40959 []\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 [637] Underfull \hbox (badness 10000) in paragraph at lines 41016--41020 []\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 [638]) (./compiler-pkg.tex Chapter 2. [639] [640] [641] [642]) (./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 [643] [644] [645] [646] [647] [648] [649] [650] [651] [652] [653] [654] [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] Underfull \vbox (badness 1515) has occurred while \output is active [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] 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 / [710] Underfull \vbox (badness 10000) has occurred while \output is active [711] [712] [713] [714] Underfull \vbox (badness 10000) has occurred while \output is active [715] Underfull \vbox (badness 10000) has occurred while \output is active [716] [717] [718] [719] [720] [721] [722] [723]) (./grDevices-pkg.tex [724] Chapter 4. [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] Underfull \hbox (badness 5175) in paragraph at lines 1066--1068 []\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 [742] [743] [744] [745] Underfull \hbox (badness 1852) in paragraph at lines 1263--1266 []\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 [746] [747] [748] Underfull \hbox (badness 1490) in paragraph at lines 1469--1474 \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 [749] Underfull \hbox (badness 2698) in paragraph at lines 1523--1526 []\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 [750] Underfull \hbox (badness 10000) in paragraph at lines 1592--1596 []\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 [751] [752] [753] [754] Underfull \hbox (badness 1325) in paragraph at lines 1875--1885 \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 , [755] [756] Underfull \hbox (badness 10000) in paragraph at lines 1980--1982 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [757] [758] [759] Underfull \hbox (badness 6758) in paragraph at lines 2141--2144 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [760] [761] [762] [763] [764] [765] [766] [767] [768] Underfull \hbox (badness 10000) in paragraph at lines 2707--2708 [769] [770] [771] [772] [773] [774] [775] Underfull \hbox (badness 1152) in paragraph at lines 3145--3147 []\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 [776] [777] [778] [779] [780] Underfull \hbox (badness 2856) in paragraph at lines 3465--3468 []\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 3479--3481 []\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 [781] [782] Underfull \hbox (badness 1173) in paragraph at lines 3595--3605 []\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 [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] Underfull \hbox (badness 1067) in paragraph at lines 4302--4309 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [794] [795] Underfull \hbox (badness 3364) in paragraph at lines 4463--4465 []\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 / [796] Underfull \hbox (badness 1789) in paragraph at lines 4540--4542 []\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 [797] Underfull \hbox (badness 1377) in paragraph at lines 4590--4595 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [798] Underfull \hbox (badness 2671) in paragraph at lines 4617--4625 \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 4666--4673 \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 4674--4683 \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 4674--4683 \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 4684--4686 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [799] [800] Underfull \hbox (badness 1057) in paragraph at lines 4795--4800 []\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 [801] Underfull \hbox (badness 7344) in paragraph at lines 4855--4857 []\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 [802] [803] Underfull \hbox (badness 2035) in paragraph at lines 4979--4988 []\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 4979--4988 \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 4979--4988 \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 , [804] Underfull \hbox (badness 10000) in paragraph at lines 5048--5055 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5048--5055 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [805] [806] [807] Underfull \hbox (badness 1546) in paragraph at lines 5186--5194 []\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 , [808] Underfull \hbox (badness 1648) in paragraph at lines 5263--5267 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [809] [810] [811] [812] [813] [814] [815] Underfull \hbox (badness 10000) in paragraph at lines 5686--5689 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [816] Underfull \vbox (badness 3803) has occurred while \output is active [817] [818] [819] [820] [821] Underfull \hbox (badness 1189) in paragraph at lines 6083--6085 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [822] [823] Underfull \hbox (badness 10000) in paragraph at lines 6181--6183 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [824] [825] [826] [827] Underfull \hbox (badness 3780) in paragraph at lines 6472--6478 []\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 , [828] [829] [830] Underfull \hbox (badness 2680) in paragraph at lines 6668--6670 []\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 [831] [832] [833]) (./graphics-pkg.tex [834] Chapter 5. [835] [836] [837] [838] [839] [840] [841] [842] [843] [844] [845] 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 [846] [847] [848] [849] Underfull \vbox (badness 3803) has occurred while \output is active [850] [851] [852] [853] [854] 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 , [855] [856] [857] [858] [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] [869] [870] [871] Underfull \hbox (badness 1009) in paragraph at lines 2277--2284 \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 [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] Underfull \vbox (badness 10000) has occurred while \output is active [894] Underfull \vbox (badness 10000) has occurred while \output is active [895] [896] [897] [898] Underfull \hbox (badness 1867) in paragraph at lines 3901--3905 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [899] [900] [901] [902] [903] [904] [905] Underfull \hbox (badness 1924) in paragraph at lines 4348--4353 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain [906] Underfull \hbox (badness 2529) in paragraph at lines 4379--4382 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used: see [907] [908] [909] [910] [911] Underfull \hbox (badness 10000) in paragraph at lines 4729--4735 []\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 4729--4735 \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 [912] Underfull \hbox (badness 10000) in paragraph at lines 4860--4863 [913] [914 ] Underfull \hbox (badness 10000) in paragraph at lines 4921--4923 [915 ] [916] Underfull \hbox (badness 10000) in paragraph at lines 5111--5113 []\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 [917] [918] [919] [920] [921] Underfull \vbox (badness 10000) has occurred while \output is active [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6581--6582 [][] [941 ] [942] Underfull \vbox (badness 10000) has occurred while \output is active [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] Underfull \hbox (badness 1048) in paragraph at lines 7290--7295 \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 [953] Underfull \hbox (badness 1038) in paragraph at lines 7406--7409 []\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 [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] [971] [972] [973] [974] Underfull \hbox (badness 6691) in paragraph at lines 8625--8628 []\T1/ptm/m/n/10 The main ti-tle (on top) us-ing font and size (char-ac-ter ex- pan-sion) Underfull \hbox (badness 2799) in paragraph at lines 8628--8630 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font and size \T1/zi4/m/n/10 par ("font.sub") \T1/ptm/m/n/10 and color [975] [976]pdfTeX warning (ext4): destination with the same identifier (name{Rf n.units}) has been already used, duplicate ignored \relax l.8710 \HeaderA{units}{Graphical Units}{units} [977] [978] [979] [980]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [981] [982] [983] [984] [985] [986] 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 [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] 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 , [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [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] Underfull \vbox (badness 3803) has occurred while \output is active [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] 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 [1054] [1055] [1056] [1057] 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 [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] Underfull \hbox (badness 10000) in paragraph at lines 5854--5860 \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., [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] Underfull \hbox (badness 7649) in paragraph at lines 6324--6327 []\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 [1087] [1088] [1089] [1090]) (./methods-pkg.tex Chapter 7. [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] 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 [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] 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 [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] 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 [1128] [1129] 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 [1130] 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 [1131] [1132] [1133] [1134] [1135] [1136] [1137] 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 [1138] [1139] [1140] [1141] [1142] 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 [1143] [1144] [1145] [1146] [1147] [1148] Underfull \vbox (badness 10000) has occurred while \output is active [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156] 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 [1157] [1158] [1159] [1160] [1161] [1162] Underfull \vbox (badness 2452) has occurred while \output is active [1163] [1164] Underfull \vbox (badness 10000) has occurred while \output is active [1165] [1166] 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 [1167] [1168] [1169] [1170] [1171] 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 [1172] [1173] [1174] [1175] 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 [1176] [1177] [1178] [1179] [1180] Underfull \hbox (badness 1675) in paragraph at lines 6343--6349 \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 [1181] [1182] [1183] [1184] Underfull \vbox (badness 10000) has occurred while \output is active [1185] [1186]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4} ) has been already used, duplicate ignored \relax l.6820 \aliasA{S4}{S3Part}{S4} [1187] [1188] [1189] [1190]pdfTeX warning (ext4) : destination with the same identifier (name{Rfn.Complex}) has been already use d, duplicate ignored \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 \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 \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 \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 \relax l.7102 \aliasA{Summary}{S4groupGeneric}{Summary} [1191] 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 [1192] [1193] [1194] 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 [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] Underfull \hbox (badness 1852) in paragraph at lines 9759--9763 []\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., [1229] [1230] [1231] [1232]) (./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 [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] Underfull \hbox (badness 3386) in paragraph at lines 1246--1249 []\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 [1253] [1254]) (./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 \T1/ptm/ m/n/10 and William N. Ven-ables [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269]) (./stats-pkg.tex [1270] Chapter 10. [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] Underfull \hbox (badness 1412) in paragraph at lines 844--846 []\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 [1284] [1285] [1286] [1287] [1288] [1289] [1290] [1291] Underfull \hbox (badness 2503) in paragraph at lines 1325--1328 []\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 , [1292] [1293] [1294] Underfull \hbox (badness 10000) in paragraph at lines 1504--1508 []\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 [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] Underfull \hbox (badness 3965) in paragraph at lines 2164--2166 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1306] [1307] [1308] [1309] [1310] Underfull \hbox (badness 3965) in paragraph at lines 2506--2508 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] Underfull \hbox (badness 2503) in paragraph at lines 3323--3326 []\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 , [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 3989) in paragraph at lines 4548--4555 []\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 = [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] Underfull \hbox (badness 2556) in paragraph at lines 5149--5152 []\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 5166--5168 []\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 [1354] [1355] [1356] [1357] Underfull \hbox (badness 1142) in paragraph at lines 5407--5419 \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. [1358] [1359] Underfull \hbox (badness 2503) in paragraph at lines 5546--5550 []\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 , [1360] Underfull \hbox (badness 1168) in paragraph at lines 5607--5612 []\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 [1361] [1362] [1363] [1364] [1365] [1366] [1367] Underfull \hbox (badness 8132) in paragraph at lines 6049--6054 \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, [1368] [1369] [1370] [1371] [1372] Underfull \hbox (badness 7081) in paragraph at lines 6324--6327 []\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 6328--6330 []\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 [1373] [1374] [1375] [1376] [1377] Underfull \vbox (badness 3803) has occurred while \output is active [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] Underfull \hbox (badness 10000) in paragraph at lines 7136--7139 []\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 [1386] [1387] Underfull \hbox (badness 10000) in paragraph at lines 7273--7276 []\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 / [1388] [1389] [1390] [1391] Underfull \vbox (badness 3803) has occurred while \output is active [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] Underfull \hbox (badness 2626) in paragraph at lines 8771--8774 []\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 [1413] Underfull \hbox (badness 2503) in paragraph at lines 8871--8875 []\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 , [1414] [1415] [1416] [1417] [1418] Overfull \hbox (6.88992pt too wide) in paragraph at lines 9205--9207 []\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 . [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] Underfull \hbox (badness 4518) in paragraph at lines 10132--10137 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1434] [1435] [1436] [1437] Underfull \hbox (badness 2142) in paragraph at lines 10474--10477 []\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 ^^@ [1438] Underfull \hbox (badness 1253) in paragraph at lines 10493--10496 []\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, [1439] Underfull \hbox (badness 1708) in paragraph at lines 10555--10559 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1440] [1441] [1442] [1443] [1444] [1445] Underfull \hbox (badness 1694) in paragraph at lines 10951--10954 []\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 10970--10979 \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- [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453]pdfTeX warning (ext4): d estination with the same identifier (name{Rfn.hat}) has been already used, dupl icate ignored \relax l.11417 \aliasA{hat}{influence.measures}{hat} [1454] [1455] Underfull \hbox (badness 1484) in paragraph at lines 11540--11542 []\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 [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 4441) in paragraph at lines 12098--12100 []\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 12105--12107 []\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 [1465] [1466] [1467] [1468] [1469] [1470] Underfull \hbox (badness 2894) in paragraph at lines 12439--12443 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] Underfull \hbox (badness 4518) in paragraph at lines 13134--13139 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1482] [1483] [1484] [1485] [1486] [1487] [1488] [1489] [1490] [1491] Underfull \hbox (badness 4518) in paragraph at lines 13781--13786 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1492] [1493] Underfull \hbox (badness 10000) in paragraph at lines 13919--13923 []\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 13926--13928 []\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 [1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] [1509] [1510] [1511] Underfull \hbox (badness 2503) in paragraph at lines 14990--14994 []\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 , [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] Underfull \hbox (badness 1418) in paragraph at lines 15499--15505 []\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 [1520] [1521] [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] Underfull \hbox (badness 2359) in paragraph at lines 17123--17125 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1546] [1547] Underfull \vbox (badness 10000) has occurred while \output is active [1548] Underfull \vbox (badness 10000) has occurred while \output is active [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] Underfull \hbox (badness 1377) in paragraph at lines 18034--18039 []\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 18039--18042 []\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 18052--18056 \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 18060--18064 []\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 [1562] [1563] [1564] Underfull \vbox (badness 10000) has occurred while \output is active [1565] [1566] [1567] [1568] [1569] [1570] [1571] Underfull \hbox (badness 1337) in paragraph at lines 18676--18679 []\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 [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] Underfull \hbox (badness 5563) in paragraph at lines 19406--19408 []\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 19409--19412 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1585] [1586] [1587] [1588] [1589] [1590] Underfull \hbox (badness 2503) in paragraph at lines 19776--19779 []\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 , [1591] Underfull \hbox (badness 10000) in paragraph at lines 19803--19805 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602] [1603] [1604] [1605] [1606] [1607] Underfull \hbox (badness 10000) in paragraph at lines 20803--20809 []\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 , [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] Underfull \hbox (badness 1337) in paragraph at lines 22138--22144 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1631] [1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] Underfull \hbox (badness 10000) in paragraph at lines 22931--22934 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1643] [1644] [1645] [1646] [1647] [1648] [1649] [1650] [1651] Underfull \hbox (badness 10000) in paragraph at lines 23508--23511 []\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 [1652] Underfull \hbox (badness 3690) in paragraph at lines 23559--23563 [][][]\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 [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] Underfull \hbox (badness 3439) in paragraph at lines 24029--24035 [][]\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 , [1661] [1662] [1663] [1664] [1665] [1666] [1667] [1668] [1669] Underfull \hbox (badness 10000) in paragraph at lines 24577--24582 []\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 [1670] [1671] [1672] [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] Underfull \vbox (badness 3803) has occurred while \output is active [1685] [1686] Underfull \hbox (badness 3514) in paragraph at lines 25593--25598 []\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 [1687] Underfull \hbox (badness 3514) in paragraph at lines 25655--25660 []\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 [1688] Underfull \hbox (badness 3514) in paragraph at lines 25712--25717 []\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 [1689] Underfull \hbox (badness 3514) in paragraph at lines 25773--25779 []\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 [1690] [1691] [1692] [1693] Underfull \hbox (badness 3514) in paragraph at lines 25986--25991 []\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 Underfull \hbox (badness 3514) in paragraph at lines 26042--26047 []\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 [1694] Underfull \hbox (badness 3514) in paragraph at lines 26099--26104 []\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 [1695] Underfull \hbox (badness 3514) in paragraph at lines 26154--26159 []\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 [1696] [1697] Underfull \hbox (badness 6691) in paragraph at lines 26223--26228 []\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 [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] Underfull \hbox (badness 10000) in paragraph at lines 26747--26750 []\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 26747--26750 \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, [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] Underfull \hbox (badness 5431) in paragraph at lines 27353--27355 []\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 [1716] [1717] [1718] [1719] Underfull \hbox (badness 5431) in paragraph at lines 27563--27566 []\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 [1720] [1721] [1722] [1723] [1724] Underfull \hbox (badness 1337) in paragraph at lines 27875--27879 []\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 [1725] [1726] Underfull \hbox (badness 10000) in paragraph at lines 27992--27995 []\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 [1727] [1728] [1729] Underfull \hbox (badness 1616) in paragraph at lines 28175--28178 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] Underfull \hbox (badness 10000) in paragraph at lines 29302--29306 []\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 [1749] [1750] [1751] Underfull \vbox (badness 10000) has occurred while \output is active [1752] [1753] [1754] Underfull \hbox (badness 1337) in paragraph at lines 29666--29670 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] Underfull \hbox (badness 1337) in paragraph at lines 30150--30154 []\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 [1763] Underfull \hbox (badness 5161) in paragraph at lines 30243--30245 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1764] [1765] [1766] [1767] [1768] [1769] Underfull \hbox (badness 10000) in paragraph at lines 30607--30612 []\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 [1770] [1771] [1772]) (./stats4-pkg.tex Chapter 11. [1773] [1774] [1775] [1776] [1777] [1778]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1779] [1780] [1781] [1782]) (./tcltk-pkg.tex Chapter 12. [1783] [1784] [1785] [1786] [1787] [1788] [1789] Underfull \vbox (badness 10000) has occurred while \output is active [1790] Underfull \vbox (badness 10000) has occurred while \output is active [1791] 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 [1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] 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 [1803]) (./tools-pkg.tex [1804] Chapter 13. [1805] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1806] 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 [1807] [1808] 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 [1809] [1810] 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 [1811] [1812] [1813] [1814] [1815] [1816] [1817] [1818] [1819] [1820] [1821] 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 [1822] 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- [1823] 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 , [1824] [1825] [1826] 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 [1827] [1828] [1829] Underfull \hbox (badness 7981) in paragraph at lines 1518--1522 []\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 1524--1526 []\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 [1830] [1831] [1832] [1833]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1721 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1834] [1835] Underfull \hbox (badness 5726) in paragraph at lines 1847--1852 []\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 1847--1852 \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 [1836] [1837] [1838] [1839] [1840] [1841] [1842] [1843] Underfull \hbox (badness 7981) in paragraph at lines 2323--2329 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1844] [1845] [1846] [1847] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2607. [1848] [1849] [1850] [1851] Underfull \hbox (badness 1424) in paragraph at lines 2844--2846 []\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 [1852] [1853] [1854] [1855] [1856] [1857] [1858] [1859] [1860] [1861] [1862] Underfull \hbox (badness 10000) in paragraph at lines 3539--3541 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1863] [1864] [1865] [1866] [1867] [1868] Underfull \hbox (badness 1838) in paragraph at lines 3919--3925 []\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 3919--3925 \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 [1869] [1870] Underfull \hbox (badness 5726) in paragraph at lines 3999--4004 []\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 3999--4004 \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 [1871] [1872] Underfull \hbox (badness 1688) in paragraph at lines 4142--4154 []\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 [1873] [1874] [1875] [1876]) (./utils-pkg.tex Chapter 14. [1877] 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 ', [1878] [1879] 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 [1880] [1881] [1882] [1883] [1884] [1885] 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 [1886] Underfull \hbox (badness 5847) in paragraph at lines 656--662 []\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 656--662 \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 [1887] Underfull \hbox (badness 3861) in paragraph at lines 724--729 []\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 , [1888] [1889] [1890] [1891] [1892] Underfull \vbox (badness 10000) has occurred while \output is active [1893] [1894] [1895] [1896] [1897] Underfull \hbox (badness 1371) in paragraph at lines 1320--1322 []\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 [1898] [1899] [1900] [1901] [1902] [1903] [1904] Underfull \hbox (badness 2057) in paragraph at lines 1812--1814 []\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 [1905] [1906] Underfull \hbox (badness 10000) in paragraph at lines 1913--1915 []\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 [1907] Underfull \hbox (badness 5189) in paragraph at lines 2003--2005 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1908] [1909] [1910] [1911] Underfull \hbox (badness 1661) in paragraph at lines 2221--2228 []\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 2238--2241 []\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 [1912] [1913] [1914] [1915] [1916] [1917] [1918] [1919] [1920] [1921] [1922] [1923] [1924] [1925] [1926] Underfull \hbox (badness 1412) in paragraph at lines 3235--3239 []\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 [1927] Underfull \hbox (badness 1430) in paragraph at lines 3259--3267 []\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 3302--3308 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1928] [1929] [1930] [1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940] [1941]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4123 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4123 ...mat Unordered and Ordered Lists}{format} [1942] [1943] [1944] [1945] [1946] [1947] [1948] [1949] [1950] [1951] [1952] [1953] [1954] [1955] [1956] Underfull \hbox (badness 1371) in paragraph at lines 5073--5075 []\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 [1957] Underfull \hbox (badness 1502) in paragraph at lines 5162--5167 []\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 5162--5167 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1958] [1959] [1960] Underfull \hbox (badness 10000) in paragraph at lines 5335--5344 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [1961] Underfull \hbox (badness 2150) in paragraph at lines 5398--5401 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [1962] [1963] Underfull \hbox (badness 3118) in paragraph at lines 5535--5537 []\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 [1964] Underfull \hbox (badness 2409) in paragraph at lines 5568--5572 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [1965] Underfull \hbox (badness 1325) in paragraph at lines 5676--5680 []\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 [1966] Underfull \hbox (badness 10000) in paragraph at lines 5759--5762 []\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 5759--5762 \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., [1967] Underfull \hbox (badness 3219) in paragraph at lines 5832--5839 []\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 5832--5839 \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 5832--5839 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [1968] Underfull \hbox (badness 10000) in paragraph at lines 5912--5917 [][][]\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 , [1969] [1970] [1971] [1972] [1973] [1974] [1975] [1976] [1977] [1978] [1979] [1980] [1981] [1982] [1983] [1984] [1985] [1986] [1987] [1988] Underfull \hbox (badness 10000) in paragraph at lines 7124--7126 []\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 7129--7134 []\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, [1989] [1990] [1991] [1992] [1993] [1994] [1995] [1996] [1997] Underfull \hbox (badness 1789) in paragraph at lines 7679--7681 []\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 [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] Underfull \hbox (badness 1097) in paragraph at lines 8504--8507 []\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 [2010] [2011] Underfull \hbox (badness 3000) in paragraph at lines 8640--8645 [][][]\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 ; [2012] [2013] [2014] [2015] [2016] [2017] [2018] [2019] [2020] Underfull \hbox (badness 2134) in paragraph at lines 9222--9227 [][][]\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 ; [2021] [2022] [2023] [2024] [2025] [2026] [2027] Underfull \hbox (badness 2469) in paragraph at lines 9655--9659 []\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 9655--9659 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2028] [2029] [2030] [2031] [2032] [2033] Underfull \hbox (badness 10000) in paragraph at lines 9996--9998 []\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 [2034] [2035] Underfull \hbox (badness 2150) in paragraph at lines 10172--10174 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2036] [2037] [2038] Underfull \hbox (badness 10000) in paragraph at lines 10350--10354 []\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 [2039] Underfull \hbox (badness 10000) in paragraph at lines 10381--10387 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2040] Underfull \hbox (badness 2096) in paragraph at lines 10499--10502 []\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 10503--10506 []\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 [2041] Underfull \hbox (badness 1009) in paragraph at lines 10569--10580 []\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 [2042] [2043] [2044] [2045] [2046] Underfull \hbox (badness 3780) in paragraph at lines 10868--10872 []\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 10884--10887 []\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 [2047] [2048] [2049] [2050] [2051] [2052] Underfull \hbox (badness 5970) in paragraph at lines 11258--11261 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2053] [2054] [2055] Underfull \hbox (badness 10000) in paragraph at lines 11437--11439 []\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 [2056] [2057] [2058] [2059] [2060] [2061] Underfull \hbox (badness 10000) in paragraph at lines 11838--11841 [][][]$\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 11838--11841 \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 [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] [2070] Underfull \hbox (badness 10000) in paragraph at lines 12368--12370 []\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 12371--12373 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2071] Underfull \hbox (badness 10000) in paragraph at lines 12401--12406 []\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 12401--12406 [][]\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 12430--12433 [][][]\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 , [2072] [2073] [2074] [2075] Overfull \hbox (25.86961pt too wide) in paragraph at lines 12669--12672 [][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi -gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](, package = "") [2076] [2077] Underfull \hbox (badness 1454) in paragraph at lines 12747--12751 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, [2078] Underfull \hbox (badness 10000) in paragraph at lines 12817--12819 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion [2079] [2080] [2081]) [2082] No file refman.ind. (./refman.aux) Package rerunfilecheck Warning: File `refman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. 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 pdfTeX warning (dest): name{Rfn.gamma.shape} has been referenced but does not e xist, replaced by a fixed one pdfTeX 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but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, replaced by a fixed one {/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/ texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dis t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}< /usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb> Output written on refman.pdf (2085 pages, 5139397 bytes). Transcript written on refman.log. This is makeindex, version 2.15 [TeX Live 2015] (kpathsea + Thai support). Scanning input file refman.idx................done (12900 entries accepted, 33 rejected). Sorting entries......................................................................................................................................done (196192 comparisons). Generating output file refman.ind................done (12825 lines written, 43 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 <2015/01/01> Babel <3.9l> and hyphenation patterns for 2 languages 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? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 511--517 []\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 1122--1125 []\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 1339--1345 []\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] Overfull \hbox (26.88089pt too wide) in paragraph at lines 1849--1849 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [30] [31] [32] Underfull \hbox (badness 10000) in paragraph at lines 2034--2036 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] Underfull \hbox (badness 10000) in paragraph at lines 3532--3534 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [56] [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 4728--4730 []\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] [93] Underfull \hbox (badness 2096) in paragraph at lines 5945--5958 []\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 [94] [95] [96] Overfull \hbox (58.35893pt too wide) in paragraph at lines 6146--6149 []\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 : [97] [98] Underfull \hbox (badness 10000) in paragraph at lines 6290--6293 []\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 [99] [100] Underfull \hbox (badness 1442) in paragraph at lines 6451--6457 []\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 6451--6457 \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 6451--6457 \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 [101] Underfull \hbox (badness 3568) in paragraph at lines 6512--6519 \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 [102] [103] Underfull \vbox (badness 10000) has occurred while \output is active [104] [105] [106] [107] [108] [109] [110] [111] Underfull \hbox (badness 2096) in paragraph at lines 7149--7153 \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 . [112] Underfull \hbox (badness 4595) in paragraph at lines 7206--7209 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [113] Underfull \hbox (badness 3000) in paragraph at lines 7242--7244 []\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 7267--7270 [][][]\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 , [114] [115] [116] [117] Underfull \hbox (badness 10000) in paragraph at lines 7517--7528 []\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 [118] Underfull \hbox (badness 4479) in paragraph at lines 7589--7598 [][][]\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 7589--7598 [][]\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 [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] Underfull \hbox (badness 1394) in paragraph at lines 9200--9205 []\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 [144] [145] [146] [147] [148] Underfull \hbox (badness 1052) in paragraph at lines 9537--9542 []\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 9537--9542 \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 [149] [150] Underfull \hbox (badness 1735) in paragraph at lines 9675--9679 \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 . [151] [152] [153] [154] [155] [156] Underfull \hbox (badness 2150) in paragraph at lines 10079--10082 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse [157] Underfull \hbox (badness 6396) in paragraph at lines 10093--10101 []\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 10134--10141 []\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 [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] Underfull \hbox (badness 4569) in paragraph at lines 11178--11182 []\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 11178--11182 \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 [174] [175] [176] [177] [178] [179] [180] [181] Underfull \hbox (badness 2698) in paragraph at lines 11754--11763 []\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 11754--11763 \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 [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] Underfull \hbox (badness 6236) in paragraph at lines 12398--12401 []\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 [192] [193] [194] [195] [196] [197] Underfull \hbox (badness 2253) in paragraph at lines 12776--12778 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [198] Underfull \hbox (badness 1565) in paragraph at lines 12847--12851 [][][]\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 [199] Underfull \hbox (badness 10000) in paragraph at lines 12891--12893 []\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 [200] [201] Underfull \hbox (badness 1466) in paragraph at lines 13032--13035 []\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 [202] [203] Underfull \hbox (badness 10000) in paragraph at lines 13140--13144 [][][]\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 13151--13154 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [204] [205] [206] [207] Underfull \hbox (badness 3965) in paragraph at lines 13403--13407 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] Underfull \hbox (badness 4429) in paragraph at lines 14133--14136 []\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 [219] Underfull \hbox (badness 10000) in paragraph at lines 14225--14227 []\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 14231--14235 []\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 [220] Underfull \hbox (badness 10000) in paragraph at lines 14273--14277 []\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 14273--14277 \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 [221] Underfull \vbox (badness 3803) has occurred while \output is active [222] [223] [224] [225] [226] [227] [228] [229] Underfull \hbox (badness 2452) in paragraph at lines 14853--14857 []\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 14853--14857 \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 [230] [231] [232] Underfull \hbox (badness 1092) in paragraph at lines 15026--15031 [][]\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 [233] [234] [235] [236] Underfull \hbox (badness 6741) in paragraph at lines 15274--15278 \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 , [237] [238] [239] [240] Underfull \hbox (badness 1867) in paragraph at lines 15580--15587 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [241] [242] [243] [244] Underfull \vbox (badness 10000) has occurred while \output is active [245] [246] Underfull \hbox (badness 3679) in paragraph at lines 15960--15962 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [247] [248] [249] [250] [251] [252] [253] Underfull \hbox (badness 1478) in paragraph at lines 16440--16443 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [254] [255] [256] [257] Underfull \hbox (badness 10000) in paragraph at lines 16693--16695 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [258] [259] [260] [261] [262] [263] [264] [265] [266] Underfull \hbox (badness 1442) in paragraph at lines 17256--17258 []\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 [267] Underfull \hbox (badness 2452) in paragraph at lines 17348--17364 [][][]\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 , [268] [269] [270] [271] [272] [273] [274] Underfull \hbox (badness 1248) in paragraph at lines 17756--17759 []\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 , [275] [276] [277] [278] Underfull \hbox (badness 4739) in paragraph at lines 18012--18014 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [279] [280] [281] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] Underfull \hbox (badness 1360) in paragraph at lines 18960--18965 \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 18983--18989 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / Underfull \hbox (badness 1127) in paragraph at lines 18983--18989 \T1/zi4/m/n/10 ssl-[]compared . html$[][] \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 [295] Underfull \hbox (badness 10000) in paragraph at lines 19056--19060 []\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 19056--19060 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [296] [297] Underfull \hbox (badness 1509) in paragraph at lines 19191--19198 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1354) in paragraph at lines 19191--19198 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19207--19212 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] [309] Underfull \hbox (badness 1264) in paragraph at lines 19938--19943 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] Underfull \hbox (badness 10000) in paragraph at lines 20692--20694 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] Underfull \hbox (badness 1077) in paragraph at lines 21690--21696 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [337] [338] [339] Underfull \hbox (badness 1484) in paragraph at lines 21851--21859 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [340] [341] [342] [343] Underfull \hbox (badness 2790) in paragraph at lines 22122--22125 []\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 22122--22125 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [344] [345] [346] [347] Underfull \hbox (badness 1194) in paragraph at lines 22403--22406 []\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 [348] [349] [350] [351] Underfull \hbox (badness 10000) in paragraph at lines 22609--22615 []\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 22609--22615 \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 22619--22622 []\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 22619--22622 \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 [352] [353] [354] [355] [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] Underfull \hbox (badness 10000) in paragraph at lines 23544--23546 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [366] [367] [368] [369] Underfull \hbox (badness 1199) in paragraph at lines 23771--23777 []\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 23771--23777 \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, [370] [371] [372] [373] [374] [375] [376] [377] Underfull \hbox (badness 1038) in paragraph at lines 24336--24344 []\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 24345--24348 []\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 24364--24366 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [378] Underfull \hbox (badness 10000) in paragraph at lines 24436--24446 []\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 24447--24453 []\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 24460--24465 []\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 24470--24472 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [379] [380] [381] Underfull \hbox (badness 10000) in paragraph at lines 24721--24727 []\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 24721--24727 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "http://bioconductor.org"\T1/p tm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 24721--24727 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "http://bioconductor.statistik.tu-dortmund.de"\T 1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 24734--24737 []\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 [382] Underfull \hbox (badness 2689) in paragraph at lines 24758--24760 []\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 24790--24795 []\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 24796--24807 \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 24808--24811 []\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 Underfull \hbox (badness 4084) in paragraph at lines 24818--24830 \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 24818--24830 \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 24818--24830 \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 24832--24839 []\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 24832--24839 \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 24832--24839 \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 24832--24839 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [383] [384] [385] [386] [387] Underfull \hbox (badness 10000) in paragraph at lines 25153--25157 []\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 25153--25157 \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)] [388] [389] [390] [391] [392] Underfull \hbox (badness 1735) in paragraph at lines 25471--25475 []\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 [393] [394] [395] [396] [397] [398] [399] [400] [401] [402] Underfull \hbox (badness 2726) in paragraph at lines 26030--26033 []\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 [403] [404] [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] [415] Underfull \hbox (badness 1052) in paragraph at lines 26849--26854 []\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 [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] Underfull \hbox (badness 1533) in paragraph at lines 27577--27580 []\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 [427] [428] Underfull \hbox (badness 1163) in paragraph at lines 27739--27749 []\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 [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] Underfull \hbox (badness 10000) in paragraph at lines 29241--29245 []\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 29241--29245 \T1/zi4/m/n/10 "(?[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 29263--29265 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [453] [454] [455] [456] [457] [458] [459] [460] [461] Underfull \hbox (badness 1655) in paragraph at lines 29808--29810 []\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 [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] Underfull \hbox (badness 10000) in paragraph at lines 30476--30480 []\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., [473] [474] [475] Underfull \hbox (badness 2302) in paragraph at lines 30716--30723 []\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 30716--30723 \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 30716--30723 \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 30716--30723 \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 [476] [477] [478] Underfull \hbox (badness 2261) in paragraph at lines 30870--30875 []\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 30897--30903 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [479] Underfull \hbox (badness 10000) in paragraph at lines 30973--30978 []\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 [480] [481] [482] [483] [484] [485] [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] Underfull \hbox (badness 1072) in paragraph at lines 33757--33761 []\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 33762--33766 []\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 ', [523] Underfull \hbox (badness 10000) in paragraph at lines 33790--33796 []\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 33790--33796 \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 33790--33796 \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 33803--33810 \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 33803--33810 \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 33803--33810 \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 [524] [525] [526] [527] [528] Underfull \hbox (badness 10000) in paragraph at lines 34094--34100 []\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 34094--34100 \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 [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] Underfull \hbox (badness 3333) in paragraph at lines 35877--35882 []\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 [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] Underfull \hbox (badness 1472) in paragraph at lines 36497--36500 []\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 [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] Underfull \hbox (badness 2671) in paragraph at lines 37159--37162 []\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 [578] [579] [580] [581] [582] [583] Underfull \hbox (badness 10000) in paragraph at lines 37563--37566 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$http : / / developer . r-[]project . org / [584] [585] Underfull \hbox (badness 10000) in paragraph at lines 37684--37688 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 http : / / developer . [586] Underfull \hbox (badness 10000) in paragraph at lines 37746--37750 [][][]\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 http : / / developer . [587] [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] Underfull \hbox (badness 1990) in paragraph at lines 39041--39049 []\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 39041--39049 \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 [606] [607] [608] [609] [610] Underfull \hbox (badness 1515) in paragraph at lines 39313--39318 []\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 [611] [612] [613] Underfull \hbox (badness 1917) in paragraph at lines 39543--39550 []\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 [614] [615] [616] [617] [618] [619] [620] [621] [622] Underfull \hbox (badness 3668) in paragraph at lines 40128--40130 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [623] [624] Underfull \hbox (badness 2401) in paragraph at lines 40233--40237 []\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 [625] [626] [627] Underfull \hbox (badness 2111) in paragraph at lines 40402--40407 \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. Underfull \hbox (badness 6542) in paragraph at lines 40418--40423 []\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 [628] [629] [630] [631] [632] [633] [634] Underfull \hbox (badness 10000) in paragraph at lines 40863--40868 []\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 40863--40868 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to [635] [636] Underfull \hbox (badness 5417) in paragraph at lines 40955--40959 []\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 [637] Underfull \hbox (badness 10000) in paragraph at lines 41016--41020 []\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 [638]) (./compiler-pkg.tex Chapter 2. [639] [640] [641] [642]) (./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 [643] [644] [645] [646] [647] [648] [649] [650] [651] [652] [653] [654] [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] Underfull \vbox (badness 1515) has occurred while \output is active [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] 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 / [710] Underfull \vbox (badness 10000) has occurred while \output is active [711] [712] [713] [714] Underfull \vbox (badness 10000) has occurred while \output is active [715] Underfull \vbox (badness 10000) has occurred while \output is active [716] [717] [718] [719] [720] [721] [722] [723]) (./grDevices-pkg.tex [724] Chapter 4. [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] Underfull \hbox (badness 5175) in paragraph at lines 1066--1068 []\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 [742] [743] [744] [745] Underfull \hbox (badness 1852) in paragraph at lines 1263--1266 []\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 [746] [747] [748] Underfull \hbox (badness 1490) in paragraph at lines 1469--1474 \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 [749] Underfull \hbox (badness 2698) in paragraph at lines 1523--1526 []\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 [750] Underfull \hbox (badness 10000) in paragraph at lines 1592--1596 []\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 [751] [752] [753] [754] Underfull \hbox (badness 1325) in paragraph at lines 1875--1885 \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 , [755] [756] Underfull \hbox (badness 10000) in paragraph at lines 1980--1982 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [757] [758] [759] Underfull \hbox (badness 6758) in paragraph at lines 2141--2144 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [760] [761] [762] [763] [764] [765] [766] [767] [768] Underfull \hbox (badness 10000) in paragraph at lines 2707--2708 [769] [770] [771] [772] [773] [774] [775] Underfull \hbox (badness 1152) in paragraph at lines 3145--3147 []\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 [776] [777] [778] [779] [780] Underfull \hbox (badness 2856) in paragraph at lines 3465--3468 []\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 3479--3481 []\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 [781] [782] Underfull \hbox (badness 1173) in paragraph at lines 3595--3605 []\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 [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] Underfull \hbox (badness 1067) in paragraph at lines 4302--4309 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [794] [795] Underfull \hbox (badness 3364) in paragraph at lines 4463--4465 []\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 / [796] Underfull \hbox (badness 1789) in paragraph at lines 4540--4542 []\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 [797] Underfull \hbox (badness 1377) in paragraph at lines 4590--4595 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [798] Underfull \hbox (badness 2671) in paragraph at lines 4617--4625 \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 4666--4673 \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 4674--4683 \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 4674--4683 \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 4684--4686 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [799] [800] Underfull \hbox (badness 1057) in paragraph at lines 4795--4800 []\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 [801] Underfull \hbox (badness 7344) in paragraph at lines 4855--4857 []\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 [802] [803] Underfull \hbox (badness 2035) in paragraph at lines 4979--4988 []\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 4979--4988 \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 4979--4988 \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 , [804] Underfull \hbox (badness 10000) in paragraph at lines 5048--5055 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5048--5055 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [805] [806] [807] Underfull \hbox (badness 1546) in paragraph at lines 5186--5194 []\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 , [808] Underfull \hbox (badness 1648) in paragraph at lines 5263--5267 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [809] [810] [811] [812] [813] [814] [815] Underfull \hbox (badness 10000) in paragraph at lines 5686--5689 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [816] Underfull \vbox (badness 3803) has occurred while \output is active [817] [818] [819] [820] [821] Underfull \hbox (badness 1189) in paragraph at lines 6083--6085 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [822] [823] Underfull \hbox (badness 10000) in paragraph at lines 6181--6183 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [824] [825] [826] [827] Underfull \hbox (badness 3780) in paragraph at lines 6472--6478 []\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 , [828] [829] [830] Underfull \hbox (badness 2680) in paragraph at lines 6668--6670 []\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 [831] [832] [833]) (./graphics-pkg.tex [834] Chapter 5. [835] [836] [837] [838] [839] [840] [841] [842] [843] [844] [845] 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 [846] [847] [848] [849] Underfull \vbox (badness 3803) has occurred while \output is active [850] [851] [852] [853] [854] 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 , [855] [856] [857] [858] [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] [869] [870] [871] Underfull \hbox (badness 1009) in paragraph at lines 2277--2284 \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 [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] Underfull \vbox (badness 10000) has occurred while \output is active [894] Underfull \vbox (badness 10000) has occurred while \output is active [895] [896] [897] [898] Underfull \hbox (badness 1867) in paragraph at lines 3901--3905 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [899] [900] [901] [902] [903] [904] [905] Underfull \hbox (badness 1924) in paragraph at lines 4348--4353 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain [906] Underfull \hbox (badness 2529) in paragraph at lines 4379--4382 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used: see [907] [908] [909] [910] [911] Underfull \hbox (badness 10000) in paragraph at lines 4729--4735 []\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 4729--4735 \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 [912] Underfull \hbox (badness 10000) in paragraph at lines 4860--4863 [913] [914 ] Underfull \hbox (badness 10000) in paragraph at lines 4921--4923 [915 ] [916] Underfull \hbox (badness 10000) in paragraph at lines 5111--5113 []\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 [917] [918] [919] [920] [921] Underfull \vbox (badness 10000) has occurred while \output is active [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6581--6582 [][] [941 ] [942] Underfull \vbox (badness 10000) has occurred while \output is active [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] Underfull \hbox (badness 1048) in paragraph at lines 7290--7295 \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 [953] Underfull \hbox (badness 1038) in paragraph at lines 7406--7409 []\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 [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] [971] [972] [973] [974] Underfull \hbox (badness 6691) in paragraph at lines 8625--8628 []\T1/ptm/m/n/10 The main ti-tle (on top) us-ing font and size (char-ac-ter ex- pan-sion) Underfull \hbox (badness 2799) in paragraph at lines 8628--8630 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font and size \T1/zi4/m/n/10 par ("font.sub") \T1/ptm/m/n/10 and color [975] [976]pdfTeX warning (ext4): destination with the same identifier (name{Rf n.units}) has been already used, duplicate ignored \relax l.8710 \HeaderA{units}{Graphical Units}{units} [977] [978] [979] [980]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [981] [982] [983] [984] [985] [986] 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 [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] 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 , [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [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] Underfull \vbox (badness 3803) has occurred while \output is active [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] 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 [1054] [1055] [1056] [1057] 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 [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] Underfull \hbox (badness 10000) in paragraph at lines 5854--5860 \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., [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] Underfull \hbox (badness 7649) in paragraph at lines 6324--6327 []\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 [1087] [1088] [1089] [1090]) (./methods-pkg.tex Chapter 7. [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] 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 [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] 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 [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] 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 [1128] [1129] 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 [1130] 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 [1131] [1132] [1133] [1134] [1135] [1136] [1137] 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 [1138] [1139] [1140] [1141] [1142] 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 [1143] [1144] [1145] [1146] [1147] [1148] Underfull \vbox (badness 10000) has occurred while \output is active [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156] 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 [1157] [1158] [1159] [1160] [1161] [1162] Underfull \vbox (badness 2452) has occurred while \output is active [1163] [1164] Underfull \vbox (badness 10000) has occurred while \output is active [1165] [1166] 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 [1167] [1168] [1169] [1170] [1171] 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 [1172] [1173] [1174] [1175] 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 [1176] [1177] [1178] [1179] [1180] Underfull \hbox (badness 1675) in paragraph at lines 6343--6349 \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 [1181] [1182] [1183] [1184] Underfull \vbox (badness 10000) has occurred while \output is active [1185] [1186]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4} ) has been already used, duplicate ignored \relax l.6820 \aliasA{S4}{S3Part}{S4} [1187] [1188] [1189] [1190]pdfTeX warning (ext4) : destination with the same identifier (name{Rfn.Complex}) has been already use d, duplicate ignored \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 \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 \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 \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 \relax l.7102 \aliasA{Summary}{S4groupGeneric}{Summary} [1191] 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 [1192] [1193] [1194] 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 [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] Underfull \hbox (badness 1852) in paragraph at lines 9759--9763 []\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., [1229] [1230] [1231] [1232]) (./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 [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] Underfull \hbox (badness 3386) in paragraph at lines 1246--1249 []\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 [1253] [1254]) (./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 \T1/ptm/ m/n/10 and William N. Ven-ables [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269]) (./stats-pkg.tex [1270] Chapter 10. [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] Underfull \hbox (badness 1412) in paragraph at lines 844--846 []\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 [1284] [1285] [1286] [1287] [1288] [1289] [1290] [1291] Underfull \hbox (badness 2503) in paragraph at lines 1325--1328 []\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 , [1292] [1293] [1294] Underfull \hbox (badness 10000) in paragraph at lines 1504--1508 []\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 [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] Underfull \hbox (badness 3965) in paragraph at lines 2164--2166 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1306] [1307] [1308] [1309] [1310] Underfull \hbox (badness 3965) in paragraph at lines 2506--2508 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] Underfull \hbox (badness 2503) in paragraph at lines 3323--3326 []\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 , [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 3989) in paragraph at lines 4548--4555 []\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 = [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] Underfull \hbox (badness 2556) in paragraph at lines 5149--5152 []\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 5166--5168 []\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 [1354] [1355] [1356] [1357] Underfull \hbox (badness 1142) in paragraph at lines 5407--5419 \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. [1358] [1359] Underfull \hbox (badness 2503) in paragraph at lines 5546--5550 []\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 , [1360] Underfull \hbox (badness 1168) in paragraph at lines 5607--5612 []\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 [1361] [1362] [1363] [1364] [1365] [1366] [1367] Underfull \hbox (badness 8132) in paragraph at lines 6049--6054 \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, [1368] [1369] [1370] [1371] [1372] Underfull \hbox (badness 7081) in paragraph at lines 6324--6327 []\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 6328--6330 []\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 [1373] [1374] [1375] [1376] [1377] Underfull \vbox (badness 3803) has occurred while \output is active [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] Underfull \hbox (badness 10000) in paragraph at lines 7136--7139 []\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 [1386] [1387] Underfull \hbox (badness 10000) in paragraph at lines 7273--7276 []\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 / [1388] [1389] [1390] [1391] Underfull \vbox (badness 3803) has occurred while \output is active [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] Underfull \hbox (badness 2626) in paragraph at lines 8771--8774 []\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 [1413] Underfull \hbox (badness 2503) in paragraph at lines 8871--8875 []\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 , [1414] [1415] [1416] [1417] [1418] Overfull \hbox (6.88992pt too wide) in paragraph at lines 9205--9207 []\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 . [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] Underfull \hbox (badness 4518) in paragraph at lines 10132--10137 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1434] [1435] [1436] [1437] Underfull \hbox (badness 2142) in paragraph at lines 10474--10477 []\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 ^^@ [1438] Underfull \hbox (badness 1253) in paragraph at lines 10493--10496 []\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, [1439] Underfull \hbox (badness 1708) in paragraph at lines 10555--10559 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1440] [1441] [1442] [1443] [1444] [1445] Underfull \hbox (badness 1694) in paragraph at lines 10951--10954 []\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 10970--10979 \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- [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453]pdfTeX warning (ext4): d estination with the same identifier (name{Rfn.hat}) has been already used, dupl icate ignored \relax l.11417 \aliasA{hat}{influence.measures}{hat} [1454] [1455] Underfull \hbox (badness 1484) in paragraph at lines 11540--11542 []\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 [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 4441) in paragraph at lines 12098--12100 []\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 12105--12107 []\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 [1465] [1466] [1467] [1468] [1469] [1470] Underfull \hbox (badness 2894) in paragraph at lines 12439--12443 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] Underfull \hbox (badness 4518) in paragraph at lines 13134--13139 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1482] [1483] [1484] [1485] [1486] [1487] [1488] [1489] [1490] [1491] Underfull \hbox (badness 4518) in paragraph at lines 13781--13786 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1492] [1493] Underfull \hbox (badness 10000) in paragraph at lines 13919--13923 []\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 13926--13928 []\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 [1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] [1509] [1510] [1511] Underfull \hbox (badness 2503) in paragraph at lines 14990--14994 []\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 , [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] Underfull \hbox (badness 1418) in paragraph at lines 15499--15505 []\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 [1520] [1521] [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] Underfull \hbox (badness 2359) in paragraph at lines 17123--17125 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1546] [1547] Underfull \vbox (badness 10000) has occurred while \output is active [1548] Underfull \vbox (badness 10000) has occurred while \output is active [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] Underfull \hbox (badness 1377) in paragraph at lines 18034--18039 []\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 18039--18042 []\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 18052--18056 \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 18060--18064 []\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 [1562] [1563] [1564] Underfull \vbox (badness 10000) has occurred while \output is active [1565] [1566] [1567] [1568] [1569] [1570] [1571] Underfull \hbox (badness 1337) in paragraph at lines 18676--18679 []\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 [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] Underfull \hbox (badness 5563) in paragraph at lines 19406--19408 []\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 19409--19412 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1585] [1586] [1587] [1588] [1589] [1590] Underfull \hbox (badness 2503) in paragraph at lines 19776--19779 []\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 , [1591] Underfull \hbox (badness 10000) in paragraph at lines 19803--19805 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602] [1603] [1604] [1605] [1606] [1607] Underfull \hbox (badness 10000) in paragraph at lines 20803--20809 []\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 , [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] Underfull \hbox (badness 1337) in paragraph at lines 22138--22144 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1631] [1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] Underfull \hbox (badness 10000) in paragraph at lines 22931--22934 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1643] [1644] [1645] [1646] [1647] [1648] [1649] [1650] [1651] Underfull \hbox (badness 10000) in paragraph at lines 23508--23511 []\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 [1652] Underfull \hbox (badness 3690) in paragraph at lines 23559--23563 [][][]\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 [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] Underfull \hbox (badness 3439) in paragraph at lines 24029--24035 [][]\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 , [1661] [1662] [1663] [1664] [1665] [1666] [1667] [1668] [1669] Underfull \hbox (badness 10000) in paragraph at lines 24577--24582 []\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 [1670] [1671] [1672] [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] Underfull \vbox (badness 3803) has occurred while \output is active [1685] [1686] Underfull \hbox (badness 3514) in paragraph at lines 25593--25598 []\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 [1687] Underfull \hbox (badness 3514) in paragraph at lines 25655--25660 []\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 [1688] Underfull \hbox (badness 3514) in paragraph at lines 25712--25717 []\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 [1689] Underfull \hbox (badness 3514) in paragraph at lines 25773--25779 []\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 [1690] [1691] [1692] [1693] Underfull \hbox (badness 3514) in paragraph at lines 25986--25991 []\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 Underfull \hbox (badness 3514) in paragraph at lines 26042--26047 []\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 [1694] Underfull \hbox (badness 3514) in paragraph at lines 26099--26104 []\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 [1695] Underfull \hbox (badness 3514) in paragraph at lines 26154--26159 []\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 [1696] [1697] Underfull \hbox (badness 6691) in paragraph at lines 26223--26228 []\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 [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] Underfull \hbox (badness 10000) in paragraph at lines 26747--26750 []\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 26747--26750 \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, [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] Underfull \hbox (badness 5431) in paragraph at lines 27353--27355 []\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 [1716] [1717] [1718] [1719] Underfull \hbox (badness 5431) in paragraph at lines 27563--27566 []\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 [1720] [1721] [1722] [1723] [1724] Underfull \hbox (badness 1337) in paragraph at lines 27875--27879 []\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 [1725] [1726] Underfull \hbox (badness 10000) in paragraph at lines 27992--27995 []\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 [1727] [1728] [1729] Underfull \hbox (badness 1616) in paragraph at lines 28175--28178 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] Underfull \hbox (badness 10000) in paragraph at lines 29302--29306 []\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 [1749] [1750] [1751] Underfull \vbox (badness 10000) has occurred while \output is active [1752] [1753] [1754] Underfull \hbox (badness 1337) in paragraph at lines 29666--29670 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] Underfull \hbox (badness 1337) in paragraph at lines 30150--30154 []\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 [1763] Underfull \hbox (badness 5161) in paragraph at lines 30243--30245 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1764] [1765] [1766] [1767] [1768] [1769] Underfull \hbox (badness 10000) in paragraph at lines 30607--30612 []\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 [1770] [1771] [1772]) (./stats4-pkg.tex Chapter 11. [1773] [1774] [1775] [1776] [1777] [1778]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1779] [1780] [1781] [1782]) (./tcltk-pkg.tex Chapter 12. [1783] [1784] [1785] [1786] [1787] [1788] [1789] Underfull \vbox (badness 10000) has occurred while \output is active [1790] Underfull \vbox (badness 10000) has occurred while \output is active [1791] 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 [1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] 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 [1803]) (./tools-pkg.tex [1804] Chapter 13. [1805] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1806] 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 [1807] [1808] 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 [1809] [1810] 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 [1811] [1812] [1813] [1814] [1815] [1816] [1817] [1818] [1819] [1820] [1821] 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 [1822] 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- [1823] 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 , [1824] [1825] [1826] 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 [1827] [1828] [1829] Underfull \hbox (badness 7981) in paragraph at lines 1518--1522 []\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 1524--1526 []\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 [1830] [1831] [1832] [1833]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1721 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1834] [1835] Underfull \hbox (badness 5726) in paragraph at lines 1847--1852 []\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 1847--1852 \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 [1836] [1837] [1838] [1839] [1840] [1841] [1842] [1843] Underfull \hbox (badness 7981) in paragraph at lines 2323--2329 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1844] [1845] [1846] [1847] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2607. [1848] [1849] [1850] [1851] Underfull \hbox (badness 1424) in paragraph at lines 2844--2846 []\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 [1852] [1853] [1854] [1855] [1856] [1857] [1858] [1859] [1860] [1861] [1862] Underfull \hbox (badness 10000) in paragraph at lines 3539--3541 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1863] [1864] [1865] [1866] [1867] [1868] Underfull \hbox (badness 1838) in paragraph at lines 3919--3925 []\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 3919--3925 \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 [1869] [1870] Underfull \hbox (badness 5726) in paragraph at lines 3999--4004 []\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 3999--4004 \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 [1871] [1872] Underfull \hbox (badness 1688) in paragraph at lines 4142--4154 []\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 [1873] [1874] [1875] [1876]) (./utils-pkg.tex Chapter 14. [1877] 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 ', [1878] [1879] 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 [1880] [1881] [1882] [1883] [1884] [1885] 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 [1886] Underfull \hbox (badness 5847) in paragraph at lines 656--662 []\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 656--662 \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 [1887] Underfull \hbox (badness 3861) in paragraph at lines 724--729 []\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 , [1888] [1889] [1890] [1891] [1892] Underfull \vbox (badness 10000) has occurred while \output is active [1893] [1894] [1895] [1896] [1897] Underfull \hbox (badness 1371) in paragraph at lines 1320--1322 []\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 [1898] [1899] [1900] [1901] [1902] [1903] [1904] Underfull \hbox (badness 2057) in paragraph at lines 1812--1814 []\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 [1905] [1906] Underfull \hbox (badness 10000) in paragraph at lines 1913--1915 []\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 [1907] Underfull \hbox (badness 5189) in paragraph at lines 2003--2005 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1908] [1909] [1910] [1911] Underfull \hbox (badness 1661) in paragraph at lines 2221--2228 []\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 2238--2241 []\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 [1912] [1913] [1914] [1915] [1916] [1917] [1918] [1919] [1920] [1921] [1922] [1923] [1924] [1925] [1926] Underfull \hbox (badness 1412) in paragraph at lines 3235--3239 []\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 [1927] Underfull \hbox (badness 1430) in paragraph at lines 3259--3267 []\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 3302--3308 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1928] [1929] [1930] [1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940] [1941]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4123 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4123 ...mat Unordered and Ordered Lists}{format} [1942] [1943] [1944] [1945] [1946] [1947] [1948] [1949] [1950] [1951] [1952] [1953] [1954] [1955] [1956] Underfull \hbox (badness 1371) in paragraph at lines 5073--5075 []\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 [1957] Underfull \hbox (badness 1502) in paragraph at lines 5162--5167 []\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 5162--5167 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1958] [1959] [1960] Underfull \hbox (badness 10000) in paragraph at lines 5335--5344 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [1961] Underfull \hbox (badness 2150) in paragraph at lines 5398--5401 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [1962] [1963] Underfull \hbox (badness 3118) in paragraph at lines 5535--5537 []\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 [1964] Underfull \hbox (badness 2409) in paragraph at lines 5568--5572 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [1965] Underfull \hbox (badness 1325) in paragraph at lines 5676--5680 []\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 [1966] Underfull \hbox (badness 10000) in paragraph at lines 5759--5762 []\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 5759--5762 \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., [1967] Underfull \hbox (badness 3219) in paragraph at lines 5832--5839 []\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 5832--5839 \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 5832--5839 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [1968] Underfull \hbox (badness 10000) in paragraph at lines 5912--5917 [][][]\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 , [1969] [1970] [1971] [1972] [1973] [1974] [1975] [1976] [1977] [1978] [1979] [1980] [1981] [1982] [1983] [1984] [1985] [1986] [1987] [1988] Underfull \hbox (badness 10000) in paragraph at lines 7124--7126 []\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 7129--7134 []\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, [1989] [1990] [1991] [1992] [1993] [1994] [1995] [1996] [1997] Underfull \hbox (badness 1789) in paragraph at lines 7679--7681 []\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 [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] Underfull \hbox (badness 1097) in paragraph at lines 8504--8507 []\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 [2010] [2011] Underfull \hbox (badness 3000) in paragraph at lines 8640--8645 [][][]\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 ; [2012] [2013] [2014] [2015] [2016] [2017] [2018] [2019] [2020] Underfull \hbox (badness 2134) in paragraph at lines 9222--9227 [][][]\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 ; [2021] [2022] [2023] [2024] [2025] [2026] [2027] Underfull \hbox (badness 2469) in paragraph at lines 9655--9659 []\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 9655--9659 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2028] [2029] [2030] [2031] [2032] [2033] Underfull \hbox (badness 10000) in paragraph at lines 9996--9998 []\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 [2034] [2035] Underfull \hbox (badness 2150) in paragraph at lines 10172--10174 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2036] [2037] [2038] Underfull \hbox (badness 10000) in paragraph at lines 10350--10354 []\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 [2039] Underfull \hbox (badness 10000) in paragraph at lines 10381--10387 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2040] Underfull \hbox (badness 2096) in paragraph at lines 10499--10502 []\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 10503--10506 []\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 [2041] Underfull \hbox (badness 1009) in paragraph at lines 10569--10580 []\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 [2042] [2043] [2044] [2045] [2046] Underfull \hbox (badness 3780) in paragraph at lines 10868--10872 []\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 10884--10887 []\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 [2047] [2048] [2049] [2050] [2051] [2052] Underfull \hbox (badness 5970) in paragraph at lines 11258--11261 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2053] [2054] [2055] Underfull \hbox (badness 10000) in paragraph at lines 11437--11439 []\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 [2056] [2057] [2058] [2059] [2060] [2061] Underfull \hbox (badness 10000) in paragraph at lines 11838--11841 [][][]$\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 11838--11841 \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 [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] [2070] Underfull \hbox (badness 10000) in paragraph at lines 12368--12370 []\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 12371--12373 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2071] Underfull \hbox (badness 10000) in paragraph at lines 12401--12406 []\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 12401--12406 [][]\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 12430--12433 [][][]\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 , [2072] [2073] [2074] [2075] Overfull \hbox (25.86961pt too wide) in paragraph at lines 12669--12672 [][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi -gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](, package = "") [2076] [2077] Underfull \hbox (badness 1454) in paragraph at lines 12747--12751 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, [2078] Underfull \hbox (badness 10000) in paragraph at lines 12817--12819 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion [2079] [2080] [2081]) [2082] (./refman.ind [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] [2102] [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] Overfull \hbox (5.8567pt too wide) in paragraph at lines 11156--11158 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_depends Overfull \hbox (5.8567pt too wide) in paragraph at lines 11158--11160 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_results Overfull \hbox (5.8567pt too wide) in paragraph at lines 11160--11162 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_timings [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151]) (./refman.aux) Package rerunfilecheck Warning: File `refman.out' has changed. 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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 pdfTeX warning (dest): name{Rfn.gamma.shape} has been referenced but does not e xist, replaced by a fixed one pdfTeX 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Transcript written on refman.log. 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 <2015/01/01> Babel <3.9l> and hyphenation patterns for 2 languages 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? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 511--517 []\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 1122--1125 []\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 1339--1345 []\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] Overfull \hbox (26.88089pt too wide) in paragraph at lines 1849--1849 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [30] [31] [32] Underfull \hbox (badness 10000) in paragraph at lines 2034--2036 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] Underfull \hbox (badness 10000) in paragraph at lines 3532--3534 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [56] [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 4728--4730 []\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] [93] Underfull \hbox (badness 2096) in paragraph at lines 5945--5958 []\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 [94] [95] [96] Overfull \hbox (58.35893pt too wide) in paragraph at lines 6146--6149 []\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 : [97] [98] Underfull \hbox (badness 10000) in paragraph at lines 6290--6293 []\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 [99] [100] Underfull \hbox (badness 1442) in paragraph at lines 6451--6457 []\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 6451--6457 \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 6451--6457 \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 [101] Underfull \hbox (badness 3568) in paragraph at lines 6512--6519 \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 [102] [103] Underfull \vbox (badness 10000) has occurred while \output is active [104] [105] [106] [107] [108] [109] [110] [111] Underfull \hbox (badness 2096) in paragraph at lines 7149--7153 \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 . [112] Underfull \hbox (badness 4595) in paragraph at lines 7206--7209 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [113] Underfull \hbox (badness 3000) in paragraph at lines 7242--7244 []\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 7267--7270 [][][]\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 , [114] [115] [116] [117] Underfull \hbox (badness 10000) in paragraph at lines 7517--7528 []\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 [118] Underfull \hbox (badness 4479) in paragraph at lines 7589--7598 [][][]\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 7589--7598 [][]\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 [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] Underfull \hbox (badness 1394) in paragraph at lines 9200--9205 []\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 [144] [145] [146] [147] [148] Underfull \hbox (badness 1052) in paragraph at lines 9537--9542 []\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 9537--9542 \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 [149] [150] Underfull \hbox (badness 1735) in paragraph at lines 9675--9679 \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 . [151] [152] [153] [154] [155] [156] Underfull \hbox (badness 2150) in paragraph at lines 10079--10082 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse [157] Underfull \hbox (badness 6396) in paragraph at lines 10093--10101 []\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 10134--10141 []\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 [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] Underfull \hbox (badness 4569) in paragraph at lines 11178--11182 []\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 11178--11182 \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 [174] [175] [176] [177] [178] [179] [180] [181] Underfull \hbox (badness 2698) in paragraph at lines 11754--11763 []\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 11754--11763 \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 [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] Underfull \hbox (badness 6236) in paragraph at lines 12398--12401 []\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 [192] [193] [194] [195] [196] [197] Underfull \hbox (badness 2253) in paragraph at lines 12776--12778 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [198] Underfull \hbox (badness 1565) in paragraph at lines 12847--12851 [][][]\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 [199] Underfull \hbox (badness 10000) in paragraph at lines 12891--12893 []\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 [200] [201] Underfull \hbox (badness 1466) in paragraph at lines 13032--13035 []\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 [202] [203] Underfull \hbox (badness 10000) in paragraph at lines 13140--13144 [][][]\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 13151--13154 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [204] [205] [206] [207] Underfull \hbox (badness 3965) in paragraph at lines 13403--13407 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] Underfull \hbox (badness 4429) in paragraph at lines 14133--14136 []\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 [219] Underfull \hbox (badness 10000) in paragraph at lines 14225--14227 []\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 14231--14235 []\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 [220] Underfull \hbox (badness 10000) in paragraph at lines 14273--14277 []\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 14273--14277 \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 [221] Underfull \vbox (badness 3803) has occurred while \output is active [222] [223] [224] [225] [226] [227] [228] [229] Underfull \hbox (badness 2452) in paragraph at lines 14853--14857 []\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 14853--14857 \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 [230] [231] [232] Underfull \hbox (badness 1092) in paragraph at lines 15026--15031 [][]\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 [233] [234] [235] [236] Underfull \hbox (badness 6741) in paragraph at lines 15274--15278 \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 , [237] [238] [239] [240] Underfull \hbox (badness 1867) in paragraph at lines 15580--15587 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [241] [242] [243] [244] Underfull \vbox (badness 10000) has occurred while \output is active [245] [246] Underfull \hbox (badness 3679) in paragraph at lines 15960--15962 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [247] [248] [249] [250] [251] [252] [253] Underfull \hbox (badness 1478) in paragraph at lines 16440--16443 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [254] [255] [256] [257] Underfull \hbox (badness 10000) in paragraph at lines 16693--16695 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [258] [259] [260] [261] [262] [263] [264] [265] [266] Underfull \hbox (badness 1442) in paragraph at lines 17256--17258 []\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 [267] Underfull \hbox (badness 2452) in paragraph at lines 17348--17364 [][][]\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 , [268] [269] [270] [271] [272] [273] [274] Underfull \hbox (badness 1248) in paragraph at lines 17756--17759 []\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 , [275] [276] [277] [278] Underfull \hbox (badness 4739) in paragraph at lines 18012--18014 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [279] [280] [281] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] Underfull \hbox (badness 1360) in paragraph at lines 18960--18965 \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 18983--18989 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / Underfull \hbox (badness 1127) in paragraph at lines 18983--18989 \T1/zi4/m/n/10 ssl-[]compared . html$[][] \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 [295] Underfull \hbox (badness 10000) in paragraph at lines 19056--19060 []\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 19056--19060 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [296] [297] Underfull \hbox (badness 1509) in paragraph at lines 19191--19198 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1354) in paragraph at lines 19191--19198 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19207--19212 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] [309] Underfull \hbox (badness 1264) in paragraph at lines 19938--19943 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] Underfull \hbox (badness 10000) in paragraph at lines 20692--20694 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] Underfull \hbox (badness 1077) in paragraph at lines 21690--21696 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [337] [338] [339] Underfull \hbox (badness 1484) in paragraph at lines 21851--21859 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [340] [341] [342] [343] Underfull \hbox (badness 2790) in paragraph at lines 22122--22125 []\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 22122--22125 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [344] [345] [346] [347] Underfull \hbox (badness 1194) in paragraph at lines 22403--22406 []\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 [348] [349] [350] [351] Underfull \hbox (badness 10000) in paragraph at lines 22609--22615 []\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 22609--22615 \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 22619--22622 []\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 22619--22622 \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 [352] [353] [354] [355] [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] Underfull \hbox (badness 10000) in paragraph at lines 23544--23546 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [366] [367] [368] [369] Underfull \hbox (badness 1199) in paragraph at lines 23771--23777 []\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 23771--23777 \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, [370] [371] [372] [373] [374] [375] [376] [377] Underfull \hbox (badness 1038) in paragraph at lines 24336--24344 []\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 24345--24348 []\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 24364--24366 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [378] Underfull \hbox (badness 10000) in paragraph at lines 24436--24446 []\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 24447--24453 []\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 24460--24465 []\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 24470--24472 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [379] [380] [381] Underfull \hbox (badness 10000) in paragraph at lines 24721--24727 []\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 24721--24727 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "http://bioconductor.org"\T1/p tm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 24721--24727 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "http://bioconductor.statistik.tu-dortmund.de"\T 1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 24734--24737 []\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 [382] Underfull \hbox (badness 2689) in paragraph at lines 24758--24760 []\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 24790--24795 []\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 24796--24807 \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 24808--24811 []\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 Underfull \hbox (badness 4084) in paragraph at lines 24818--24830 \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 24818--24830 \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 24818--24830 \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 24832--24839 []\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 24832--24839 \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 24832--24839 \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 24832--24839 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [383] [384] [385] [386] [387] Underfull \hbox (badness 10000) in paragraph at lines 25153--25157 []\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 25153--25157 \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)] [388] [389] [390] [391] [392] Underfull \hbox (badness 1735) in paragraph at lines 25471--25475 []\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 [393] [394] [395] [396] [397] [398] [399] [400] [401] [402] Underfull \hbox (badness 2726) in paragraph at lines 26030--26033 []\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 [403] [404] [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] [415] Underfull \hbox (badness 1052) in paragraph at lines 26849--26854 []\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 [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] Underfull \hbox (badness 1533) in paragraph at lines 27577--27580 []\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 [427] [428] Underfull \hbox (badness 1163) in paragraph at lines 27739--27749 []\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 [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] Underfull \hbox (badness 10000) in paragraph at lines 29241--29245 []\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 29241--29245 \T1/zi4/m/n/10 "(?[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 29263--29265 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [453] [454] [455] [456] [457] [458] [459] [460] [461] Underfull \hbox (badness 1655) in paragraph at lines 29808--29810 []\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 [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] Underfull \hbox (badness 10000) in paragraph at lines 30476--30480 []\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., [473] [474] [475] Underfull \hbox (badness 2302) in paragraph at lines 30716--30723 []\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 30716--30723 \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 30716--30723 \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 30716--30723 \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 [476] [477] [478] Underfull \hbox (badness 2261) in paragraph at lines 30870--30875 []\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 30897--30903 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [479] Underfull \hbox (badness 10000) in paragraph at lines 30973--30978 []\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 [480] [481] [482] [483] [484] [485] [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] Underfull \hbox (badness 1072) in paragraph at lines 33757--33761 []\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 33762--33766 []\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 ', [523] Underfull \hbox (badness 10000) in paragraph at lines 33790--33796 []\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 33790--33796 \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 33790--33796 \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 33803--33810 \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 33803--33810 \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 33803--33810 \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 [524] [525] [526] [527] [528] Underfull \hbox (badness 10000) in paragraph at lines 34094--34100 []\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 34094--34100 \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 [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] Underfull \hbox (badness 3333) in paragraph at lines 35877--35882 []\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 [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] Underfull \hbox (badness 1472) in paragraph at lines 36497--36500 []\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 [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] Underfull \hbox (badness 2671) in paragraph at lines 37159--37162 []\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 [578] [579] [580] [581] [582] [583] Underfull \hbox (badness 10000) in paragraph at lines 37563--37566 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$http : / / developer . r-[]project . org / [584] [585] Underfull \hbox (badness 10000) in paragraph at lines 37684--37688 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 http : / / developer . [586] Underfull \hbox (badness 10000) in paragraph at lines 37746--37750 [][][]\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 http : / / developer . [587] [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] Underfull \hbox (badness 1990) in paragraph at lines 39041--39049 []\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 39041--39049 \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 [606] [607] [608] [609] [610] Underfull \hbox (badness 1515) in paragraph at lines 39313--39318 []\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 [611] [612] [613] Underfull \hbox (badness 1917) in paragraph at lines 39543--39550 []\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 [614] [615] [616] [617] [618] [619] [620] [621] [622] Underfull \hbox (badness 3668) in paragraph at lines 40128--40130 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [623] [624] Underfull \hbox (badness 2401) in paragraph at lines 40233--40237 []\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 [625] [626] [627] Underfull \hbox (badness 2111) in paragraph at lines 40402--40407 \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. Underfull \hbox (badness 6542) in paragraph at lines 40418--40423 []\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 [628] [629] [630] [631] [632] [633] [634] Underfull \hbox (badness 10000) in paragraph at lines 40863--40868 []\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 40863--40868 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to [635] [636] Underfull \hbox (badness 5417) in paragraph at lines 40955--40959 []\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 [637] Underfull \hbox (badness 10000) in paragraph at lines 41016--41020 []\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 [638]) (./compiler-pkg.tex Chapter 2. [639] [640] [641] [642]) (./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 [643] [644] [645] [646] [647] [648] [649] [650] [651] [652] [653] [654] [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] Underfull \vbox (badness 1515) has occurred while \output is active [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] 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 / [710] Underfull \vbox (badness 10000) has occurred while \output is active [711] [712] [713] [714] Underfull \vbox (badness 10000) has occurred while \output is active [715] Underfull \vbox (badness 10000) has occurred while \output is active [716] [717] [718] [719] [720] [721] [722] [723]) (./grDevices-pkg.tex [724] Chapter 4. [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] Underfull \hbox (badness 5175) in paragraph at lines 1066--1068 []\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 [742] [743] [744] [745] Underfull \hbox (badness 1852) in paragraph at lines 1263--1266 []\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 [746] [747] [748] Underfull \hbox (badness 1490) in paragraph at lines 1469--1474 \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 [749] Underfull \hbox (badness 2698) in paragraph at lines 1523--1526 []\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 [750] Underfull \hbox (badness 10000) in paragraph at lines 1592--1596 []\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 [751] [752] [753] [754] Underfull \hbox (badness 1325) in paragraph at lines 1875--1885 \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 , [755] [756] Underfull \hbox (badness 10000) in paragraph at lines 1980--1982 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [757] [758] [759] Underfull \hbox (badness 6758) in paragraph at lines 2141--2144 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [760] [761] [762] [763] [764] [765] [766] [767] [768] Underfull \hbox (badness 10000) in paragraph at lines 2707--2708 [769] [770] [771] [772] [773] [774] [775] Underfull \hbox (badness 1152) in paragraph at lines 3145--3147 []\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 [776] [777] [778] [779] [780] Underfull \hbox (badness 2856) in paragraph at lines 3465--3468 []\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 3479--3481 []\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 [781] [782] Underfull \hbox (badness 1173) in paragraph at lines 3595--3605 []\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 [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] Underfull \hbox (badness 1067) in paragraph at lines 4302--4309 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [794] [795] Underfull \hbox (badness 3364) in paragraph at lines 4463--4465 []\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 / [796] Underfull \hbox (badness 1789) in paragraph at lines 4540--4542 []\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 [797] Underfull \hbox (badness 1377) in paragraph at lines 4590--4595 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [798] Underfull \hbox (badness 2671) in paragraph at lines 4617--4625 \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 4666--4673 \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 4674--4683 \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 4674--4683 \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 4684--4686 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [799] [800] Underfull \hbox (badness 1057) in paragraph at lines 4795--4800 []\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 [801] Underfull \hbox (badness 7344) in paragraph at lines 4855--4857 []\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 [802] [803] Underfull \hbox (badness 2035) in paragraph at lines 4979--4988 []\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 4979--4988 \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 4979--4988 \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 , [804] Underfull \hbox (badness 10000) in paragraph at lines 5048--5055 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5048--5055 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [805] [806] [807] Underfull \hbox (badness 1546) in paragraph at lines 5186--5194 []\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 , [808] Underfull \hbox (badness 1648) in paragraph at lines 5263--5267 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [809] [810] [811] [812] [813] [814] [815] Underfull \hbox (badness 10000) in paragraph at lines 5686--5689 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [816] Underfull \vbox (badness 3803) has occurred while \output is active [817] [818] [819] [820] [821] Underfull \hbox (badness 1189) in paragraph at lines 6083--6085 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [822] [823] Underfull \hbox (badness 10000) in paragraph at lines 6181--6183 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [824] [825] [826] [827] Underfull \hbox (badness 3780) in paragraph at lines 6472--6478 []\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 , [828] [829] [830] Underfull \hbox (badness 2680) in paragraph at lines 6668--6670 []\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 [831] [832] [833]) (./graphics-pkg.tex [834] Chapter 5. [835] [836] [837] [838] [839] [840] [841] [842] [843] [844] [845] 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 [846] [847] [848] [849] Underfull \vbox (badness 3803) has occurred while \output is active [850] [851] [852] [853] [854] 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 , [855] [856] [857] [858] [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] [869] [870] [871] Underfull \hbox (badness 1009) in paragraph at lines 2277--2284 \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 [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] Underfull \vbox (badness 10000) has occurred while \output is active [894] Underfull \vbox (badness 10000) has occurred while \output is active [895] [896] [897] [898] Underfull \hbox (badness 1867) in paragraph at lines 3901--3905 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [899] [900] [901] [902] [903] [904] [905] Underfull \hbox (badness 1924) in paragraph at lines 4348--4353 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain [906] Underfull \hbox (badness 2529) in paragraph at lines 4379--4382 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used: see [907] [908] [909] [910] [911] Underfull \hbox (badness 10000) in paragraph at lines 4729--4735 []\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 4729--4735 \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 [912] Underfull \hbox (badness 10000) in paragraph at lines 4860--4863 [913] [914 ] Underfull \hbox (badness 10000) in paragraph at lines 4921--4923 [915 ] [916] Underfull \hbox (badness 10000) in paragraph at lines 5111--5113 []\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 [917] [918] [919] [920] [921] Underfull \vbox (badness 10000) has occurred while \output is active [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6581--6582 [][] [941 ] [942] Underfull \vbox (badness 10000) has occurred while \output is active [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] Underfull \hbox (badness 1048) in paragraph at lines 7290--7295 \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 [953] Underfull \hbox (badness 1038) in paragraph at lines 7406--7409 []\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 [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] [971] [972] [973] [974] Underfull \hbox (badness 6691) in paragraph at lines 8625--8628 []\T1/ptm/m/n/10 The main ti-tle (on top) us-ing font and size (char-ac-ter ex- pan-sion) Underfull \hbox (badness 2799) in paragraph at lines 8628--8630 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font and size \T1/zi4/m/n/10 par ("font.sub") \T1/ptm/m/n/10 and color [975] [976]pdfTeX warning (ext4): destination with the same identifier (name{Rf n.units}) has been already used, duplicate ignored \relax l.8710 \HeaderA{units}{Graphical Units}{units} [977] [978] [979] [980]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [981] [982] [983] [984] [985] [986] 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 [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] 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 , [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [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] Underfull \vbox (badness 3803) has occurred while \output is active [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] 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 [1054] [1055] [1056] [1057] 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 [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] Underfull \hbox (badness 10000) in paragraph at lines 5854--5860 \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., [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] Underfull \hbox (badness 7649) in paragraph at lines 6324--6327 []\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 [1087] [1088] [1089] [1090]) (./methods-pkg.tex Chapter 7. [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] 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 [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] 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 [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] 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 [1128] [1129] 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 [1130] 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 [1131] [1132] [1133] [1134] [1135] [1136] [1137] 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 [1138] [1139] [1140] [1141] [1142] 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 [1143] [1144] [1145] [1146] [1147] [1148] Underfull \vbox (badness 10000) has occurred while \output is active [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156] 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 [1157] [1158] [1159] [1160] [1161] [1162] Underfull \vbox (badness 2452) has occurred while \output is active [1163] [1164] Underfull \vbox (badness 10000) has occurred while \output is active [1165] [1166] 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 [1167] [1168] [1169] [1170] [1171] 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 [1172] [1173] [1174] [1175] 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 [1176] [1177] [1178] [1179] [1180] Underfull \hbox (badness 1675) in paragraph at lines 6343--6349 \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 [1181] [1182] [1183] [1184] Underfull \vbox (badness 10000) has occurred while \output is active [1185] [1186]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4} ) has been already used, duplicate ignored \relax l.6820 \aliasA{S4}{S3Part}{S4} [1187] [1188] [1189] [1190]pdfTeX warning (ext4) : destination with the same identifier (name{Rfn.Complex}) has been already use d, duplicate ignored \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 \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 \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 \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 \relax l.7102 \aliasA{Summary}{S4groupGeneric}{Summary} [1191] 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 [1192] [1193] [1194] 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 [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] Underfull \hbox (badness 1852) in paragraph at lines 9759--9763 []\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., [1229] [1230] [1231] [1232]) (./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 [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] Underfull \hbox (badness 3386) in paragraph at lines 1246--1249 []\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 [1253] [1254]) (./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 \T1/ptm/ m/n/10 and William N. Ven-ables [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269]) (./stats-pkg.tex [1270] Chapter 10. [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] Underfull \hbox (badness 1412) in paragraph at lines 844--846 []\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 [1284] [1285] [1286] [1287] [1288] [1289] [1290] [1291] Underfull \hbox (badness 2503) in paragraph at lines 1325--1328 []\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 , [1292] [1293] [1294] Underfull \hbox (badness 10000) in paragraph at lines 1504--1508 []\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 [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] Underfull \hbox (badness 3965) in paragraph at lines 2164--2166 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1306] [1307] [1308] [1309] [1310] Underfull \hbox (badness 3965) in paragraph at lines 2506--2508 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] Underfull \hbox (badness 2503) in paragraph at lines 3323--3326 []\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 , [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 3989) in paragraph at lines 4548--4555 []\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 = [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] Underfull \hbox (badness 2556) in paragraph at lines 5149--5152 []\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 5166--5168 []\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 [1354] [1355] [1356] [1357] Underfull \hbox (badness 1142) in paragraph at lines 5407--5419 \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. [1358] [1359] Underfull \hbox (badness 2503) in paragraph at lines 5546--5550 []\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 , [1360] Underfull \hbox (badness 1168) in paragraph at lines 5607--5612 []\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 [1361] [1362] [1363] [1364] [1365] [1366] [1367] Underfull \hbox (badness 8132) in paragraph at lines 6049--6054 \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, [1368] [1369] [1370] [1371] [1372] Underfull \hbox (badness 7081) in paragraph at lines 6324--6327 []\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 6328--6330 []\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 [1373] [1374] [1375] [1376] [1377] Underfull \vbox (badness 3803) has occurred while \output is active [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] Underfull \hbox (badness 10000) in paragraph at lines 7136--7139 []\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 [1386] [1387] Underfull \hbox (badness 10000) in paragraph at lines 7273--7276 []\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 / [1388] [1389] [1390] [1391] Underfull \vbox (badness 3803) has occurred while \output is active [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] Underfull \hbox (badness 2626) in paragraph at lines 8771--8774 []\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 [1413] Underfull \hbox (badness 2503) in paragraph at lines 8871--8875 []\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 , [1414] [1415] [1416] [1417] [1418] Overfull \hbox (6.88992pt too wide) in paragraph at lines 9205--9207 []\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 . [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] Underfull \hbox (badness 4518) in paragraph at lines 10132--10137 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1434] [1435] [1436] [1437] Underfull \hbox (badness 2142) in paragraph at lines 10474--10477 []\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 ^^@ [1438] Underfull \hbox (badness 1253) in paragraph at lines 10493--10496 []\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, [1439] Underfull \hbox (badness 1708) in paragraph at lines 10555--10559 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1440] [1441] [1442] [1443] [1444] [1445] Underfull \hbox (badness 1694) in paragraph at lines 10951--10954 []\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 10970--10979 \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- [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453]pdfTeX warning (ext4): d estination with the same identifier (name{Rfn.hat}) has been already used, dupl icate ignored \relax l.11417 \aliasA{hat}{influence.measures}{hat} [1454] [1455] Underfull \hbox (badness 1484) in paragraph at lines 11540--11542 []\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 [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 4441) in paragraph at lines 12098--12100 []\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 12105--12107 []\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 [1465] [1466] [1467] [1468] [1469] [1470] Underfull \hbox (badness 2894) in paragraph at lines 12439--12443 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] Underfull \hbox (badness 4518) in paragraph at lines 13134--13139 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1482] [1483] [1484] [1485] [1486] [1487] [1488] [1489] [1490] [1491] Underfull \hbox (badness 4518) in paragraph at lines 13781--13786 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1492] [1493] Underfull \hbox (badness 10000) in paragraph at lines 13919--13923 []\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 13926--13928 []\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 [1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] [1509] [1510] [1511] Underfull \hbox (badness 2503) in paragraph at lines 14990--14994 []\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 , [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] Underfull \hbox (badness 1418) in paragraph at lines 15499--15505 []\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 [1520] [1521] [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] Underfull \hbox (badness 2359) in paragraph at lines 17123--17125 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1546] [1547] Underfull \vbox (badness 10000) has occurred while \output is active [1548] Underfull \vbox (badness 10000) has occurred while \output is active [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] Underfull \hbox (badness 1377) in paragraph at lines 18034--18039 []\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 18039--18042 []\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 18052--18056 \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 18060--18064 []\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 [1562] [1563] [1564] Underfull \vbox (badness 10000) has occurred while \output is active [1565] [1566] [1567] [1568] [1569] [1570] [1571] Underfull \hbox (badness 1337) in paragraph at lines 18676--18679 []\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 [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] Underfull \hbox (badness 5563) in paragraph at lines 19406--19408 []\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 19409--19412 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1585] [1586] [1587] [1588] [1589] [1590] Underfull \hbox (badness 2503) in paragraph at lines 19776--19779 []\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 , [1591] Underfull \hbox (badness 10000) in paragraph at lines 19803--19805 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602] [1603] [1604] [1605] [1606] [1607] Underfull \hbox (badness 10000) in paragraph at lines 20803--20809 []\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 , [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] Underfull \hbox (badness 1337) in paragraph at lines 22138--22144 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1631] [1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] Underfull \hbox (badness 10000) in paragraph at lines 22931--22934 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1643] [1644] [1645] [1646] [1647] [1648] [1649] [1650] [1651] Underfull \hbox (badness 10000) in paragraph at lines 23508--23511 []\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 [1652] Underfull \hbox (badness 3690) in paragraph at lines 23559--23563 [][][]\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 [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] Underfull \hbox (badness 3439) in paragraph at lines 24029--24035 [][]\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 , [1661] [1662] [1663] [1664] [1665] [1666] [1667] [1668] [1669] Underfull \hbox (badness 10000) in paragraph at lines 24577--24582 []\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 [1670] [1671] [1672] [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] Underfull \vbox (badness 3803) has occurred while \output is active [1685] [1686] Underfull \hbox (badness 3514) in paragraph at lines 25593--25598 []\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 [1687] Underfull \hbox (badness 3514) in paragraph at lines 25655--25660 []\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 [1688] Underfull \hbox (badness 3514) in paragraph at lines 25712--25717 []\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 [1689] Underfull \hbox (badness 3514) in paragraph at lines 25773--25779 []\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 [1690] [1691] [1692] [1693] Underfull \hbox (badness 3514) in paragraph at lines 25986--25991 []\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 Underfull \hbox (badness 3514) in paragraph at lines 26042--26047 []\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 [1694] Underfull \hbox (badness 3514) in paragraph at lines 26099--26104 []\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 [1695] Underfull \hbox (badness 3514) in paragraph at lines 26154--26159 []\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 [1696] [1697] Underfull \hbox (badness 6691) in paragraph at lines 26223--26228 []\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 [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] Underfull \hbox (badness 10000) in paragraph at lines 26747--26750 []\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 26747--26750 \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, [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] Underfull \hbox (badness 5431) in paragraph at lines 27353--27355 []\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 [1716] [1717] [1718] [1719] Underfull \hbox (badness 5431) in paragraph at lines 27563--27566 []\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 [1720] [1721] [1722] [1723] [1724] Underfull \hbox (badness 1337) in paragraph at lines 27875--27879 []\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 [1725] [1726] Underfull \hbox (badness 10000) in paragraph at lines 27992--27995 []\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 [1727] [1728] [1729] Underfull \hbox (badness 1616) in paragraph at lines 28175--28178 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] Underfull \hbox (badness 10000) in paragraph at lines 29302--29306 []\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 [1749] [1750] [1751] Underfull \vbox (badness 10000) has occurred while \output is active [1752] [1753] [1754] Underfull \hbox (badness 1337) in paragraph at lines 29666--29670 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] Underfull \hbox (badness 1337) in paragraph at lines 30150--30154 []\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 [1763] Underfull \hbox (badness 5161) in paragraph at lines 30243--30245 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1764] [1765] [1766] [1767] [1768] [1769] Underfull \hbox (badness 10000) in paragraph at lines 30607--30612 []\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 [1770] [1771] [1772]) (./stats4-pkg.tex Chapter 11. [1773] [1774] [1775] [1776] [1777] [1778]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1779] [1780] [1781] [1782]) (./tcltk-pkg.tex Chapter 12. [1783] [1784] [1785] [1786] [1787] [1788] [1789] Underfull \vbox (badness 10000) has occurred while \output is active [1790] Underfull \vbox (badness 10000) has occurred while \output is active [1791] 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 [1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] 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 [1803]) (./tools-pkg.tex [1804] Chapter 13. [1805] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1806] 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 [1807] [1808] 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 [1809] [1810] 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 [1811] [1812] [1813] [1814] [1815] [1816] [1817] [1818] [1819] [1820] [1821] 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 [1822] 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- [1823] 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 , [1824] [1825] [1826] 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 [1827] [1828] [1829] Underfull \hbox (badness 7981) in paragraph at lines 1518--1522 []\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 1524--1526 []\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 [1830] [1831] [1832] [1833]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1721 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1834] [1835] Underfull \hbox (badness 5726) in paragraph at lines 1847--1852 []\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 1847--1852 \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 [1836] [1837] [1838] [1839] [1840] [1841] [1842] [1843] Underfull \hbox (badness 7981) in paragraph at lines 2323--2329 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1844] [1845] [1846] [1847] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2607. [1848] [1849] [1850] [1851] Underfull \hbox (badness 1424) in paragraph at lines 2844--2846 []\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 [1852] [1853] [1854] [1855] [1856] [1857] [1858] [1859] [1860] [1861] [1862] Underfull \hbox (badness 10000) in paragraph at lines 3539--3541 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1863] [1864] [1865] [1866] [1867] [1868] Underfull \hbox (badness 1838) in paragraph at lines 3919--3925 []\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 3919--3925 \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 [1869] [1870] Underfull \hbox (badness 5726) in paragraph at lines 3999--4004 []\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 3999--4004 \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 [1871] [1872] Underfull \hbox (badness 1688) in paragraph at lines 4142--4154 []\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 [1873] [1874] [1875] [1876]) (./utils-pkg.tex Chapter 14. [1877] 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 ', [1878] [1879] 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 [1880] [1881] [1882] [1883] [1884] [1885] 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 [1886] Underfull \hbox (badness 5847) in paragraph at lines 656--662 []\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 656--662 \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 [1887] Underfull \hbox (badness 3861) in paragraph at lines 724--729 []\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 , [1888] [1889] [1890] [1891] [1892] Underfull \vbox (badness 10000) has occurred while \output is active [1893] [1894] [1895] [1896] [1897] Underfull \hbox (badness 1371) in paragraph at lines 1320--1322 []\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 [1898] [1899] [1900] [1901] [1902] [1903] [1904] Underfull \hbox (badness 2057) in paragraph at lines 1812--1814 []\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 [1905] [1906] Underfull \hbox (badness 10000) in paragraph at lines 1913--1915 []\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 [1907] Underfull \hbox (badness 5189) in paragraph at lines 2003--2005 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1908] [1909] [1910] [1911] Underfull \hbox (badness 1661) in paragraph at lines 2221--2228 []\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 2238--2241 []\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 [1912] [1913] [1914] [1915] [1916] [1917] [1918] [1919] [1920] [1921] [1922] [1923] [1924] [1925] [1926] Underfull \hbox (badness 1412) in paragraph at lines 3235--3239 []\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 [1927] Underfull \hbox (badness 1430) in paragraph at lines 3259--3267 []\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 3302--3308 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1928] [1929] [1930] [1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940] [1941]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4123 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4123 ...mat Unordered and Ordered Lists}{format} [1942] [1943] [1944] [1945] [1946] [1947] [1948] [1949] [1950] [1951] [1952] [1953] [1954] [1955] [1956] Underfull \hbox (badness 1371) in paragraph at lines 5073--5075 []\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 [1957] Underfull \hbox (badness 1502) in paragraph at lines 5162--5167 []\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 5162--5167 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1958] [1959] [1960] Underfull \hbox (badness 10000) in paragraph at lines 5335--5344 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [1961] Underfull \hbox (badness 2150) in paragraph at lines 5398--5401 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [1962] [1963] Underfull \hbox (badness 3118) in paragraph at lines 5535--5537 []\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 [1964] Underfull \hbox (badness 2409) in paragraph at lines 5568--5572 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [1965] Underfull \hbox (badness 1325) in paragraph at lines 5676--5680 []\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 [1966] Underfull \hbox (badness 10000) in paragraph at lines 5759--5762 []\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 5759--5762 \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., [1967] Underfull \hbox (badness 3219) in paragraph at lines 5832--5839 []\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 5832--5839 \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 5832--5839 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [1968] Underfull \hbox (badness 10000) in paragraph at lines 5912--5917 [][][]\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 , [1969] [1970] [1971] [1972] [1973] [1974] [1975] [1976] [1977] [1978] [1979] [1980] [1981] [1982] [1983] [1984] [1985] [1986] [1987] [1988] Underfull \hbox (badness 10000) in paragraph at lines 7124--7126 []\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 7129--7134 []\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, [1989] [1990] [1991] [1992] [1993] [1994] [1995] [1996] [1997] Underfull \hbox (badness 1789) in paragraph at lines 7679--7681 []\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 [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] Underfull \hbox (badness 1097) in paragraph at lines 8504--8507 []\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 [2010] [2011] Underfull \hbox (badness 3000) in paragraph at lines 8640--8645 [][][]\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 ; [2012] [2013] [2014] [2015] [2016] [2017] [2018] [2019] [2020] Underfull \hbox (badness 2134) in paragraph at lines 9222--9227 [][][]\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 ; [2021] [2022] [2023] [2024] [2025] [2026] [2027] Underfull \hbox (badness 2469) in paragraph at lines 9655--9659 []\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 9655--9659 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2028] [2029] [2030] [2031] [2032] [2033] Underfull \hbox (badness 10000) in paragraph at lines 9996--9998 []\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 [2034] [2035] Underfull \hbox (badness 2150) in paragraph at lines 10172--10174 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2036] [2037] [2038] Underfull \hbox (badness 10000) in paragraph at lines 10350--10354 []\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 [2039] Underfull \hbox (badness 10000) in paragraph at lines 10381--10387 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2040] Underfull \hbox (badness 2096) in paragraph at lines 10499--10502 []\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 10503--10506 []\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 [2041] Underfull \hbox (badness 1009) in paragraph at lines 10569--10580 []\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 [2042] [2043] [2044] [2045] [2046] Underfull \hbox (badness 3780) in paragraph at lines 10868--10872 []\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 10884--10887 []\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 [2047] [2048] [2049] [2050] [2051] [2052] Underfull \hbox (badness 5970) in paragraph at lines 11258--11261 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2053] [2054] [2055] Underfull \hbox (badness 10000) in paragraph at lines 11437--11439 []\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 [2056] [2057] [2058] [2059] [2060] [2061] Underfull \hbox (badness 10000) in paragraph at lines 11838--11841 [][][]$\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 11838--11841 \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 [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] [2070] Underfull \hbox (badness 10000) in paragraph at lines 12368--12370 []\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 12371--12373 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2071] Underfull \hbox (badness 10000) in paragraph at lines 12401--12406 []\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 12401--12406 [][]\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 12430--12433 [][][]\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 , [2072] [2073] [2074] [2075] Overfull \hbox (25.86961pt too wide) in paragraph at lines 12669--12672 [][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi -gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](, package = "") [2076] [2077] Underfull \hbox (badness 1454) in paragraph at lines 12747--12751 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, [2078] Underfull \hbox (badness 10000) in paragraph at lines 12817--12819 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion [2079] [2080] [2081]) [2082] (./refman.ind [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] [2102] [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] Overfull \hbox (5.8567pt too wide) in paragraph at lines 11156--11158 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_depends Overfull \hbox (5.8567pt too wide) in paragraph at lines 11158--11160 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_results Overfull \hbox (5.8567pt too wide) in paragraph at lines 11160--11162 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_timings [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151]) (./refman.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 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-ad min.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/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] [20] Underfull \hbox (badness 10000) in paragraph at lines 1795--1804 @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 1924--1924 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [24] [25] Underfull \hbox (badness 6842) in paragraph at lines 2115--2124 []@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 2214--2224 []@textrm The de-fault com-pil-ers spec-i-fied in @texttt /Library/Frameworks/R .framework/Resources/etc/Makeconf[] [27] [28] [29] [30] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2500--2500 []@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 2520--2520 []@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 2521--2521 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [31] [32] [33] Chapter 8 [34] Chapter 9 [35] [36] [37] Appendix A [38] [39] [40] [41] [42] [43] [44] [45] [46] Overfull \hbox (26.43913pt too wide) in paragraph at lines 3745--3745 []@texttt ln -s /opt/acml5.1.0/gfortran64_mp/lib/libacml_mp.so @textttsl R_HOM E@texttt /lib/libRblas.so[] [47] Appendix B [48] [49] [50] [51] [52] [53] Appendix C [54] [55] [56] [57] Overfull \hbox (22.38167pt too wide) in paragraph at lines 4603--4607 []@textrm Others have re-ported suc-cess with ver-sions 10.x and 11.x. % https: //stat.ethz.ch/pipermail/r- [58] [59] [60] Overfull \hbox (106.92076pt too wide) in paragraph at lines 4792--4792 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [61] [62] Overfull \hbox (66.67995pt too wide) in paragraph at lines 4932--4932 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig[] [63] Underfull \hbox (badness 10000) in paragraph at lines 5062--5067 []@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled , run [64] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5085--5085 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_51.jdk/Contents /Home[] [65] [66] Underfull \hbox (badness 10000) in paragraph at lines 5243--5249 @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 5252--5252 []@texttt PKG_CONFIG_PATH=/opt/csw/lib/sparcv9/pkgconfig:/usr/lib/sparcv9/pkgc onfig[] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5259--5259 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s olaris"[] [67] [68] [69] [70] [71] [72] Appendix D [73] [74] [75] (Function and variable index) [76] (Concept index) [77] (Environment variable index) [78] [79] ) (see the transcript file for additional information) Output written on R-admin.pdf (82 pages, 459694 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-ad min.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-admin.aux) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-admin.toc [-1] [-2]) [-3] [-4] (./R-admin.toc) (./R-admin.toc) Chapter 1 [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] [20] Underfull \hbox (badness 10000) in paragraph at lines 1795--1804 @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 1924--1924 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [24] [25] Underfull \hbox (badness 6842) in paragraph at lines 2115--2124 []@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 2214--2224 []@textrm The de-fault com-pil-ers spec-i-fied in @texttt /Library/Frameworks/R .framework/Resources/etc/Makeconf[] [27] [28] [29] [30] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2500--2500 []@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 2520--2520 []@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 2521--2521 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [31] [32] [33] Chapter 8 [34] Chapter 9 [35] [36] [37] Appendix A [38] [39] [40] [41] [42] [43] [44] [45] [46] Overfull \hbox (26.43913pt too wide) in paragraph at lines 3745--3745 []@texttt ln -s /opt/acml5.1.0/gfortran64_mp/lib/libacml_mp.so @textttsl R_HOM E@texttt /lib/libRblas.so[] [47] Appendix B [48] [49] [50] [51] [52] [53] Appendix C [54] [55] [56] [57] Overfull \hbox (22.38167pt too wide) in paragraph at lines 4603--4607 []@textrm Others have re-ported suc-cess with ver-sions 10.x and 11.x. % https: //stat.ethz.ch/pipermail/r- [58] [59] [60] Overfull \hbox (106.92076pt too wide) in paragraph at lines 4792--4792 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [61] [62] Overfull \hbox (66.67995pt too wide) in paragraph at lines 4932--4932 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig[] [63] Underfull \hbox (badness 10000) in paragraph at lines 5062--5067 []@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled , run [64] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5085--5085 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_51.jdk/Contents /Home[] [65] [66] Underfull \hbox (badness 10000) in paragraph at lines 5243--5249 @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 5252--5252 []@texttt PKG_CONFIG_PATH=/opt/csw/lib/sparcv9/pkgconfig:/usr/lib/sparcv9/pkgc onfig[] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5259--5259 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s olaris"[] [67] [68] [69] [70] [71] [72] Appendix D [73] [74] [75] (Function and variable index) [76] (./R-admin.vrs) (Concept index) [77] (./R-admin.cps) (Environment variable index) [78] (./R-admin.ens) [79] ) (see the transcript file for additional information) Output written on R-admin.pdf (85 pages, 506144 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-ad min.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-admin.aux) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-admin.toc [-1] [-2]) [-3] [-4] (./R-admin.toc) (./R-admin.toc) Chapter 1 [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] [20] Underfull \hbox (badness 10000) in paragraph at lines 1795--1804 @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 1924--1924 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [24] [25] Underfull \hbox (badness 6842) in paragraph at lines 2115--2124 []@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 2214--2224 []@textrm The de-fault com-pil-ers spec-i-fied in @texttt /Library/Frameworks/R .framework/Resources/etc/Makeconf[] [27] [28] [29] [30] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2500--2500 []@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 2520--2520 []@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 2521--2521 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [31] [32] [33] Chapter 8 [34] Chapter 9 [35] [36] [37] Appendix A [38] [39] [40] [41] [42] [43] [44] [45] [46] Overfull \hbox (26.43913pt too wide) in paragraph at lines 3745--3745 []@texttt ln -s /opt/acml5.1.0/gfortran64_mp/lib/libacml_mp.so @textttsl R_HOM E@texttt /lib/libRblas.so[] [47] Appendix B [48] [49] [50] [51] [52] [53] Appendix C [54] [55] [56] [57] Overfull \hbox (22.38167pt too wide) in paragraph at lines 4603--4607 []@textrm Others have re-ported suc-cess with ver-sions 10.x and 11.x. % https: //stat.ethz.ch/pipermail/r- [58] [59] [60] Overfull \hbox (106.92076pt too wide) in paragraph at lines 4792--4792 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [61] [62] Overfull \hbox (66.67995pt too wide) in paragraph at lines 4932--4932 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig[] [63] Underfull \hbox (badness 10000) in paragraph at lines 5062--5067 []@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled , run [64] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5085--5085 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_51.jdk/Contents /Home[] [65] [66] Underfull \hbox (badness 10000) in paragraph at lines 5243--5249 @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 5252--5252 []@texttt PKG_CONFIG_PATH=/opt/csw/lib/sparcv9/pkgconfig:/usr/lib/sparcv9/pkgc onfig[] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5259--5259 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s olaris"[] [67] [68] [69] [70] [71] [72] Appendix D [73] [74] [75] (Function and variable index) [76] (./R-admin.vrs) (Concept index) [77] (./R-admin.cps) (Environment variable index) [78] (./R-admin.ens) [79] ) (see the transcript file for additional information) Output written on R-admin.pdf (85 pages, 506143 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-dat a.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/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) Output written on R-data.pdf (39 pages, 276106 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-dat a.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-data.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-data.toc [-1]) [-2] (./R-data.toc) (./R-data.toc) (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] [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] (./R-data.vrs [35]) (Concept index) [36] (./R-data.cps) [37] ) (see the transcript file for additional information) Output written on R-data.pdf (41 pages, 315447 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-dat a.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-data.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-data.toc [-1]) [-2] (./R-data.toc) (./R-data.toc) (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] [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] (./R-data.vrs [35]) (Concept index) [36] (./R-data.cps) [37] ) (see the transcript file for additional information) Output written on R-data.pdf (41 pages, 315451 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-ext s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/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] Underfull \hbox (badness 10000) in paragraph at lines 1820--1823 []@textrm [@texttt libRlapack[] @textrm in-cludes all the double-precision LA- PACK rou-tines Overfull \hbox (14.94176pt too wide) in paragraph at lines 1864--1864 []@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 2162--2162 []@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 2164--2164 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [28] [29] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2303--2303 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [30] [31] [32] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2526--2528 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [33] [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 4434--4434 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [58] [59] [60] [61] Overfull \hbox (13.62822pt too wide) in paragraph at lines 4764--4764 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [62] [63] Chapter 2 [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 10000) in paragraph at lines 6018--6025 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [79] [80] [81] [82] Underfull \hbox (badness 10000) in paragraph at lines 6337--6341 []@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file [83] [84] Chapter 3 [85] [86] [87] [88] [89] [90] Overfull \hbox (20.69044pt too wide) in paragraph at lines 6939--6939 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [91] [92] [93] Chapter 4 [94] [95] [96] Overfull \hbox (14.94176pt too wide) in paragraph at lines 7312--7312 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [97] Overfull \hbox (25.25755pt too wide) in paragraph at lines 7352--7352 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [98] Overfull \hbox (20.53261pt too wide) in paragraph at lines 7456--7456 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] Overfull \hbox (38.96663pt too wide) in paragraph at lines 7486--7495 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [99] [100] [101] [102] [103] [104] Overfull \hbox (78.17732pt too wide) in paragraph at lines 7878--7878 []@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 7909--7911 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] [105] [106] Overfull \hbox (72.42863pt too wide) in paragraph at lines 8042--8042 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8091--8091 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8094--8094 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [107] [108] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8173--8173 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [109] [110] Chapter 5 [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] Overfull \hbox (37.93651pt too wide) in paragraph at lines 9352--9352 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10123--10123 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [134] Underfull \hbox (badness 10000) in paragraph at lines 10184--10186 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [135] [136] [137] [138] [139] [140] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10693--10693 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [141] [142] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10816--10816 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [143] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10821--10821 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10876--10876 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10888--10888 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [144] [145] [146] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11113--11113 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [147] Overfull \hbox (43.6852pt too wide) in paragraph at lines 11195--11195 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [148] [149] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11281--11281 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] Chapter 7 [170] [171] Chapter 8 [172] [173] [174] Overfull \hbox (43.6852pt too wide) in paragraph at lines 13305--13305 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [175] Overfull \hbox (20.69044pt too wide) in paragraph at lines 13337--13337 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 13353--13353 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [176] [177] [178] Underfull \hbox (badness 10000) in paragraph at lines 13596--13603 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [179] [180] [181] [182] [183] [184] Underfull \hbox (badness 10000) in paragraph at lines 13985--13989 []@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; 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Output written on ecrm1095.603gf (256 characters, 55528 bytes). Transcript written on ecrm1095.log. mktexpk: /home/buildd/.texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1095.603pk: successfully generated. (Function and variable index) [185] (Concept index) [186] [187] ) (see the transcript file for additional information) Output written on R-exts.pdf (190 pages, 839638 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-ext s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-exts.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-exts.toc [-1] [-2] [-3] [-4]) [-5] (./R-exts.toc) (./R-exts.toc) (Acknowledgements) 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] Underfull \hbox (badness 10000) in paragraph at lines 1820--1823 []@textrm [@texttt libRlapack[] @textrm in-cludes all the double-precision LA- PACK rou-tines Overfull \hbox (14.94176pt too wide) in paragraph at lines 1864--1864 []@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 2162--2162 []@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 2164--2164 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [28] [29] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2303--2303 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [30] [31] [32] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2526--2528 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [33] [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 4434--4434 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [58] [59] [60] [61] Overfull \hbox (13.62822pt too wide) in paragraph at lines 4764--4764 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [62] [63] Chapter 2 [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 10000) in paragraph at lines 6018--6025 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [79] [80] [81] [82] Underfull \hbox (badness 10000) in paragraph at lines 6337--6341 []@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file [83] [84] Chapter 3 [85] [86] [87] [88] [89] [90] Overfull \hbox (20.69044pt too wide) in paragraph at lines 6939--6939 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [91] [92] [93] Chapter 4 [94] [95] [96] Overfull \hbox (14.94176pt too wide) in paragraph at lines 7312--7312 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [97] Overfull \hbox (25.25755pt too wide) in paragraph at lines 7352--7352 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [98] Overfull \hbox (20.53261pt too wide) in paragraph at lines 7456--7456 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] Overfull \hbox (38.96663pt too wide) in paragraph at lines 7486--7495 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [99] [100] [101] [102] [103] [104] Overfull \hbox (78.17732pt too wide) in paragraph at lines 7878--7878 []@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 7909--7911 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] [105] [106] Overfull \hbox (72.42863pt too wide) in paragraph at lines 8042--8042 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8091--8091 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8094--8094 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [107] [108] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8173--8173 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [109] [110] Chapter 5 [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] Overfull \hbox (37.93651pt too wide) in paragraph at lines 9352--9352 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10123--10123 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [134] Underfull \hbox (badness 10000) in paragraph at lines 10184--10186 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [135] [136] [137] [138] [139] [140] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10693--10693 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [141] [142] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10816--10816 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [143] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10821--10821 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10876--10876 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10888--10888 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [144] [145] [146] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11113--11113 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [147] Overfull \hbox (43.6852pt too wide) in paragraph at lines 11195--11195 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [148] [149] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11281--11281 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] Chapter 7 [170] [171] Chapter 8 [172] [173] [174] Overfull \hbox (43.6852pt too wide) in paragraph at lines 13305--13305 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [175] Overfull \hbox (20.69044pt too wide) in paragraph at lines 13337--13337 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 13353--13353 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [176] [177] [178] Underfull \hbox (badness 10000) in paragraph at lines 13596--13603 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [179] [180] [181] [182] [183] [184] Underfull \hbox (badness 10000) in paragraph at lines 13985--13989 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [185] (./R-exts.vrs [186] [187] [188]) (Concept index) [189] (./R-exts.cps [190]) [191] ) (see the transcript file for additional information) Output written on R-exts.pdf (198 pages, 901166 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-ext s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-exts.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-exts.toc [-1] [-2] [-3] [-4]) [-5] (./R-exts.toc) (./R-exts.toc) (Acknowledgements) 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] Underfull \hbox (badness 10000) in paragraph at lines 1820--1823 []@textrm [@texttt libRlapack[] @textrm in-cludes all the double-precision LA- PACK rou-tines Overfull \hbox (14.94176pt too wide) in paragraph at lines 1864--1864 []@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 2162--2162 []@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 2164--2164 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [28] [29] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2303--2303 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [30] [31] [32] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2526--2528 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [33] [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 4434--4434 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [58] [59] [60] [61] Overfull \hbox (13.62822pt too wide) in paragraph at lines 4764--4764 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [62] [63] Chapter 2 [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 10000) in paragraph at lines 6018--6025 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [79] [80] [81] [82] Underfull \hbox (badness 10000) in paragraph at lines 6337--6341 []@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file [83] [84] Chapter 3 [85] [86] [87] [88] [89] [90] Overfull \hbox (20.69044pt too wide) in paragraph at lines 6939--6939 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [91] [92] [93] Chapter 4 [94] [95] [96] Overfull \hbox (14.94176pt too wide) in paragraph at lines 7312--7312 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [97] Overfull \hbox (25.25755pt too wide) in paragraph at lines 7352--7352 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [98] Overfull \hbox (20.53261pt too wide) in paragraph at lines 7456--7456 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] Overfull \hbox (38.96663pt too wide) in paragraph at lines 7486--7495 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [99] [100] [101] [102] [103] [104] Overfull \hbox (78.17732pt too wide) in paragraph at lines 7878--7878 []@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 7909--7911 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] [105] [106] Overfull \hbox (72.42863pt too wide) in paragraph at lines 8042--8042 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8091--8091 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8094--8094 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [107] [108] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8173--8173 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [109] [110] Chapter 5 [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] Overfull \hbox (37.93651pt too wide) in paragraph at lines 9352--9352 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10123--10123 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [134] Underfull \hbox (badness 10000) in paragraph at lines 10184--10186 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [135] [136] [137] [138] [139] [140] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10693--10693 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [141] [142] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10816--10816 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [143] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10821--10821 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10876--10876 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10888--10888 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [144] [145] [146] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11113--11113 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [147] Overfull \hbox (43.6852pt too wide) in paragraph at lines 11195--11195 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [148] [149] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11281--11281 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] Chapter 7 [170] [171] Chapter 8 [172] [173] [174] Overfull \hbox (43.6852pt too wide) in paragraph at lines 13305--13305 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [175] Overfull \hbox (20.69044pt too wide) in paragraph at lines 13337--13337 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 13353--13353 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [176] [177] [178] Underfull \hbox (badness 10000) in paragraph at lines 13596--13603 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [179] [180] [181] [182] [183] [184] Underfull \hbox (badness 10000) in paragraph at lines 13985--13989 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [185] (./R-exts.vrs [186] [187] [188]) (Concept index) [189] (./R-exts.cps [190]) [191] ) (see the transcript file for additional information) Output written on R-exts.pdf (198 pages, 901172 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-ext s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-exts.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-exts.toc [-1] [-2] [-3] [-4]) [-5] (./R-exts.toc) (./R-exts.toc) (Acknowledgements) 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] Underfull \hbox (badness 10000) in paragraph at lines 1820--1823 []@textrm [@texttt libRlapack[] @textrm in-cludes all the double-precision LA- PACK rou-tines Overfull \hbox (14.94176pt too wide) in paragraph at lines 1864--1864 []@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 2162--2162 []@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 2164--2164 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [28] [29] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2303--2303 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [30] [31] [32] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2526--2528 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [33] [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 4434--4434 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [58] [59] [60] [61] Overfull \hbox (13.62822pt too wide) in paragraph at lines 4764--4764 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [62] [63] Chapter 2 [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 10000) in paragraph at lines 6018--6025 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [79] [80] [81] [82] Underfull \hbox (badness 10000) in paragraph at lines 6337--6341 []@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file [83] [84] Chapter 3 [85] [86] [87] [88] [89] [90] Overfull \hbox (20.69044pt too wide) in paragraph at lines 6939--6939 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [91] [92] [93] Chapter 4 [94] [95] [96] Overfull \hbox (14.94176pt too wide) in paragraph at lines 7312--7312 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [97] Overfull \hbox (25.25755pt too wide) in paragraph at lines 7352--7352 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [98] Overfull \hbox (20.53261pt too wide) in paragraph at lines 7456--7456 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] Overfull \hbox (38.96663pt too wide) in paragraph at lines 7486--7495 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [99] [100] [101] [102] [103] [104] Overfull \hbox (78.17732pt too wide) in paragraph at lines 7878--7878 []@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 7909--7911 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] [105] [106] Overfull \hbox (72.42863pt too wide) in paragraph at lines 8042--8042 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8091--8091 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8094--8094 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [107] [108] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8173--8173 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [109] [110] Chapter 5 [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] Overfull \hbox (37.93651pt too wide) in paragraph at lines 9352--9352 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10123--10123 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [134] Underfull \hbox (badness 10000) in paragraph at lines 10184--10186 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [135] [136] [137] [138] [139] [140] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10693--10693 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [141] [142] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10816--10816 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [143] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10821--10821 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10876--10876 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10888--10888 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [144] [145] [146] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11113--11113 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [147] Overfull \hbox (43.6852pt too wide) in paragraph at lines 11195--11195 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [148] [149] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11281--11281 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] Chapter 7 [170] [171] Chapter 8 [172] [173] [174] Overfull \hbox (43.6852pt too wide) in paragraph at lines 13305--13305 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [175] Overfull \hbox (20.69044pt too wide) in paragraph at lines 13337--13337 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 13353--13353 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [176] [177] [178] Underfull \hbox (badness 10000) in paragraph at lines 13596--13603 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [179] [180] [181] [182] [183] [184] Underfull \hbox (badness 10000) in paragraph at lines 13985--13989 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [185] (./R-exts.vrs [186] [187] [188]) (Concept index) [189] (./R-exts.cps [190]) [191] ) (see the transcript file for additional information) Output written on R-exts.pdf (198 pages, 901172 bytes). Transcript written on R-exts.log. TEXINPUTS=".:$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 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./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] Chapter 4 [18] [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3362--3370 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the Overfull \hbox (50.07326pt too wide) in paragraph at lines 3377--3377 []@texttt options(download.file.method = "wininet", url.method = "wininet") @textrm (Windows)[] Overfull \hbox (81.49376pt too wide) in paragraph at lines 3378--3378 []@texttt options(download.file.method = "libcurl", url.method = "libcurl") @textrm (Linux and OS X)[] Chapter 8 [42] Chapter 9 [43] [44] Chapter 10 [45] [46] [47] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (49 pages, 364948 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 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-FAQ.aux) (/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/var/lib/texmf/fonts/map/pdftex/up dmap/pdftex.map}] (./R-FAQ.toc [-1] [-2]) [-3] (./R-FAQ.toc) (./R-FAQ.toc) Chapter 1 [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] Chapter 4 [18] [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3362--3370 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the Overfull \hbox (50.07326pt too wide) in paragraph at lines 3377--3377 []@texttt options(download.file.method = "wininet", url.method = "wininet") @textrm (Windows)[] Overfull \hbox (81.49376pt too wide) in paragraph at lines 3378--3378 []@texttt options(download.file.method = "libcurl", url.method = "libcurl") @textrm (Linux and OS X)[] Chapter 8 [42] Chapter 9 [43] [44] Chapter 10 [45] [46] [47] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (51 pages, 380786 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 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-FAQ.aux) (/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/var/lib/texmf/fonts/map/pdftex/up dmap/pdftex.map}] (./R-FAQ.toc [-1] [-2]) [-3] (./R-FAQ.toc) (./R-FAQ.toc) Chapter 1 [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] Chapter 4 [18] [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3362--3370 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the Overfull \hbox (50.07326pt too wide) in paragraph at lines 3377--3377 []@texttt options(download.file.method = "wininet", url.method = "wininet") @textrm (Windows)[] Overfull \hbox (81.49376pt too wide) in paragraph at lines 3378--3378 []@texttt options(download.file.method = "libcurl", url.method = "libcurl") @textrm (Linux and OS X)[] Chapter 8 [42] Chapter 9 [43] [44] Chapter 10 [45] [46] [47] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (51 pages, 380786 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-in tro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/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] Chapter 3 [12] [13] [14] Chapter 4 [15] [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24] [25] [26] Chapter 6 [27] [28] [29] [30] Chapter 7 [31] [32] [33] Chapter 8 [34] [35] [36] <./images/hist.pdf> <./images/ecdf.pdf> [37] <./images/QQ.pdf> [38] <./images/ice.pdf> [39] [40] Chapter 9 [41] [42] Chapter 10 [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] Chapter 11 [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] Chapter 12 [66] [67] [68] [69] [70] 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})))[] [71] [72] [73] [74] [75] <./images/fig11.pdf> [76] <./images/fig12.pdf> [77] [78] [79] [80] Chapter 13 [81] 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 [82] Chapter 14 [83] [84] Underfull \hbox (badness 10000) in paragraph at lines 6650--6655 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and [85] Appendix A [86] [87] [88] [89] Appendix B [90] [91] [92] [93] [94] [95] [96] [97] Appendix C [98] [99] Appendix D [100] Appendix E [101] Appendix F [102] [103] ) (see the transcript file for additional information) Output written on R-intro.pdf (106 pages, 584565 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-in tro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-intro.aux) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-intro.toc [-1] [-2] [-3]) [-4] (./R-intro.toc) (./R-intro.toc) (Preface) Chapter 1 [1] [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] Chapter 4 [15] [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24] [25] [26] Chapter 6 [27] [28] [29] [30] Chapter 7 [31] [32] [33] Chapter 8 [34] [35] [36] <./images/hist.pdf> <./images/ecdf.pdf> [37] <./images/QQ.pdf> [38] <./images/ice.pdf> [39] [40] Chapter 9 [41] [42] Chapter 10 [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] Chapter 11 [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] Chapter 12 [66] [67] [68] [69] [70] 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})))[] [71] [72] [73] [74] [75] <./images/fig11.pdf> [76] <./images/fig12.pdf> [77] [78] [79] [80] Chapter 13 [81] 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 [82] Chapter 14 [83] [84] Underfull \hbox (badness 10000) in paragraph at lines 6650--6655 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and [85] Appendix A [86] [87] [88] [89] Appendix B [90] [91] [92] [93] [94] [95] [96] [97] Appendix C [98] [99] Appendix D [100] (./R-intro.vrs [101] [102]) Appendix E [103] (./R-intro.cps [104]) Appendix F [105] [106] ) (see the transcript file for additional information) < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi7.pfb> Output written on R-intro.pdf (112 pages, 633842 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-in tro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-intro.aux) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-intro.toc [-1] [-2] [-3]) [-4] (./R-intro.toc) (./R-intro.toc) (Preface) Chapter 1 [1] [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] Chapter 4 [15] [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24] [25] [26] Chapter 6 [27] [28] [29] [30] Chapter 7 [31] [32] [33] Chapter 8 [34] [35] [36] <./images/hist.pdf> <./images/ecdf.pdf> [37] <./images/QQ.pdf> [38] <./images/ice.pdf> [39] [40] Chapter 9 [41] [42] Chapter 10 [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] Chapter 11 [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] Chapter 12 [66] [67] [68] [69] [70] 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})))[] [71] [72] [73] [74] [75] <./images/fig11.pdf> [76] <./images/fig12.pdf> [77] [78] [79] [80] Chapter 13 [81] 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 [82] Chapter 14 [83] [84] Underfull \hbox (badness 10000) in paragraph at lines 6650--6655 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and [85] Appendix A [86] [87] [88] [89] Appendix B [90] [91] [92] [93] [94] [95] [96] [97] Appendix C [98] [99] Appendix D [100] (./R-intro.vrs [101] [102]) Appendix E [103] (./R-intro.cps [104]) Appendix F [105] [106] ) (see the transcript file for additional information) < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi7.pfb> Output written on R-intro.pdf (112 pages, 633814 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-int s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/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 3989--3997 @texttt CRAN . R-project . org / package=codetools[]@textrm )[][] func-tions u sed for Underfull \hbox (badness 7869) in paragraph at lines 3989--3997 @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 3989--3997 @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) Output written on R-ints.pdf (69 pages, 383247 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-int s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-ints.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-ints.toc [-1] [-2]) [-3] (./R-ints.toc) (./R-ints.toc) 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 3989--3997 @texttt CRAN . R-project . org / package=codetools[]@textrm )[][] func-tions u sed for Underfull \hbox (badness 7869) in paragraph at lines 3989--3997 @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 3989--3997 @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] (./R-ints.vrs [65]) (Concept index) [66] (./R-ints.cps) [67] ) (see the transcript file for additional information) Output written on R-ints.pdf (72 pages, 431143 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-int s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-ints.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-ints.toc [-1] [-2]) [-3] (./R-ints.toc) (./R-ints.toc) 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 3989--3997 @texttt CRAN . R-project . org / package=codetools[]@textrm )[][] func-tions u sed for Underfull \hbox (badness 7869) in paragraph at lines 3989--3997 @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 3989--3997 @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] (./R-ints.vrs [65]) (Concept index) [66] (./R-ints.cps) [67] ) (see the transcript file for additional information) Output written on R-ints.pdf (72 pages, 431143 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-lan g.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/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) Output written on R-lang.pdf (65 pages, 331061 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-lan g.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-lang.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-lang.toc [-1] [-2]) [-3] (./R-lang.toc) (./R-lang.toc) Chapter 1 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] (./R-lang.vrs [60]) (Concept Index) [61] (./R-lang.cps) Appendix A [62] [63] ) (see the transcript file for additional information) Output written on R-lang.pdf (68 pages, 379658 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-lan g.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2015-06-24.23]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (./epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (./R-lang.aux ) (./R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (./version.texi) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./R-lang.toc [-1] [-2]) [-3] (./R-lang.toc) (./R-lang.toc) Chapter 1 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] (./R-lang.vrs [60]) (Concept Index) [61] (./R-lang.cps) Appendix A [62] [63] ) (see the transcript file for additional information) Output written on R-lang.pdf (68 pages, 379659 bytes). Transcript written on R-lang.log. make[1]: Leaving directory '/«PKGBUILDDIR»/doc/manual' /usr/bin/make 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 <2015/01/01> Babel <3.9l> and hyphenation patterns for 2 languages 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 511--517 []\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 1122--1125 []\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 1339--1345 []\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] Overfull \hbox (26.88089pt too wide) in paragraph at lines 1849--1849 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [30] [31] [32] Underfull \hbox (badness 10000) in paragraph at lines 2034--2036 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] Underfull \hbox (badness 10000) in paragraph at lines 3532--3534 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [56] [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 4728--4730 []\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] [93] Underfull \hbox (badness 2096) in paragraph at lines 5945--5958 []\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 [94] [95] [96] Overfull \hbox (58.35893pt too wide) in paragraph at lines 6146--6149 []\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 : [97] [98] Underfull \hbox (badness 10000) in paragraph at lines 6290--6293 []\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 [99] [100] Underfull \hbox (badness 1442) in paragraph at lines 6451--6457 []\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 6451--6457 \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 6451--6457 \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 [101] Underfull \hbox (badness 3568) in paragraph at lines 6512--6519 \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 [102] [103] Underfull \vbox (badness 10000) has occurred while \output is active [104] [105] [106] [107] [108] [109] [110] [111] Underfull \hbox (badness 2096) in paragraph at lines 7149--7153 \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 . [112] Underfull \hbox (badness 4595) in paragraph at lines 7206--7209 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [113] Underfull \hbox (badness 3000) in paragraph at lines 7242--7244 []\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 7267--7270 [][][]\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 , [114] [115] [116] [117] Underfull \hbox (badness 10000) in paragraph at lines 7517--7528 []\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 [118] Underfull \hbox (badness 4479) in paragraph at lines 7589--7598 [][][]\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 7589--7598 [][]\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 [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] Underfull \hbox (badness 1394) in paragraph at lines 9200--9205 []\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 [144] [145] [146] [147] [148] Underfull \hbox (badness 1052) in paragraph at lines 9537--9542 []\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 9537--9542 \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 [149] [150] Underfull \hbox (badness 1735) in paragraph at lines 9675--9679 \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 . [151] [152] [153] [154] [155] [156] Underfull \hbox (badness 2150) in paragraph at lines 10079--10082 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse [157] Underfull \hbox (badness 6396) in paragraph at lines 10093--10101 []\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 10134--10141 []\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 [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] Underfull \hbox (badness 4569) in paragraph at lines 11178--11182 []\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 11178--11182 \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 [174] [175] [176] [177] [178] [179] [180] [181] Underfull \hbox (badness 2698) in paragraph at lines 11754--11763 []\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 11754--11763 \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 [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] Underfull \hbox (badness 6236) in paragraph at lines 12398--12401 []\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 [192] [193] [194] [195] [196] [197] Underfull \hbox (badness 2253) in paragraph at lines 12776--12778 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [198] Underfull \hbox (badness 1565) in paragraph at lines 12847--12851 [][][]\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 [199] Underfull \hbox (badness 10000) in paragraph at lines 12891--12893 []\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 [200] [201] Underfull \hbox (badness 1466) in paragraph at lines 13032--13035 []\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 [202] [203] Underfull \hbox (badness 10000) in paragraph at lines 13140--13144 [][][]\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 13151--13154 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [204] [205] [206] [207] Underfull \hbox (badness 3965) in paragraph at lines 13403--13407 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] Underfull \hbox (badness 4429) in paragraph at lines 14133--14136 []\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 [219] Underfull \hbox (badness 10000) in paragraph at lines 14225--14227 []\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 14231--14235 []\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 [220] Underfull \hbox (badness 10000) in paragraph at lines 14273--14277 []\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 14273--14277 \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 [221] Underfull \vbox (badness 3803) has occurred while \output is active [222] [223] [224] [225] [226] [227] [228] [229] Underfull \hbox (badness 2452) in paragraph at lines 14853--14857 []\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 14853--14857 \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 [230] [231] [232] Underfull \hbox (badness 1092) in paragraph at lines 15026--15031 [][]\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 [233] [234] [235] [236] Underfull \hbox (badness 6741) in paragraph at lines 15274--15278 \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 , [237] [238] [239] [240] Underfull \hbox (badness 1867) in paragraph at lines 15580--15587 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [241] [242] [243] [244] Underfull \vbox (badness 10000) has occurred while \output is active [245] [246] Underfull \hbox (badness 3679) in paragraph at lines 15960--15962 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [247] [248] [249] [250] [251] [252] [253] Underfull \hbox (badness 1478) in paragraph at lines 16440--16443 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [254] [255] [256] [257] Underfull \hbox (badness 10000) in paragraph at lines 16693--16695 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [258] [259] [260] [261] [262] [263] [264] [265] [266] Underfull \hbox (badness 1442) in paragraph at lines 17256--17258 []\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 [267] Underfull \hbox (badness 2452) in paragraph at lines 17348--17364 [][][]\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 , [268] [269] [270] [271] [272] [273] [274] Underfull \hbox (badness 1248) in paragraph at lines 17756--17759 []\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 , [275] [276] [277] [278] Underfull \hbox (badness 4739) in paragraph at lines 18012--18014 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [279] [280] [281] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] Underfull \hbox (badness 1360) in paragraph at lines 18960--18965 \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 18983--18989 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / Underfull \hbox (badness 1127) in paragraph at lines 18983--18989 \T1/zi4/m/n/10 ssl-[]compared . html$[][] \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 [295] Underfull \hbox (badness 10000) in paragraph at lines 19056--19060 []\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 19056--19060 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [296] [297] Underfull \hbox (badness 1509) in paragraph at lines 19191--19198 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1354) in paragraph at lines 19191--19198 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19207--19212 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] [309] Underfull \hbox (badness 1264) in paragraph at lines 19938--19943 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] Underfull \hbox (badness 10000) in paragraph at lines 20692--20694 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] Underfull \hbox (badness 1077) in paragraph at lines 21690--21696 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [337] [338] [339] Underfull \hbox (badness 1484) in paragraph at lines 21851--21859 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [340] [341] [342] [343] Underfull \hbox (badness 2790) in paragraph at lines 22122--22125 []\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 22122--22125 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [344] [345] [346] [347] Underfull \hbox (badness 1194) in paragraph at lines 22403--22406 []\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 [348] [349] [350] [351] Underfull \hbox (badness 10000) in paragraph at lines 22609--22615 []\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 22609--22615 \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 22619--22622 []\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 22619--22622 \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 [352] [353] [354] [355] [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] Underfull \hbox (badness 10000) in paragraph at lines 23544--23546 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [366] [367] [368] [369] Underfull \hbox (badness 1199) in paragraph at lines 23771--23777 []\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 23771--23777 \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, [370] [371] [372] [373] [374] [375] [376] [377] Underfull \hbox (badness 1038) in paragraph at lines 24336--24344 []\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 24345--24348 []\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 24364--24366 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [378] Underfull \hbox (badness 10000) in paragraph at lines 24436--24446 []\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 24447--24453 []\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 24460--24465 []\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 24470--24472 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [379] [380] [381] Underfull \hbox (badness 10000) in paragraph at lines 24721--24727 []\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 24721--24727 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "http://bioconductor.org"\T1/p tm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 24721--24727 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "http://bioconductor.statistik.tu-dortmund.de"\T 1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 24734--24737 []\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 [382] Underfull \hbox (badness 2689) in paragraph at lines 24758--24760 []\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 24790--24795 []\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 24796--24807 \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 24808--24811 []\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 Underfull \hbox (badness 4084) in paragraph at lines 24818--24830 \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 24818--24830 \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 24818--24830 \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 24832--24839 []\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 24832--24839 \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 24832--24839 \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 24832--24839 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [383] [384] [385] [386] [387] Underfull \hbox (badness 10000) in paragraph at lines 25153--25157 []\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 25153--25157 \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)] [388] [389] [390] [391] [392] Underfull \hbox (badness 1735) in paragraph at lines 25471--25475 []\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 [393] [394] [395] [396] [397] [398] [399] [400] [401] [402] Underfull \hbox (badness 2726) in paragraph at lines 26030--26033 []\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 [403] [404] [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] [415] Underfull \hbox (badness 1052) in paragraph at lines 26849--26854 []\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 [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] Underfull \hbox (badness 1533) in paragraph at lines 27577--27580 []\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 [427] [428] Underfull \hbox (badness 1163) in paragraph at lines 27739--27749 []\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 [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] Underfull \hbox (badness 10000) in paragraph at lines 29241--29245 []\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 29241--29245 \T1/zi4/m/n/10 "(?[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 29263--29265 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [453] [454] [455] [456] [457] [458] [459] [460] [461] Underfull \hbox (badness 1655) in paragraph at lines 29808--29810 []\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 [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] Underfull \hbox (badness 10000) in paragraph at lines 30476--30480 []\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., [473] [474] [475] Underfull \hbox (badness 2302) in paragraph at lines 30716--30723 []\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 30716--30723 \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 30716--30723 \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 30716--30723 \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 [476] [477] [478] Underfull \hbox (badness 2261) in paragraph at lines 30870--30875 []\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 30897--30903 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [479] Underfull \hbox (badness 10000) in paragraph at lines 30973--30978 []\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 [480] [481] [482] [483] [484] [485] [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] Underfull \hbox (badness 1072) in paragraph at lines 33757--33761 []\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 33762--33766 []\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 ', [523] Underfull \hbox (badness 10000) in paragraph at lines 33790--33796 []\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 33790--33796 \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 33790--33796 \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 33803--33810 \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 33803--33810 \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 33803--33810 \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 [524] [525] [526] [527] [528] Underfull \hbox (badness 10000) in paragraph at lines 34094--34100 []\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 34094--34100 \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 [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] Underfull \hbox (badness 3333) in paragraph at lines 35877--35882 []\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 [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] Underfull \hbox (badness 1472) in paragraph at lines 36497--36500 []\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 [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] Underfull \hbox (badness 2671) in paragraph at lines 37159--37162 []\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 [578] [579] [580] [581] [582] [583] Underfull \hbox (badness 10000) in paragraph at lines 37563--37566 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$http : / / developer . r-[]project . org / [584] [585] Underfull \hbox (badness 10000) in paragraph at lines 37684--37688 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 http : / / developer . [586] Underfull \hbox (badness 10000) in paragraph at lines 37746--37750 [][][]\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 http : / / developer . [587] [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] Underfull \hbox (badness 1990) in paragraph at lines 39041--39049 []\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 39041--39049 \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 [606] [607] [608] [609] [610] Underfull \hbox (badness 1515) in paragraph at lines 39313--39318 []\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 [611] [612] [613] Underfull \hbox (badness 1917) in paragraph at lines 39543--39550 []\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 [614] [615] [616] [617] [618] [619] [620] [621] [622] Underfull \hbox (badness 3668) in paragraph at lines 40128--40130 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [623] [624] Underfull \hbox (badness 2401) in paragraph at lines 40233--40237 []\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 [625] [626] [627] Underfull \hbox (badness 2111) in paragraph at lines 40402--40407 \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. Underfull \hbox (badness 6542) in paragraph at lines 40418--40423 []\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 [628] [629] [630] [631] [632] [633] [634] Underfull \hbox (badness 10000) in paragraph at lines 40863--40868 []\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 40863--40868 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to [635] [636] Underfull \hbox (badness 5417) in paragraph at lines 40955--40959 []\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 [637] Underfull \hbox (badness 10000) in paragraph at lines 41016--41020 []\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 [638]) (./compiler-pkg.tex Chapter 2. [639] [640] [641] [642]) (./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 [643] [644] [645] [646] [647] [648] [649] [650] [651] [652] [653] [654] [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] Underfull \vbox (badness 1515) has occurred while \output is active [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] 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 / [710] Underfull \vbox (badness 10000) has occurred while \output is active [711] [712] [713] [714] Underfull \vbox (badness 10000) has occurred while \output is active [715] Underfull \vbox (badness 10000) has occurred while \output is active [716] [717] [718] [719] [720] [721] [722] [723]) (./grDevices-pkg.tex [724] Chapter 4. [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] Underfull \hbox (badness 5175) in paragraph at lines 1066--1068 []\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 [742] [743] [744] [745] Underfull \hbox (badness 1852) in paragraph at lines 1263--1266 []\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 [746] [747] [748] Underfull \hbox (badness 1490) in paragraph at lines 1469--1474 \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 [749] Underfull \hbox (badness 2698) in paragraph at lines 1523--1526 []\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 [750] Underfull \hbox (badness 10000) in paragraph at lines 1592--1596 []\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 [751] [752] [753] [754] Underfull \hbox (badness 1325) in paragraph at lines 1875--1885 \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 , [755] [756] Underfull \hbox (badness 10000) in paragraph at lines 1980--1982 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [757] [758] [759] Underfull \hbox (badness 6758) in paragraph at lines 2141--2144 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [760] [761] [762] [763] [764] [765] [766] [767] [768] Underfull \hbox (badness 10000) in paragraph at lines 2707--2708 [769] [770] [771] [772] [773] [774] [775] Underfull \hbox (badness 1152) in paragraph at lines 3145--3147 []\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 [776] [777] [778] [779] [780] Underfull \hbox (badness 2856) in paragraph at lines 3465--3468 []\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 3479--3481 []\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 [781] [782] Underfull \hbox (badness 1173) in paragraph at lines 3595--3605 []\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 [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] Underfull \hbox (badness 1067) in paragraph at lines 4302--4309 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [794] [795] Underfull \hbox (badness 3364) in paragraph at lines 4463--4465 []\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 / [796] Underfull \hbox (badness 1789) in paragraph at lines 4540--4542 []\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 [797] Underfull \hbox (badness 1377) in paragraph at lines 4590--4595 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [798] Underfull \hbox (badness 2671) in paragraph at lines 4617--4625 \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 4666--4673 \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 4674--4683 \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 4674--4683 \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 4684--4686 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [799] [800] Underfull \hbox (badness 1057) in paragraph at lines 4795--4800 []\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 [801] Underfull \hbox (badness 7344) in paragraph at lines 4855--4857 []\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 [802] [803] Underfull \hbox (badness 2035) in paragraph at lines 4979--4988 []\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 4979--4988 \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 4979--4988 \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 , [804] Underfull \hbox (badness 10000) in paragraph at lines 5048--5055 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5048--5055 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [805] [806] [807] Underfull \hbox (badness 1546) in paragraph at lines 5186--5194 []\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 , [808] Underfull \hbox (badness 1648) in paragraph at lines 5263--5267 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [809] [810] [811] [812] [813] [814] [815] Underfull \hbox (badness 10000) in paragraph at lines 5686--5689 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [816] Underfull \vbox (badness 3803) has occurred while \output is active [817] [818] [819] [820] [821] Underfull \hbox (badness 1189) in paragraph at lines 6083--6085 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [822] [823] Underfull \hbox (badness 10000) in paragraph at lines 6181--6183 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [824] [825] [826] [827] Underfull \hbox (badness 3780) in paragraph at lines 6472--6478 []\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 , [828] [829] [830] Underfull \hbox (badness 2680) in paragraph at lines 6668--6670 []\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 [831] [832] [833]) (./graphics-pkg.tex [834] Chapter 5. [835] [836] [837] [838] [839] [840] [841] [842] [843] [844] [845] 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 [846] [847] [848] [849] Underfull \vbox (badness 3803) has occurred while \output is active [850] [851] [852] [853] [854] 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 , [855] [856] [857] [858] [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] [869] [870] [871] Underfull \hbox (badness 1009) in paragraph at lines 2277--2284 \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 [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] Underfull \vbox (badness 10000) has occurred while \output is active [894] Underfull \vbox (badness 10000) has occurred while \output is active [895] [896] [897] [898] Underfull \hbox (badness 1867) in paragraph at lines 3901--3905 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [899] [900] [901] [902] [903] [904] [905] Underfull \hbox (badness 1924) in paragraph at lines 4348--4353 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain [906] Underfull \hbox (badness 2529) in paragraph at lines 4379--4382 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used: see [907] [908] [909] [910] [911] Underfull \hbox (badness 10000) in paragraph at lines 4729--4735 []\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 4729--4735 \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 [912] Underfull \hbox (badness 10000) in paragraph at lines 4860--4863 [913] [914 ] Underfull \hbox (badness 10000) in paragraph at lines 4921--4923 [915 ] [916] Underfull \hbox (badness 10000) in paragraph at lines 5111--5113 []\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 [917] [918] [919] [920] [921] Underfull \vbox (badness 10000) has occurred while \output is active [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6581--6582 [][] [941 ] [942] Underfull \vbox (badness 10000) has occurred while \output is active [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] Underfull \hbox (badness 1048) in paragraph at lines 7290--7295 \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 [953] Underfull \hbox (badness 1038) in paragraph at lines 7406--7409 []\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 [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] [971] [972] [973] [974] Underfull \hbox (badness 6691) in paragraph at lines 8625--8628 []\T1/ptm/m/n/10 The main ti-tle (on top) us-ing font and size (char-ac-ter ex- pan-sion) Underfull \hbox (badness 2799) in paragraph at lines 8628--8630 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font and size \T1/zi4/m/n/10 par ("font.sub") \T1/ptm/m/n/10 and color [975] [976]pdfTeX warning (ext4): destination with the same identifier (name{Rf n.units}) has been already used, duplicate ignored \relax l.8710 \HeaderA{units}{Graphical Units}{units} [977] [978] [979] [980]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [981] [982] [983] [984] [985] [986] 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 [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] 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 , [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [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] Underfull \vbox (badness 3803) has occurred while \output is active [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] 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 [1054] [1055] [1056] [1057] 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 [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] Underfull \hbox (badness 10000) in paragraph at lines 5854--5860 \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., [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] Underfull \hbox (badness 7649) in paragraph at lines 6324--6327 []\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 [1087] [1088] [1089] [1090]) (./methods-pkg.tex Chapter 7. [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] 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 [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] 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 [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] 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 [1128] [1129] 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 [1130] 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 [1131] [1132] [1133] [1134] [1135] [1136] [1137] 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 [1138] [1139] [1140] [1141] [1142] 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 [1143] [1144] [1145] [1146] [1147] [1148] Underfull \vbox (badness 10000) has occurred while \output is active [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156] 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 [1157] [1158] [1159] [1160] [1161] [1162] Underfull \vbox (badness 2452) has occurred while \output is active [1163] [1164] Underfull \vbox (badness 10000) has occurred while \output is active [1165] [1166] 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 [1167] [1168] [1169] [1170] [1171] 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 [1172] [1173] [1174] [1175] 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 [1176] [1177] [1178] [1179] [1180] Underfull \hbox (badness 1675) in paragraph at lines 6343--6349 \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 [1181] [1182] [1183] [1184] Underfull \vbox (badness 10000) has occurred while \output is active [1185] [1186]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4} ) has been already used, duplicate ignored \relax l.6820 \aliasA{S4}{S3Part}{S4} [1187] [1188] [1189] [1190]pdfTeX warning (ext4) : destination with the same identifier (name{Rfn.Complex}) has been already use d, duplicate ignored \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 \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 \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 \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 \relax l.7102 \aliasA{Summary}{S4groupGeneric}{Summary} [1191] 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 [1192] [1193] [1194] 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 [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] Underfull \hbox (badness 1852) in paragraph at lines 9759--9763 []\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., [1229] [1230] [1231] [1232]) (./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 [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] Underfull \hbox (badness 3386) in paragraph at lines 1246--1249 []\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 [1253] [1254]) (./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 \T1/ptm/ m/n/10 and William N. Ven-ables [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269]) (./stats-pkg.tex [1270] Chapter 10. [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] Underfull \hbox (badness 1412) in paragraph at lines 844--846 []\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 [1284] [1285] [1286] [1287] [1288] [1289] [1290] [1291] Underfull \hbox (badness 2503) in paragraph at lines 1325--1328 []\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 , [1292] [1293] [1294] Underfull \hbox (badness 10000) in paragraph at lines 1504--1508 []\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 [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] Underfull \hbox (badness 3965) in paragraph at lines 2164--2166 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1306] [1307] [1308] [1309] [1310] Underfull \hbox (badness 3965) in paragraph at lines 2506--2508 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] Underfull \hbox (badness 2503) in paragraph at lines 3323--3326 []\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 , [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 3989) in paragraph at lines 4548--4555 []\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 = [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] Underfull \hbox (badness 2556) in paragraph at lines 5149--5152 []\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 5166--5168 []\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 [1354] [1355] [1356] [1357] Underfull \hbox (badness 1142) in paragraph at lines 5407--5419 \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. [1358] [1359] Underfull \hbox (badness 2503) in paragraph at lines 5546--5550 []\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 , [1360] Underfull \hbox (badness 1168) in paragraph at lines 5607--5612 []\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 [1361] [1362] [1363] [1364] [1365] [1366] [1367] Underfull \hbox (badness 8132) in paragraph at lines 6049--6054 \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, [1368] [1369] [1370] [1371] [1372] Underfull \hbox (badness 7081) in paragraph at lines 6324--6327 []\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 6328--6330 []\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 [1373] [1374] [1375] [1376] [1377] Underfull \vbox (badness 3803) has occurred while \output is active [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] Underfull \hbox (badness 10000) in paragraph at lines 7136--7139 []\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 [1386] [1387] Underfull \hbox (badness 10000) in paragraph at lines 7273--7276 []\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 / [1388] [1389] [1390] [1391] Underfull \vbox (badness 3803) has occurred while \output is active [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] Underfull \hbox (badness 2626) in paragraph at lines 8771--8774 []\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 [1413] Underfull \hbox (badness 2503) in paragraph at lines 8871--8875 []\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 , [1414] [1415] [1416] [1417] [1418] Overfull \hbox (6.88992pt too wide) in paragraph at lines 9205--9207 []\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 . [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] Underfull \hbox (badness 4518) in paragraph at lines 10132--10137 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1434] [1435] [1436] [1437] Underfull \hbox (badness 2142) in paragraph at lines 10474--10477 []\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 ^^@ [1438] Underfull \hbox (badness 1253) in paragraph at lines 10493--10496 []\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, [1439] Underfull \hbox (badness 1708) in paragraph at lines 10555--10559 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1440] [1441] [1442] [1443] [1444] [1445] Underfull \hbox (badness 1694) in paragraph at lines 10951--10954 []\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 10970--10979 \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- [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453]pdfTeX warning (ext4): d estination with the same identifier (name{Rfn.hat}) has been already used, dupl icate ignored \relax l.11417 \aliasA{hat}{influence.measures}{hat} [1454] [1455] Underfull \hbox (badness 1484) in paragraph at lines 11540--11542 []\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 [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 4441) in paragraph at lines 12098--12100 []\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 12105--12107 []\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 [1465] [1466] [1467] [1468] [1469] [1470] Underfull \hbox (badness 2894) in paragraph at lines 12439--12443 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] Underfull \hbox (badness 4518) in paragraph at lines 13134--13139 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1482] [1483] [1484] [1485] [1486] [1487] [1488] [1489] [1490] [1491] Underfull \hbox (badness 4518) in paragraph at lines 13781--13786 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1492] [1493] Underfull \hbox (badness 10000) in paragraph at lines 13919--13923 []\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 13926--13928 []\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 [1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] [1509] [1510] [1511] Underfull \hbox (badness 2503) in paragraph at lines 14990--14994 []\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 , [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] Underfull \hbox (badness 1418) in paragraph at lines 15499--15505 []\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 [1520] [1521] [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] Underfull \hbox (badness 2359) in paragraph at lines 17123--17125 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1546] [1547] Underfull \vbox (badness 10000) has occurred while \output is active [1548] Underfull \vbox (badness 10000) has occurred while \output is active [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] Underfull \hbox (badness 1377) in paragraph at lines 18034--18039 []\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 18039--18042 []\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 18052--18056 \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 18060--18064 []\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 [1562] [1563] [1564] Underfull \vbox (badness 10000) has occurred while \output is active [1565] [1566] [1567] [1568] [1569] [1570] [1571] Underfull \hbox (badness 1337) in paragraph at lines 18676--18679 []\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 [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] Underfull \hbox (badness 5563) in paragraph at lines 19406--19408 []\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 19409--19412 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1585] [1586] [1587] [1588] [1589] [1590] Underfull \hbox (badness 2503) in paragraph at lines 19776--19779 []\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 , [1591] Underfull \hbox (badness 10000) in paragraph at lines 19803--19805 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602] [1603] [1604] [1605] [1606] [1607] Underfull \hbox (badness 10000) in paragraph at lines 20803--20809 []\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 , [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] Underfull \hbox (badness 1337) in paragraph at lines 22138--22144 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1631] [1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] Underfull \hbox (badness 10000) in paragraph at lines 22931--22934 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1643] [1644] [1645] [1646] [1647] [1648] [1649] [1650] [1651] Underfull \hbox (badness 10000) in paragraph at lines 23508--23511 []\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 [1652] Underfull \hbox (badness 3690) in paragraph at lines 23559--23563 [][][]\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 [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] Underfull \hbox (badness 3439) in paragraph at lines 24029--24035 [][]\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 , [1661] [1662] [1663] [1664] [1665] [1666] [1667] [1668] [1669] Underfull \hbox (badness 10000) in paragraph at lines 24577--24582 []\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 [1670] [1671] [1672] [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] Underfull \vbox (badness 3803) has occurred while \output is active [1685] [1686] Underfull \hbox (badness 3514) in paragraph at lines 25593--25598 []\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 [1687] Underfull \hbox (badness 3514) in paragraph at lines 25655--25660 []\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 [1688] Underfull \hbox (badness 3514) in paragraph at lines 25712--25717 []\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 [1689] Underfull \hbox (badness 3514) in paragraph at lines 25773--25779 []\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 [1690] [1691] [1692] [1693] Underfull \hbox (badness 3514) in paragraph at lines 25986--25991 []\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 Underfull \hbox (badness 3514) in paragraph at lines 26042--26047 []\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 [1694] Underfull \hbox (badness 3514) in paragraph at lines 26099--26104 []\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 [1695] Underfull \hbox (badness 3514) in paragraph at lines 26154--26159 []\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 [1696] [1697] Underfull \hbox (badness 6691) in paragraph at lines 26223--26228 []\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 [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] Underfull \hbox (badness 10000) in paragraph at lines 26747--26750 []\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 26747--26750 \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, [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] Underfull \hbox (badness 5431) in paragraph at lines 27353--27355 []\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 [1716] [1717] [1718] [1719] Underfull \hbox (badness 5431) in paragraph at lines 27563--27566 []\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 [1720] [1721] [1722] [1723] [1724] Underfull \hbox (badness 1337) in paragraph at lines 27875--27879 []\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 [1725] [1726] Underfull \hbox (badness 10000) in paragraph at lines 27992--27995 []\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 [1727] [1728] [1729] Underfull \hbox (badness 1616) in paragraph at lines 28175--28178 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] Underfull \hbox (badness 10000) in paragraph at lines 29302--29306 []\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 [1749] [1750] [1751] Underfull \vbox (badness 10000) has occurred while \output is active [1752] [1753] [1754] Underfull \hbox (badness 1337) in paragraph at lines 29666--29670 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] Underfull \hbox (badness 1337) in paragraph at lines 30150--30154 []\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 [1763] Underfull \hbox (badness 5161) in paragraph at lines 30243--30245 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1764] [1765] [1766] [1767] [1768] [1769] Underfull \hbox (badness 10000) in paragraph at lines 30607--30612 []\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 [1770] [1771] [1772]) (./stats4-pkg.tex Chapter 11. [1773] [1774] [1775] [1776] [1777] [1778]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1779] [1780] [1781] [1782]) (./tcltk-pkg.tex Chapter 12. [1783] [1784] [1785] [1786] [1787] [1788] [1789] Underfull \vbox (badness 10000) has occurred while \output is active [1790] Underfull \vbox (badness 10000) has occurred while \output is active [1791] 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 [1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] 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 [1803]) (./tools-pkg.tex [1804] Chapter 13. [1805] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1806] 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 [1807] [1808] 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 [1809] [1810] 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 [1811] [1812] [1813] [1814] [1815] [1816] [1817] [1818] [1819] [1820] [1821] 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 [1822] 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- [1823] 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 , [1824] [1825] [1826] 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 [1827] [1828] [1829] Underfull \hbox (badness 7981) in paragraph at lines 1518--1522 []\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 1524--1526 []\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 [1830] [1831] [1832] [1833]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1721 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1834] [1835] Underfull \hbox (badness 5726) in paragraph at lines 1847--1852 []\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 1847--1852 \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 [1836] [1837] [1838] [1839] [1840] [1841] [1842] [1843] Underfull \hbox (badness 7981) in paragraph at lines 2323--2329 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1844] [1845] [1846] [1847] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2607. [1848] [1849] [1850] [1851] Underfull \hbox (badness 1424) in paragraph at lines 2844--2846 []\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 [1852] [1853] [1854] [1855] [1856] [1857] [1858] [1859] [1860] [1861] [1862] Underfull \hbox (badness 10000) in paragraph at lines 3539--3541 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1863] [1864] [1865] [1866] [1867] [1868] Underfull \hbox (badness 1838) in paragraph at lines 3919--3925 []\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 3919--3925 \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 [1869] [1870] Underfull \hbox (badness 5726) in paragraph at lines 3999--4004 []\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 3999--4004 \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 [1871] [1872] Underfull \hbox (badness 1688) in paragraph at lines 4142--4154 []\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 [1873] [1874] [1875] [1876]) (./utils-pkg.tex Chapter 14. [1877] 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 ', [1878] [1879] 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 [1880] [1881] [1882] [1883] [1884] [1885] 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 [1886] Underfull \hbox (badness 5847) in paragraph at lines 656--662 []\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 656--662 \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 [1887] Underfull \hbox (badness 3861) in paragraph at lines 724--729 []\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 , [1888] [1889] [1890] [1891] [1892] Underfull \vbox (badness 10000) has occurred while \output is active [1893] [1894] [1895] [1896] [1897] Underfull \hbox (badness 1371) in paragraph at lines 1320--1322 []\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 [1898] [1899] [1900] [1901] [1902] [1903] [1904] Underfull \hbox (badness 2057) in paragraph at lines 1812--1814 []\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 [1905] [1906] Underfull \hbox (badness 10000) in paragraph at lines 1913--1915 []\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 [1907] Underfull \hbox (badness 5189) in paragraph at lines 2003--2005 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1908] [1909] [1910] [1911] Underfull \hbox (badness 1661) in paragraph at lines 2221--2228 []\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 2238--2241 []\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 [1912] [1913] [1914] [1915] [1916] [1917] [1918] [1919] [1920] [1921] [1922] [1923] [1924] [1925] [1926] Underfull \hbox (badness 1412) in paragraph at lines 3235--3239 []\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 [1927] Underfull \hbox (badness 1430) in paragraph at lines 3259--3267 []\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 3302--3308 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1928] [1929] [1930] [1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940] [1941]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4123 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4123 ...mat Unordered and Ordered Lists}{format} [1942] [1943] [1944] [1945] [1946] [1947] [1948] [1949] [1950] [1951] [1952] [1953] [1954] [1955] [1956] Underfull \hbox (badness 1371) in paragraph at lines 5073--5075 []\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 [1957] Underfull \hbox (badness 1502) in paragraph at lines 5162--5167 []\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 5162--5167 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1958] [1959] [1960] Underfull \hbox (badness 10000) in paragraph at lines 5335--5344 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [1961] Underfull \hbox (badness 2150) in paragraph at lines 5398--5401 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [1962] [1963] Underfull \hbox (badness 3118) in paragraph at lines 5535--5537 []\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 [1964] Underfull \hbox (badness 2409) in paragraph at lines 5568--5572 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [1965] Underfull \hbox (badness 1325) in paragraph at lines 5676--5680 []\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 [1966] Underfull \hbox (badness 10000) in paragraph at lines 5759--5762 []\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 5759--5762 \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., [1967] Underfull \hbox (badness 3219) in paragraph at lines 5832--5839 []\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 5832--5839 \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 5832--5839 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [1968] Underfull \hbox (badness 10000) in paragraph at lines 5912--5917 [][][]\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 , [1969] [1970] [1971] [1972] [1973] [1974] [1975] [1976] [1977] [1978] [1979] [1980] [1981] [1982] [1983] [1984] [1985] [1986] [1987] [1988] Underfull \hbox (badness 10000) in paragraph at lines 7124--7126 []\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 7129--7134 []\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, [1989] [1990] [1991] [1992] [1993] [1994] [1995] [1996] [1997] Underfull \hbox (badness 1789) in paragraph at lines 7679--7681 []\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 [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] Underfull \hbox (badness 1097) in paragraph at lines 8504--8507 []\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 [2010] [2011] Underfull \hbox (badness 3000) in paragraph at lines 8640--8645 [][][]\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 ; [2012] [2013] [2014] [2015] [2016] [2017] [2018] [2019] [2020] Underfull \hbox (badness 2134) in paragraph at lines 9222--9227 [][][]\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 ; [2021] [2022] [2023] [2024] [2025] [2026] [2027] Underfull \hbox (badness 2469) in paragraph at lines 9655--9659 []\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 9655--9659 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2028] [2029] [2030] [2031] [2032] [2033] Underfull \hbox (badness 10000) in paragraph at lines 9996--9998 []\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 [2034] [2035] Underfull \hbox (badness 2150) in paragraph at lines 10172--10174 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2036] [2037] [2038] Underfull \hbox (badness 10000) in paragraph at lines 10350--10354 []\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 [2039] Underfull \hbox (badness 10000) in paragraph at lines 10381--10387 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2040] Underfull \hbox (badness 2096) in paragraph at lines 10499--10502 []\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 10503--10506 []\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 [2041] Underfull \hbox (badness 1009) in paragraph at lines 10569--10580 []\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 [2042] [2043] [2044] [2045] [2046] Underfull \hbox (badness 3780) in paragraph at lines 10868--10872 []\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 10884--10887 []\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 [2047] [2048] [2049] [2050] [2051] [2052] Underfull \hbox (badness 5970) in paragraph at lines 11258--11261 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2053] [2054] [2055] Underfull \hbox (badness 10000) in paragraph at lines 11437--11439 []\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 [2056] [2057] [2058] [2059] [2060] [2061] Underfull \hbox (badness 10000) in paragraph at lines 11838--11841 [][][]$\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 11838--11841 \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 [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] [2070] Underfull \hbox (badness 10000) in paragraph at lines 12368--12370 []\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 12371--12373 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2071] Underfull \hbox (badness 10000) in paragraph at lines 12401--12406 []\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 12401--12406 [][]\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 12430--12433 [][][]\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 , [2072] [2073] [2074] [2075] Overfull \hbox (25.86961pt too wide) in paragraph at lines 12669--12672 [][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi -gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](, package = "") [2076] [2077] Underfull \hbox (badness 1454) in paragraph at lines 12747--12751 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, [2078] Underfull \hbox (badness 10000) in paragraph at lines 12817--12819 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion [2079] [2080] [2081]) [2082] No file fullrefman.ind. (./fullrefman.aux) Package rerunfilecheck Warning: File `fullrefman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. 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 pdfTeX warning (dest): name{Rfn.gamma.shape} has been referenced but does not e xist, replaced by a fixed one pdfTeX 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but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, replaced by a fixed one {/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/ texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dis t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}< /usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb> Output written on fullrefman.pdf (2085 pages, 5139397 bytes). Transcript written on fullrefman.log. This is makeindex, version 2.15 [TeX Live 2015] (kpathsea + Thai support). Scanning input file fullrefman.idx................done (12900 entries accepted, 33 rejected). Sorting entries......................................................................................................................................done (196192 comparisons). Generating output file fullrefman.ind................done (12825 lines written, 43 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 <2015/01/01> Babel <3.9l> and hyphenation patterns for 2 languages 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? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 511--517 []\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 1122--1125 []\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 1339--1345 []\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] Overfull \hbox (26.88089pt too wide) in paragraph at lines 1849--1849 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [30] [31] [32] Underfull \hbox (badness 10000) in paragraph at lines 2034--2036 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] Underfull \hbox (badness 10000) in paragraph at lines 3532--3534 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [56] [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 4728--4730 []\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] [93] Underfull \hbox (badness 2096) in paragraph at lines 5945--5958 []\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 [94] [95] [96] Overfull \hbox (58.35893pt too wide) in paragraph at lines 6146--6149 []\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 : [97] [98] Underfull \hbox (badness 10000) in paragraph at lines 6290--6293 []\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 [99] [100] Underfull \hbox (badness 1442) in paragraph at lines 6451--6457 []\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 6451--6457 \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 6451--6457 \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 [101] Underfull \hbox (badness 3568) in paragraph at lines 6512--6519 \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 [102] [103] Underfull \vbox (badness 10000) has occurred while \output is active [104] [105] [106] [107] [108] [109] [110] [111] Underfull \hbox (badness 2096) in paragraph at lines 7149--7153 \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 . [112] Underfull \hbox (badness 4595) in paragraph at lines 7206--7209 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [113] Underfull \hbox (badness 3000) in paragraph at lines 7242--7244 []\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 7267--7270 [][][]\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 , [114] [115] [116] [117] Underfull \hbox (badness 10000) in paragraph at lines 7517--7528 []\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 [118] Underfull \hbox (badness 4479) in paragraph at lines 7589--7598 [][][]\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 7589--7598 [][]\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 [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] Underfull \hbox (badness 1394) in paragraph at lines 9200--9205 []\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 [144] [145] [146] [147] [148] Underfull \hbox (badness 1052) in paragraph at lines 9537--9542 []\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 9537--9542 \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 [149] [150] Underfull \hbox (badness 1735) in paragraph at lines 9675--9679 \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 . [151] [152] [153] [154] [155] [156] Underfull \hbox (badness 2150) in paragraph at lines 10079--10082 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse [157] Underfull \hbox (badness 6396) in paragraph at lines 10093--10101 []\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 10134--10141 []\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 [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] Underfull \hbox (badness 4569) in paragraph at lines 11178--11182 []\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 11178--11182 \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 [174] [175] [176] [177] [178] [179] [180] [181] Underfull \hbox (badness 2698) in paragraph at lines 11754--11763 []\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 11754--11763 \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 [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] Underfull \hbox (badness 6236) in paragraph at lines 12398--12401 []\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 [192] [193] [194] [195] [196] [197] Underfull \hbox (badness 2253) in paragraph at lines 12776--12778 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [198] Underfull \hbox (badness 1565) in paragraph at lines 12847--12851 [][][]\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 [199] Underfull \hbox (badness 10000) in paragraph at lines 12891--12893 []\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 [200] [201] Underfull \hbox (badness 1466) in paragraph at lines 13032--13035 []\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 [202] [203] Underfull \hbox (badness 10000) in paragraph at lines 13140--13144 [][][]\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 13151--13154 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [204] [205] [206] [207] Underfull \hbox (badness 3965) in paragraph at lines 13403--13407 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] Underfull \hbox (badness 4429) in paragraph at lines 14133--14136 []\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 [219] Underfull \hbox (badness 10000) in paragraph at lines 14225--14227 []\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 14231--14235 []\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 [220] Underfull \hbox (badness 10000) in paragraph at lines 14273--14277 []\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 14273--14277 \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 [221] Underfull \vbox (badness 3803) has occurred while \output is active [222] [223] [224] [225] [226] [227] [228] [229] Underfull \hbox (badness 2452) in paragraph at lines 14853--14857 []\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 14853--14857 \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 [230] [231] [232] Underfull \hbox (badness 1092) in paragraph at lines 15026--15031 [][]\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 [233] [234] [235] [236] Underfull \hbox (badness 6741) in paragraph at lines 15274--15278 \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 , [237] [238] [239] [240] Underfull \hbox (badness 1867) in paragraph at lines 15580--15587 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [241] [242] [243] [244] Underfull \vbox (badness 10000) has occurred while \output is active [245] [246] Underfull \hbox (badness 3679) in paragraph at lines 15960--15962 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [247] [248] [249] [250] [251] [252] [253] Underfull \hbox (badness 1478) in paragraph at lines 16440--16443 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [254] [255] [256] [257] Underfull \hbox (badness 10000) in paragraph at lines 16693--16695 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [258] [259] [260] [261] [262] [263] [264] [265] [266] Underfull \hbox (badness 1442) in paragraph at lines 17256--17258 []\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 [267] Underfull \hbox (badness 2452) in paragraph at lines 17348--17364 [][][]\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 , [268] [269] [270] [271] [272] [273] [274] Underfull \hbox (badness 1248) in paragraph at lines 17756--17759 []\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 , [275] [276] [277] [278] Underfull \hbox (badness 4739) in paragraph at lines 18012--18014 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [279] [280] [281] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] Underfull \hbox (badness 1360) in paragraph at lines 18960--18965 \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 18983--18989 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / Underfull \hbox (badness 1127) in paragraph at lines 18983--18989 \T1/zi4/m/n/10 ssl-[]compared . html$[][] \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 [295] Underfull \hbox (badness 10000) in paragraph at lines 19056--19060 []\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 19056--19060 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [296] [297] Underfull \hbox (badness 1509) in paragraph at lines 19191--19198 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1354) in paragraph at lines 19191--19198 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19207--19212 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] [309] Underfull \hbox (badness 1264) in paragraph at lines 19938--19943 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] Underfull \hbox (badness 10000) in paragraph at lines 20692--20694 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] Underfull \hbox (badness 1077) in paragraph at lines 21690--21696 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [337] [338] [339] Underfull \hbox (badness 1484) in paragraph at lines 21851--21859 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [340] [341] [342] [343] Underfull \hbox (badness 2790) in paragraph at lines 22122--22125 []\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 22122--22125 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [344] [345] [346] [347] Underfull \hbox (badness 1194) in paragraph at lines 22403--22406 []\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 [348] [349] [350] [351] Underfull \hbox (badness 10000) in paragraph at lines 22609--22615 []\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 22609--22615 \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 22619--22622 []\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 22619--22622 \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 [352] [353] [354] [355] [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] Underfull \hbox (badness 10000) in paragraph at lines 23544--23546 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [366] [367] [368] [369] Underfull \hbox (badness 1199) in paragraph at lines 23771--23777 []\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 23771--23777 \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, [370] [371] [372] [373] [374] [375] [376] [377] Underfull \hbox (badness 1038) in paragraph at lines 24336--24344 []\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 24345--24348 []\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 24364--24366 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [378] Underfull \hbox (badness 10000) in paragraph at lines 24436--24446 []\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 24447--24453 []\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 24460--24465 []\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 24470--24472 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [379] [380] [381] Underfull \hbox (badness 10000) in paragraph at lines 24721--24727 []\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 24721--24727 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "http://bioconductor.org"\T1/p tm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 24721--24727 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "http://bioconductor.statistik.tu-dortmund.de"\T 1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 24734--24737 []\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 [382] Underfull \hbox (badness 2689) in paragraph at lines 24758--24760 []\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 24790--24795 []\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 24796--24807 \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 24808--24811 []\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 Underfull \hbox (badness 4084) in paragraph at lines 24818--24830 \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 24818--24830 \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 24818--24830 \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 24832--24839 []\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 24832--24839 \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 24832--24839 \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 24832--24839 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [383] [384] [385] [386] [387] Underfull \hbox (badness 10000) in paragraph at lines 25153--25157 []\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 25153--25157 \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)] [388] [389] [390] [391] [392] Underfull \hbox (badness 1735) in paragraph at lines 25471--25475 []\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 [393] [394] [395] [396] [397] [398] [399] [400] [401] [402] Underfull \hbox (badness 2726) in paragraph at lines 26030--26033 []\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 [403] [404] [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] [415] Underfull \hbox (badness 1052) in paragraph at lines 26849--26854 []\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 [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] Underfull \hbox (badness 1533) in paragraph at lines 27577--27580 []\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 [427] [428] Underfull \hbox (badness 1163) in paragraph at lines 27739--27749 []\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 [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] Underfull \hbox (badness 10000) in paragraph at lines 29241--29245 []\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 29241--29245 \T1/zi4/m/n/10 "(?[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 29263--29265 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [453] [454] [455] [456] [457] [458] [459] [460] [461] Underfull \hbox (badness 1655) in paragraph at lines 29808--29810 []\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 [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] Underfull \hbox (badness 10000) in paragraph at lines 30476--30480 []\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., [473] [474] [475] Underfull \hbox (badness 2302) in paragraph at lines 30716--30723 []\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 30716--30723 \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 30716--30723 \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 30716--30723 \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 [476] [477] [478] Underfull \hbox (badness 2261) in paragraph at lines 30870--30875 []\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 30897--30903 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [479] Underfull \hbox (badness 10000) in paragraph at lines 30973--30978 []\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 [480] [481] [482] [483] [484] [485] [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] Underfull \hbox (badness 1072) in paragraph at lines 33757--33761 []\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 33762--33766 []\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 ', [523] Underfull \hbox (badness 10000) in paragraph at lines 33790--33796 []\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 33790--33796 \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 33790--33796 \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 33803--33810 \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 33803--33810 \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 33803--33810 \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 [524] [525] [526] [527] [528] Underfull \hbox (badness 10000) in paragraph at lines 34094--34100 []\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 34094--34100 \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 [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] Underfull \hbox (badness 3333) in paragraph at lines 35877--35882 []\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 [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] Underfull \hbox (badness 1472) in paragraph at lines 36497--36500 []\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 [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] Underfull \hbox (badness 2671) in paragraph at lines 37159--37162 []\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 [578] [579] [580] [581] [582] [583] Underfull \hbox (badness 10000) in paragraph at lines 37563--37566 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$http : / / developer . r-[]project . org / [584] [585] Underfull \hbox (badness 10000) in paragraph at lines 37684--37688 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 http : / / developer . [586] Underfull \hbox (badness 10000) in paragraph at lines 37746--37750 [][][]\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 http : / / developer . [587] [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] Underfull \hbox (badness 1990) in paragraph at lines 39041--39049 []\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 39041--39049 \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 [606] [607] [608] [609] [610] Underfull \hbox (badness 1515) in paragraph at lines 39313--39318 []\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 [611] [612] [613] Underfull \hbox (badness 1917) in paragraph at lines 39543--39550 []\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 [614] [615] [616] [617] [618] [619] [620] [621] [622] Underfull \hbox (badness 3668) in paragraph at lines 40128--40130 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [623] [624] Underfull \hbox (badness 2401) in paragraph at lines 40233--40237 []\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 [625] [626] [627] Underfull \hbox (badness 2111) in paragraph at lines 40402--40407 \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. Underfull \hbox (badness 6542) in paragraph at lines 40418--40423 []\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 [628] [629] [630] [631] [632] [633] [634] Underfull \hbox (badness 10000) in paragraph at lines 40863--40868 []\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 40863--40868 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to [635] [636] Underfull \hbox (badness 5417) in paragraph at lines 40955--40959 []\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 [637] Underfull \hbox (badness 10000) in paragraph at lines 41016--41020 []\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 [638]) (./compiler-pkg.tex Chapter 2. [639] [640] [641] [642]) (./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 [643] [644] [645] [646] [647] [648] [649] [650] [651] [652] [653] [654] [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] Underfull \vbox (badness 1515) has occurred while \output is active [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] 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 / [710] Underfull \vbox (badness 10000) has occurred while \output is active [711] [712] [713] [714] Underfull \vbox (badness 10000) has occurred while \output is active [715] Underfull \vbox (badness 10000) has occurred while \output is active [716] [717] [718] [719] [720] [721] [722] [723]) (./grDevices-pkg.tex [724] Chapter 4. [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] Underfull \hbox (badness 5175) in paragraph at lines 1066--1068 []\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 [742] [743] [744] [745] Underfull \hbox (badness 1852) in paragraph at lines 1263--1266 []\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 [746] [747] [748] Underfull \hbox (badness 1490) in paragraph at lines 1469--1474 \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 [749] Underfull \hbox (badness 2698) in paragraph at lines 1523--1526 []\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 [750] Underfull \hbox (badness 10000) in paragraph at lines 1592--1596 []\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 [751] [752] [753] [754] Underfull \hbox (badness 1325) in paragraph at lines 1875--1885 \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 , [755] [756] Underfull \hbox (badness 10000) in paragraph at lines 1980--1982 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [757] [758] [759] Underfull \hbox (badness 6758) in paragraph at lines 2141--2144 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [760] [761] [762] [763] [764] [765] [766] [767] [768] Underfull \hbox (badness 10000) in paragraph at lines 2707--2708 [769] [770] [771] [772] [773] [774] [775] Underfull \hbox (badness 1152) in paragraph at lines 3145--3147 []\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 [776] [777] [778] [779] [780] Underfull \hbox (badness 2856) in paragraph at lines 3465--3468 []\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 3479--3481 []\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 [781] [782] Underfull \hbox (badness 1173) in paragraph at lines 3595--3605 []\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 [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] Underfull \hbox (badness 1067) in paragraph at lines 4302--4309 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [794] [795] Underfull \hbox (badness 3364) in paragraph at lines 4463--4465 []\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 / [796] Underfull \hbox (badness 1789) in paragraph at lines 4540--4542 []\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 [797] Underfull \hbox (badness 1377) in paragraph at lines 4590--4595 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [798] Underfull \hbox (badness 2671) in paragraph at lines 4617--4625 \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 4666--4673 \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 4674--4683 \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 4674--4683 \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 4684--4686 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [799] [800] Underfull \hbox (badness 1057) in paragraph at lines 4795--4800 []\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 [801] Underfull \hbox (badness 7344) in paragraph at lines 4855--4857 []\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 [802] [803] Underfull \hbox (badness 2035) in paragraph at lines 4979--4988 []\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 4979--4988 \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 4979--4988 \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 , [804] Underfull \hbox (badness 10000) in paragraph at lines 5048--5055 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5048--5055 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [805] [806] [807] Underfull \hbox (badness 1546) in paragraph at lines 5186--5194 []\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 , [808] Underfull \hbox (badness 1648) in paragraph at lines 5263--5267 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [809] [810] [811] [812] [813] [814] [815] Underfull \hbox (badness 10000) in paragraph at lines 5686--5689 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [816] Underfull \vbox (badness 3803) has occurred while \output is active [817] [818] [819] [820] [821] Underfull \hbox (badness 1189) in paragraph at lines 6083--6085 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [822] [823] Underfull \hbox (badness 10000) in paragraph at lines 6181--6183 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [824] [825] [826] [827] Underfull \hbox (badness 3780) in paragraph at lines 6472--6478 []\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 , [828] [829] [830] Underfull \hbox (badness 2680) in paragraph at lines 6668--6670 []\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 [831] [832] [833]) (./graphics-pkg.tex [834] Chapter 5. [835] [836] [837] [838] [839] [840] [841] [842] [843] [844] [845] 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 [846] [847] [848] [849] Underfull \vbox (badness 3803) has occurred while \output is active [850] [851] [852] [853] [854] 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 , [855] [856] [857] [858] [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] [869] [870] [871] Underfull \hbox (badness 1009) in paragraph at lines 2277--2284 \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 [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] Underfull \vbox (badness 10000) has occurred while \output is active [894] Underfull \vbox (badness 10000) has occurred while \output is active [895] [896] [897] [898] Underfull \hbox (badness 1867) in paragraph at lines 3901--3905 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [899] [900] [901] [902] [903] [904] [905] Underfull \hbox (badness 1924) in paragraph at lines 4348--4353 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain [906] Underfull \hbox (badness 2529) in paragraph at lines 4379--4382 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used: see [907] [908] [909] [910] [911] Underfull \hbox (badness 10000) in paragraph at lines 4729--4735 []\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 4729--4735 \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 [912] Underfull \hbox (badness 10000) in paragraph at lines 4860--4863 [913] [914 ] Underfull \hbox (badness 10000) in paragraph at lines 4921--4923 [915 ] [916] Underfull \hbox (badness 10000) in paragraph at lines 5111--5113 []\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 [917] [918] [919] [920] [921] Underfull \vbox (badness 10000) has occurred while \output is active [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6581--6582 [][] [941 ] [942] Underfull \vbox (badness 10000) has occurred while \output is active [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] Underfull \hbox (badness 1048) in paragraph at lines 7290--7295 \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 [953] Underfull \hbox (badness 1038) in paragraph at lines 7406--7409 []\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 [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] [971] [972] [973] [974] Underfull \hbox (badness 6691) in paragraph at lines 8625--8628 []\T1/ptm/m/n/10 The main ti-tle (on top) us-ing font and size (char-ac-ter ex- pan-sion) Underfull \hbox (badness 2799) in paragraph at lines 8628--8630 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font and size \T1/zi4/m/n/10 par ("font.sub") \T1/ptm/m/n/10 and color [975] [976]pdfTeX warning (ext4): destination with the same identifier (name{Rf n.units}) has been already used, duplicate ignored \relax l.8710 \HeaderA{units}{Graphical Units}{units} [977] [978] [979] [980]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [981] [982] [983] [984] [985] [986] 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 [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] 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 , [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [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] Underfull \vbox (badness 3803) has occurred while \output is active [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] 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 [1054] [1055] [1056] [1057] 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 [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] Underfull \hbox (badness 10000) in paragraph at lines 5854--5860 \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., [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] Underfull \hbox (badness 7649) in paragraph at lines 6324--6327 []\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 [1087] [1088] [1089] [1090]) (./methods-pkg.tex Chapter 7. [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] 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 [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] 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 [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] 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 [1128] [1129] 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 [1130] 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 [1131] [1132] [1133] [1134] [1135] [1136] [1137] 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 [1138] [1139] [1140] [1141] [1142] 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 [1143] [1144] [1145] [1146] [1147] [1148] Underfull \vbox (badness 10000) has occurred while \output is active [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156] 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 [1157] [1158] [1159] [1160] [1161] [1162] Underfull \vbox (badness 2452) has occurred while \output is active [1163] [1164] Underfull \vbox (badness 10000) has occurred while \output is active [1165] [1166] 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 [1167] [1168] [1169] [1170] [1171] 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 [1172] [1173] [1174] [1175] 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 [1176] [1177] [1178] [1179] [1180] Underfull \hbox (badness 1675) in paragraph at lines 6343--6349 \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 [1181] [1182] [1183] [1184] Underfull \vbox (badness 10000) has occurred while \output is active [1185] [1186]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4} ) has been already used, duplicate ignored \relax l.6820 \aliasA{S4}{S3Part}{S4} [1187] [1188] [1189] [1190]pdfTeX warning (ext4) : destination with the same identifier (name{Rfn.Complex}) has been already use d, duplicate ignored \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 \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 \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 \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 \relax l.7102 \aliasA{Summary}{S4groupGeneric}{Summary} [1191] 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 [1192] [1193] [1194] 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 [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] Underfull \hbox (badness 1852) in paragraph at lines 9759--9763 []\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., [1229] [1230] [1231] [1232]) (./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 [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] Underfull \hbox (badness 3386) in paragraph at lines 1246--1249 []\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 [1253] [1254]) (./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 \T1/ptm/ m/n/10 and William N. Ven-ables [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269]) (./stats-pkg.tex [1270] Chapter 10. [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] Underfull \hbox (badness 1412) in paragraph at lines 844--846 []\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 [1284] [1285] [1286] [1287] [1288] [1289] [1290] [1291] Underfull \hbox (badness 2503) in paragraph at lines 1325--1328 []\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 , [1292] [1293] [1294] Underfull \hbox (badness 10000) in paragraph at lines 1504--1508 []\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 [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] Underfull \hbox (badness 3965) in paragraph at lines 2164--2166 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1306] [1307] [1308] [1309] [1310] Underfull \hbox (badness 3965) in paragraph at lines 2506--2508 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] Underfull \hbox (badness 2503) in paragraph at lines 3323--3326 []\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 , [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 3989) in paragraph at lines 4548--4555 []\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 = [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] Underfull \hbox (badness 2556) in paragraph at lines 5149--5152 []\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 5166--5168 []\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 [1354] [1355] [1356] [1357] Underfull \hbox (badness 1142) in paragraph at lines 5407--5419 \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. [1358] [1359] Underfull \hbox (badness 2503) in paragraph at lines 5546--5550 []\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 , [1360] Underfull \hbox (badness 1168) in paragraph at lines 5607--5612 []\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 [1361] [1362] [1363] [1364] [1365] [1366] [1367] Underfull \hbox (badness 8132) in paragraph at lines 6049--6054 \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, [1368] [1369] [1370] [1371] [1372] Underfull \hbox (badness 7081) in paragraph at lines 6324--6327 []\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 6328--6330 []\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 [1373] [1374] [1375] [1376] [1377] Underfull \vbox (badness 3803) has occurred while \output is active [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] Underfull \hbox (badness 10000) in paragraph at lines 7136--7139 []\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 [1386] [1387] Underfull \hbox (badness 10000) in paragraph at lines 7273--7276 []\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 / [1388] [1389] [1390] [1391] Underfull \vbox (badness 3803) has occurred while \output is active [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] Underfull \hbox (badness 2626) in paragraph at lines 8771--8774 []\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 [1413] Underfull \hbox (badness 2503) in paragraph at lines 8871--8875 []\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 , [1414] [1415] [1416] [1417] [1418] Overfull \hbox (6.88992pt too wide) in paragraph at lines 9205--9207 []\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 . [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] Underfull \hbox (badness 4518) in paragraph at lines 10132--10137 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1434] [1435] [1436] [1437] Underfull \hbox (badness 2142) in paragraph at lines 10474--10477 []\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 ^^@ [1438] Underfull \hbox (badness 1253) in paragraph at lines 10493--10496 []\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, [1439] Underfull \hbox (badness 1708) in paragraph at lines 10555--10559 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1440] [1441] [1442] [1443] [1444] [1445] Underfull \hbox (badness 1694) in paragraph at lines 10951--10954 []\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 10970--10979 \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- [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453]pdfTeX warning (ext4): d estination with the same identifier (name{Rfn.hat}) has been already used, dupl icate ignored \relax l.11417 \aliasA{hat}{influence.measures}{hat} [1454] [1455] Underfull \hbox (badness 1484) in paragraph at lines 11540--11542 []\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 [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 4441) in paragraph at lines 12098--12100 []\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 12105--12107 []\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 [1465] [1466] [1467] [1468] [1469] [1470] Underfull \hbox (badness 2894) in paragraph at lines 12439--12443 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] Underfull \hbox (badness 4518) in paragraph at lines 13134--13139 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1482] [1483] [1484] [1485] [1486] [1487] [1488] [1489] [1490] [1491] Underfull \hbox (badness 4518) in paragraph at lines 13781--13786 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1492] [1493] Underfull \hbox (badness 10000) in paragraph at lines 13919--13923 []\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 13926--13928 []\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 [1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] [1509] [1510] [1511] Underfull \hbox (badness 2503) in paragraph at lines 14990--14994 []\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 , [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] Underfull \hbox (badness 1418) in paragraph at lines 15499--15505 []\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 [1520] [1521] [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] Underfull \hbox (badness 2359) in paragraph at lines 17123--17125 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1546] [1547] Underfull \vbox (badness 10000) has occurred while \output is active [1548] Underfull \vbox (badness 10000) has occurred while \output is active [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] Underfull \hbox (badness 1377) in paragraph at lines 18034--18039 []\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 18039--18042 []\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 18052--18056 \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 18060--18064 []\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 [1562] [1563] [1564] Underfull \vbox (badness 10000) has occurred while \output is active [1565] [1566] [1567] [1568] [1569] [1570] [1571] Underfull \hbox (badness 1337) in paragraph at lines 18676--18679 []\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 [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] Underfull \hbox (badness 5563) in paragraph at lines 19406--19408 []\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 19409--19412 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1585] [1586] [1587] [1588] [1589] [1590] Underfull \hbox (badness 2503) in paragraph at lines 19776--19779 []\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 , [1591] Underfull \hbox (badness 10000) in paragraph at lines 19803--19805 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602] [1603] [1604] [1605] [1606] [1607] Underfull \hbox (badness 10000) in paragraph at lines 20803--20809 []\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 , [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] Underfull \hbox (badness 1337) in paragraph at lines 22138--22144 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1631] [1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] Underfull \hbox (badness 10000) in paragraph at lines 22931--22934 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1643] [1644] [1645] [1646] [1647] [1648] [1649] [1650] [1651] Underfull \hbox (badness 10000) in paragraph at lines 23508--23511 []\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 [1652] Underfull \hbox (badness 3690) in paragraph at lines 23559--23563 [][][]\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 [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] Underfull \hbox (badness 3439) in paragraph at lines 24029--24035 [][]\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 , [1661] [1662] [1663] [1664] [1665] [1666] [1667] [1668] [1669] Underfull \hbox (badness 10000) in paragraph at lines 24577--24582 []\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 [1670] [1671] [1672] [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] Underfull \vbox (badness 3803) has occurred while \output is active [1685] [1686] Underfull \hbox (badness 3514) in paragraph at lines 25593--25598 []\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 [1687] Underfull \hbox (badness 3514) in paragraph at lines 25655--25660 []\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 [1688] Underfull \hbox (badness 3514) in paragraph at lines 25712--25717 []\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 [1689] Underfull \hbox (badness 3514) in paragraph at lines 25773--25779 []\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 [1690] [1691] [1692] [1693] Underfull \hbox (badness 3514) in paragraph at lines 25986--25991 []\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 Underfull \hbox (badness 3514) in paragraph at lines 26042--26047 []\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 [1694] Underfull \hbox (badness 3514) in paragraph at lines 26099--26104 []\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 [1695] Underfull \hbox (badness 3514) in paragraph at lines 26154--26159 []\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 [1696] [1697] Underfull \hbox (badness 6691) in paragraph at lines 26223--26228 []\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 [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] Underfull \hbox (badness 10000) in paragraph at lines 26747--26750 []\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 26747--26750 \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, [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] Underfull \hbox (badness 5431) in paragraph at lines 27353--27355 []\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 [1716] [1717] [1718] [1719] Underfull \hbox (badness 5431) in paragraph at lines 27563--27566 []\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 [1720] [1721] [1722] [1723] [1724] Underfull \hbox (badness 1337) in paragraph at lines 27875--27879 []\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 [1725] [1726] Underfull \hbox (badness 10000) in paragraph at lines 27992--27995 []\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 [1727] [1728] [1729] Underfull \hbox (badness 1616) in paragraph at lines 28175--28178 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] Underfull \hbox (badness 10000) in paragraph at lines 29302--29306 []\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 [1749] [1750] [1751] Underfull \vbox (badness 10000) has occurred while \output is active [1752] [1753] [1754] Underfull \hbox (badness 1337) in paragraph at lines 29666--29670 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] Underfull \hbox (badness 1337) in paragraph at lines 30150--30154 []\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 [1763] Underfull \hbox (badness 5161) in paragraph at lines 30243--30245 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1764] [1765] [1766] [1767] [1768] [1769] Underfull \hbox (badness 10000) in paragraph at lines 30607--30612 []\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 [1770] [1771] [1772]) (./stats4-pkg.tex Chapter 11. [1773] [1774] [1775] [1776] [1777] [1778]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1779] [1780] [1781] [1782]) (./tcltk-pkg.tex Chapter 12. [1783] [1784] [1785] [1786] [1787] [1788] [1789] Underfull \vbox (badness 10000) has occurred while \output is active [1790] Underfull \vbox (badness 10000) has occurred while \output is active [1791] 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 [1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] 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 [1803]) (./tools-pkg.tex [1804] Chapter 13. [1805] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1806] 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 [1807] [1808] 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 [1809] [1810] 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 [1811] [1812] [1813] [1814] [1815] [1816] [1817] [1818] [1819] [1820] [1821] 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 [1822] 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- [1823] 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 , [1824] [1825] [1826] 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 [1827] [1828] [1829] Underfull \hbox (badness 7981) in paragraph at lines 1518--1522 []\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 1524--1526 []\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 [1830] [1831] [1832] [1833]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1721 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1834] [1835] Underfull \hbox (badness 5726) in paragraph at lines 1847--1852 []\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 1847--1852 \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 [1836] [1837] [1838] [1839] [1840] [1841] [1842] [1843] Underfull \hbox (badness 7981) in paragraph at lines 2323--2329 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1844] [1845] [1846] [1847] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2607. [1848] [1849] [1850] [1851] Underfull \hbox (badness 1424) in paragraph at lines 2844--2846 []\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 [1852] [1853] [1854] [1855] [1856] [1857] [1858] [1859] [1860] [1861] [1862] Underfull \hbox (badness 10000) in paragraph at lines 3539--3541 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1863] [1864] [1865] [1866] [1867] [1868] Underfull \hbox (badness 1838) in paragraph at lines 3919--3925 []\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 3919--3925 \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 [1869] [1870] Underfull \hbox (badness 5726) in paragraph at lines 3999--4004 []\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 3999--4004 \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 [1871] [1872] Underfull \hbox (badness 1688) in paragraph at lines 4142--4154 []\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 [1873] [1874] [1875] [1876]) (./utils-pkg.tex Chapter 14. [1877] 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 ', [1878] [1879] 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 [1880] [1881] [1882] [1883] [1884] [1885] 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 [1886] Underfull \hbox (badness 5847) in paragraph at lines 656--662 []\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 656--662 \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 [1887] Underfull \hbox (badness 3861) in paragraph at lines 724--729 []\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 , [1888] [1889] [1890] [1891] [1892] Underfull \vbox (badness 10000) has occurred while \output is active [1893] [1894] [1895] [1896] [1897] Underfull \hbox (badness 1371) in paragraph at lines 1320--1322 []\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 [1898] [1899] [1900] [1901] [1902] [1903] [1904] Underfull \hbox (badness 2057) in paragraph at lines 1812--1814 []\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 [1905] [1906] Underfull \hbox (badness 10000) in paragraph at lines 1913--1915 []\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 [1907] Underfull \hbox (badness 5189) in paragraph at lines 2003--2005 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1908] [1909] [1910] [1911] Underfull \hbox (badness 1661) in paragraph at lines 2221--2228 []\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 2238--2241 []\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 [1912] [1913] [1914] [1915] [1916] [1917] [1918] [1919] [1920] [1921] [1922] [1923] [1924] [1925] [1926] Underfull \hbox (badness 1412) in paragraph at lines 3235--3239 []\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 [1927] Underfull \hbox (badness 1430) in paragraph at lines 3259--3267 []\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 3302--3308 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1928] [1929] [1930] [1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940] [1941]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4123 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4123 ...mat Unordered and Ordered Lists}{format} [1942] [1943] [1944] [1945] [1946] [1947] [1948] [1949] [1950] [1951] [1952] [1953] [1954] [1955] [1956] Underfull \hbox (badness 1371) in paragraph at lines 5073--5075 []\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 [1957] Underfull \hbox (badness 1502) in paragraph at lines 5162--5167 []\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 5162--5167 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1958] [1959] [1960] Underfull \hbox (badness 10000) in paragraph at lines 5335--5344 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [1961] Underfull \hbox (badness 2150) in paragraph at lines 5398--5401 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [1962] [1963] Underfull \hbox (badness 3118) in paragraph at lines 5535--5537 []\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 [1964] Underfull \hbox (badness 2409) in paragraph at lines 5568--5572 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [1965] Underfull \hbox (badness 1325) in paragraph at lines 5676--5680 []\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 [1966] Underfull \hbox (badness 10000) in paragraph at lines 5759--5762 []\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 5759--5762 \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., [1967] Underfull \hbox (badness 3219) in paragraph at lines 5832--5839 []\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 5832--5839 \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 5832--5839 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [1968] Underfull \hbox (badness 10000) in paragraph at lines 5912--5917 [][][]\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 , [1969] [1970] [1971] [1972] [1973] [1974] [1975] [1976] [1977] [1978] [1979] [1980] [1981] [1982] [1983] [1984] [1985] [1986] [1987] [1988] Underfull \hbox (badness 10000) in paragraph at lines 7124--7126 []\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 7129--7134 []\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, [1989] [1990] [1991] [1992] [1993] [1994] [1995] [1996] [1997] Underfull \hbox (badness 1789) in paragraph at lines 7679--7681 []\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 [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] Underfull \hbox (badness 1097) in paragraph at lines 8504--8507 []\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 [2010] [2011] Underfull \hbox (badness 3000) in paragraph at lines 8640--8645 [][][]\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 ; [2012] [2013] [2014] [2015] [2016] [2017] [2018] [2019] [2020] Underfull \hbox (badness 2134) in paragraph at lines 9222--9227 [][][]\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 ; [2021] [2022] [2023] [2024] [2025] [2026] [2027] Underfull \hbox (badness 2469) in paragraph at lines 9655--9659 []\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 9655--9659 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2028] [2029] [2030] [2031] [2032] [2033] Underfull \hbox (badness 10000) in paragraph at lines 9996--9998 []\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 [2034] [2035] Underfull \hbox (badness 2150) in paragraph at lines 10172--10174 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2036] [2037] [2038] Underfull \hbox (badness 10000) in paragraph at lines 10350--10354 []\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 [2039] Underfull \hbox (badness 10000) in paragraph at lines 10381--10387 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2040] Underfull \hbox (badness 2096) in paragraph at lines 10499--10502 []\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 10503--10506 []\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 [2041] Underfull \hbox (badness 1009) in paragraph at lines 10569--10580 []\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 [2042] [2043] [2044] [2045] [2046] Underfull \hbox (badness 3780) in paragraph at lines 10868--10872 []\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 10884--10887 []\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 [2047] [2048] [2049] [2050] [2051] [2052] Underfull \hbox (badness 5970) in paragraph at lines 11258--11261 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2053] [2054] [2055] Underfull \hbox (badness 10000) in paragraph at lines 11437--11439 []\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 [2056] [2057] [2058] [2059] [2060] [2061] Underfull \hbox (badness 10000) in paragraph at lines 11838--11841 [][][]$\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 11838--11841 \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 [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] [2070] Underfull \hbox (badness 10000) in paragraph at lines 12368--12370 []\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 12371--12373 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2071] Underfull \hbox (badness 10000) in paragraph at lines 12401--12406 []\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 12401--12406 [][]\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 12430--12433 [][][]\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 , [2072] [2073] [2074] [2075] Overfull \hbox (25.86961pt too wide) in paragraph at lines 12669--12672 [][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi -gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](, package = "") [2076] [2077] Underfull \hbox (badness 1454) in paragraph at lines 12747--12751 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, [2078] Underfull \hbox (badness 10000) in paragraph at lines 12817--12819 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion [2079] [2080] [2081]) [2082] (./fullrefman.ind [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] [2102] [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] Overfull \hbox (5.8567pt too wide) in paragraph at lines 11156--11158 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_depends Overfull \hbox (5.8567pt too wide) in paragraph at lines 11158--11160 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_results Overfull \hbox (5.8567pt too wide) in paragraph at lines 11160--11162 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_timings [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151]) (./fullrefman.aux) Package rerunfilecheck Warning: File `fullrefman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. 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 pdfTeX warning (dest): name{Rfn.gamma.shape} has been referenced but does not e xist, replaced by a fixed one pdfTeX 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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? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 511--517 []\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 1122--1125 []\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 1339--1345 []\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] Overfull \hbox (26.88089pt too wide) in paragraph at lines 1849--1849 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [30] [31] [32] Underfull \hbox (badness 10000) in paragraph at lines 2034--2036 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] Underfull \hbox (badness 10000) in paragraph at lines 3532--3534 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [56] [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 4728--4730 []\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] [93] Underfull \hbox (badness 2096) in paragraph at lines 5945--5958 []\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 [94] [95] [96] Overfull \hbox (58.35893pt too wide) in paragraph at lines 6146--6149 []\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 : [97] [98] Underfull \hbox (badness 10000) in paragraph at lines 6290--6293 []\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 [99] [100] Underfull \hbox (badness 1442) in paragraph at lines 6451--6457 []\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 6451--6457 \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 6451--6457 \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 [101] Underfull \hbox (badness 3568) in paragraph at lines 6512--6519 \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 [102] [103] Underfull \vbox (badness 10000) has occurred while \output is active [104] [105] [106] [107] [108] [109] [110] [111] Underfull \hbox (badness 2096) in paragraph at lines 7149--7153 \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 . [112] Underfull \hbox (badness 4595) in paragraph at lines 7206--7209 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [113] Underfull \hbox (badness 3000) in paragraph at lines 7242--7244 []\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 7267--7270 [][][]\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 , [114] [115] [116] [117] Underfull \hbox (badness 10000) in paragraph at lines 7517--7528 []\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 [118] Underfull \hbox (badness 4479) in paragraph at lines 7589--7598 [][][]\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 7589--7598 [][]\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 [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] Underfull \hbox (badness 1394) in paragraph at lines 9200--9205 []\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 [144] [145] [146] [147] [148] Underfull \hbox (badness 1052) in paragraph at lines 9537--9542 []\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 9537--9542 \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 [149] [150] Underfull \hbox (badness 1735) in paragraph at lines 9675--9679 \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 . [151] [152] [153] [154] [155] [156] Underfull \hbox (badness 2150) in paragraph at lines 10079--10082 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse [157] Underfull \hbox (badness 6396) in paragraph at lines 10093--10101 []\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 10134--10141 []\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 [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] Underfull \hbox (badness 4569) in paragraph at lines 11178--11182 []\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 11178--11182 \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 [174] [175] [176] [177] [178] [179] [180] [181] Underfull \hbox (badness 2698) in paragraph at lines 11754--11763 []\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 11754--11763 \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 [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] Underfull \hbox (badness 6236) in paragraph at lines 12398--12401 []\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 [192] [193] [194] [195] [196] [197] Underfull \hbox (badness 2253) in paragraph at lines 12776--12778 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [198] Underfull \hbox (badness 1565) in paragraph at lines 12847--12851 [][][]\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 [199] Underfull \hbox (badness 10000) in paragraph at lines 12891--12893 []\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 [200] [201] Underfull \hbox (badness 1466) in paragraph at lines 13032--13035 []\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 [202] [203] Underfull \hbox (badness 10000) in paragraph at lines 13140--13144 [][][]\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 13151--13154 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [204] [205] [206] [207] Underfull \hbox (badness 3965) in paragraph at lines 13403--13407 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] Underfull \hbox (badness 4429) in paragraph at lines 14133--14136 []\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 [219] Underfull \hbox (badness 10000) in paragraph at lines 14225--14227 []\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 14231--14235 []\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 [220] Underfull \hbox (badness 10000) in paragraph at lines 14273--14277 []\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 14273--14277 \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 [221] Underfull \vbox (badness 3803) has occurred while \output is active [222] [223] [224] [225] [226] [227] [228] [229] Underfull \hbox (badness 2452) in paragraph at lines 14853--14857 []\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 14853--14857 \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 [230] [231] [232] Underfull \hbox (badness 1092) in paragraph at lines 15026--15031 [][]\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 [233] [234] [235] [236] Underfull \hbox (badness 6741) in paragraph at lines 15274--15278 \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 , [237] [238] [239] [240] Underfull \hbox (badness 1867) in paragraph at lines 15580--15587 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [241] [242] [243] [244] Underfull \vbox (badness 10000) has occurred while \output is active [245] [246] Underfull \hbox (badness 3679) in paragraph at lines 15960--15962 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [247] [248] [249] [250] [251] [252] [253] Underfull \hbox (badness 1478) in paragraph at lines 16440--16443 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [254] [255] [256] [257] Underfull \hbox (badness 10000) in paragraph at lines 16693--16695 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [258] [259] [260] [261] [262] [263] [264] [265] [266] Underfull \hbox (badness 1442) in paragraph at lines 17256--17258 []\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 [267] Underfull \hbox (badness 2452) in paragraph at lines 17348--17364 [][][]\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 , [268] [269] [270] [271] [272] [273] [274] Underfull \hbox (badness 1248) in paragraph at lines 17756--17759 []\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 , [275] [276] [277] [278] Underfull \hbox (badness 4739) in paragraph at lines 18012--18014 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [279] [280] [281] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] Underfull \hbox (badness 1360) in paragraph at lines 18960--18965 \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 18983--18989 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / Underfull \hbox (badness 1127) in paragraph at lines 18983--18989 \T1/zi4/m/n/10 ssl-[]compared . html$[][] \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 [295] Underfull \hbox (badness 10000) in paragraph at lines 19056--19060 []\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 19056--19060 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [296] [297] Underfull \hbox (badness 1509) in paragraph at lines 19191--19198 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1354) in paragraph at lines 19191--19198 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19207--19212 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] [309] Underfull \hbox (badness 1264) in paragraph at lines 19938--19943 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] Underfull \hbox (badness 10000) in paragraph at lines 20692--20694 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] Underfull \hbox (badness 1077) in paragraph at lines 21690--21696 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [337] [338] [339] Underfull \hbox (badness 1484) in paragraph at lines 21851--21859 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [340] [341] [342] [343] Underfull \hbox (badness 2790) in paragraph at lines 22122--22125 []\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 22122--22125 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [344] [345] [346] [347] Underfull \hbox (badness 1194) in paragraph at lines 22403--22406 []\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 [348] [349] [350] [351] Underfull \hbox (badness 10000) in paragraph at lines 22609--22615 []\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 22609--22615 \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 22619--22622 []\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 22619--22622 \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 [352] [353] [354] [355] [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] Underfull \hbox (badness 10000) in paragraph at lines 23544--23546 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [366] [367] [368] [369] Underfull \hbox (badness 1199) in paragraph at lines 23771--23777 []\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 23771--23777 \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, [370] [371] [372] [373] [374] [375] [376] [377] Underfull \hbox (badness 1038) in paragraph at lines 24336--24344 []\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 24345--24348 []\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 24364--24366 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [378] Underfull \hbox (badness 10000) in paragraph at lines 24436--24446 []\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 24447--24453 []\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 24460--24465 []\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 24470--24472 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [379] [380] [381] Underfull \hbox (badness 10000) in paragraph at lines 24721--24727 []\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 24721--24727 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "http://bioconductor.org"\T1/p tm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 24721--24727 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "http://bioconductor.statistik.tu-dortmund.de"\T 1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 24734--24737 []\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 [382] Underfull \hbox (badness 2689) in paragraph at lines 24758--24760 []\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 24790--24795 []\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 24796--24807 \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 24808--24811 []\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 Underfull \hbox (badness 4084) in paragraph at lines 24818--24830 \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 24818--24830 \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 24818--24830 \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 24832--24839 []\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 24832--24839 \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 24832--24839 \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 24832--24839 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [383] [384] [385] [386] [387] Underfull \hbox (badness 10000) in paragraph at lines 25153--25157 []\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 25153--25157 \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)] [388] [389] [390] [391] [392] Underfull \hbox (badness 1735) in paragraph at lines 25471--25475 []\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 [393] [394] [395] [396] [397] [398] [399] [400] [401] [402] Underfull \hbox (badness 2726) in paragraph at lines 26030--26033 []\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 [403] [404] [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] [415] Underfull \hbox (badness 1052) in paragraph at lines 26849--26854 []\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 [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] Underfull \hbox (badness 1533) in paragraph at lines 27577--27580 []\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 [427] [428] Underfull \hbox (badness 1163) in paragraph at lines 27739--27749 []\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 [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] Underfull \hbox (badness 10000) in paragraph at lines 29241--29245 []\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 29241--29245 \T1/zi4/m/n/10 "(?[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 29263--29265 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [453] [454] [455] [456] [457] [458] [459] [460] [461] Underfull \hbox (badness 1655) in paragraph at lines 29808--29810 []\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 [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] Underfull \hbox (badness 10000) in paragraph at lines 30476--30480 []\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., [473] [474] [475] Underfull \hbox (badness 2302) in paragraph at lines 30716--30723 []\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 30716--30723 \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 30716--30723 \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 30716--30723 \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 [476] [477] [478] Underfull \hbox (badness 2261) in paragraph at lines 30870--30875 []\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 30897--30903 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [479] Underfull \hbox (badness 10000) in paragraph at lines 30973--30978 []\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 [480] [481] [482] [483] [484] [485] [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] Underfull \hbox (badness 1072) in paragraph at lines 33757--33761 []\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 33762--33766 []\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 ', [523] Underfull \hbox (badness 10000) in paragraph at lines 33790--33796 []\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 33790--33796 \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 33790--33796 \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 33803--33810 \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 33803--33810 \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 33803--33810 \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 [524] [525] [526] [527] [528] Underfull \hbox (badness 10000) in paragraph at lines 34094--34100 []\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 34094--34100 \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 [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] Underfull \hbox (badness 3333) in paragraph at lines 35877--35882 []\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 [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] Underfull \hbox (badness 1472) in paragraph at lines 36497--36500 []\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 [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] Underfull \hbox (badness 2671) in paragraph at lines 37159--37162 []\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 [578] [579] [580] [581] [582] [583] Underfull \hbox (badness 10000) in paragraph at lines 37563--37566 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$http : / / developer . r-[]project . org / [584] [585] Underfull \hbox (badness 10000) in paragraph at lines 37684--37688 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 http : / / developer . [586] Underfull \hbox (badness 10000) in paragraph at lines 37746--37750 [][][]\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 http : / / developer . [587] [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] Underfull \hbox (badness 1990) in paragraph at lines 39041--39049 []\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 39041--39049 \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 [606] [607] [608] [609] [610] Underfull \hbox (badness 1515) in paragraph at lines 39313--39318 []\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 [611] [612] [613] Underfull \hbox (badness 1917) in paragraph at lines 39543--39550 []\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 [614] [615] [616] [617] [618] [619] [620] [621] [622] Underfull \hbox (badness 3668) in paragraph at lines 40128--40130 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [623] [624] Underfull \hbox (badness 2401) in paragraph at lines 40233--40237 []\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 [625] [626] [627] Underfull \hbox (badness 2111) in paragraph at lines 40402--40407 \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. Underfull \hbox (badness 6542) in paragraph at lines 40418--40423 []\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 [628] [629] [630] [631] [632] [633] [634] Underfull \hbox (badness 10000) in paragraph at lines 40863--40868 []\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 40863--40868 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to [635] [636] Underfull \hbox (badness 5417) in paragraph at lines 40955--40959 []\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 [637] Underfull \hbox (badness 10000) in paragraph at lines 41016--41020 []\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 [638]) (./compiler-pkg.tex Chapter 2. [639] [640] [641] [642]) (./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 [643] [644] [645] [646] [647] [648] [649] [650] [651] [652] [653] [654] [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] Underfull \vbox (badness 1515) has occurred while \output is active [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] 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 / [710] Underfull \vbox (badness 10000) has occurred while \output is active [711] [712] [713] [714] Underfull \vbox (badness 10000) has occurred while \output is active [715] Underfull \vbox (badness 10000) has occurred while \output is active [716] [717] [718] [719] [720] [721] [722] [723]) (./grDevices-pkg.tex [724] Chapter 4. [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] Underfull \hbox (badness 5175) in paragraph at lines 1066--1068 []\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 [742] [743] [744] [745] Underfull \hbox (badness 1852) in paragraph at lines 1263--1266 []\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 [746] [747] [748] Underfull \hbox (badness 1490) in paragraph at lines 1469--1474 \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 [749] Underfull \hbox (badness 2698) in paragraph at lines 1523--1526 []\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 [750] Underfull \hbox (badness 10000) in paragraph at lines 1592--1596 []\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 [751] [752] [753] [754] Underfull \hbox (badness 1325) in paragraph at lines 1875--1885 \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 , [755] [756] Underfull \hbox (badness 10000) in paragraph at lines 1980--1982 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [757] [758] [759] Underfull \hbox (badness 6758) in paragraph at lines 2141--2144 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [760] [761] [762] [763] [764] [765] [766] [767] [768] Underfull \hbox (badness 10000) in paragraph at lines 2707--2708 [769] [770] [771] [772] [773] [774] [775] Underfull \hbox (badness 1152) in paragraph at lines 3145--3147 []\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 [776] [777] [778] [779] [780] Underfull \hbox (badness 2856) in paragraph at lines 3465--3468 []\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 3479--3481 []\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 [781] [782] Underfull \hbox (badness 1173) in paragraph at lines 3595--3605 []\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 [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] Underfull \hbox (badness 1067) in paragraph at lines 4302--4309 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [794] [795] Underfull \hbox (badness 3364) in paragraph at lines 4463--4465 []\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 / [796] Underfull \hbox (badness 1789) in paragraph at lines 4540--4542 []\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 [797] Underfull \hbox (badness 1377) in paragraph at lines 4590--4595 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [798] Underfull \hbox (badness 2671) in paragraph at lines 4617--4625 \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 4666--4673 \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 4674--4683 \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 4674--4683 \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 4684--4686 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [799] [800] Underfull \hbox (badness 1057) in paragraph at lines 4795--4800 []\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 [801] Underfull \hbox (badness 7344) in paragraph at lines 4855--4857 []\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 [802] [803] Underfull \hbox (badness 2035) in paragraph at lines 4979--4988 []\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 4979--4988 \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 4979--4988 \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 , [804] Underfull \hbox (badness 10000) in paragraph at lines 5048--5055 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5048--5055 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [805] [806] [807] Underfull \hbox (badness 1546) in paragraph at lines 5186--5194 []\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 , [808] Underfull \hbox (badness 1648) in paragraph at lines 5263--5267 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [809] [810] [811] [812] [813] [814] [815] Underfull \hbox (badness 10000) in paragraph at lines 5686--5689 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [816] Underfull \vbox (badness 3803) has occurred while \output is active [817] [818] [819] [820] [821] Underfull \hbox (badness 1189) in paragraph at lines 6083--6085 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [822] [823] Underfull \hbox (badness 10000) in paragraph at lines 6181--6183 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [824] [825] [826] [827] Underfull \hbox (badness 3780) in paragraph at lines 6472--6478 []\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 , [828] [829] [830] Underfull \hbox (badness 2680) in paragraph at lines 6668--6670 []\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 [831] [832] [833]) (./graphics-pkg.tex [834] Chapter 5. [835] [836] [837] [838] [839] [840] [841] [842] [843] [844] [845] 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 [846] [847] [848] [849] Underfull \vbox (badness 3803) has occurred while \output is active [850] [851] [852] [853] [854] 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 , [855] [856] [857] [858] [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] [869] [870] [871] Underfull \hbox (badness 1009) in paragraph at lines 2277--2284 \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 [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] Underfull \vbox (badness 10000) has occurred while \output is active [894] Underfull \vbox (badness 10000) has occurred while \output is active [895] [896] [897] [898] Underfull \hbox (badness 1867) in paragraph at lines 3901--3905 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [899] [900] [901] [902] [903] [904] [905] Underfull \hbox (badness 1924) in paragraph at lines 4348--4353 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain [906] Underfull \hbox (badness 2529) in paragraph at lines 4379--4382 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used: see [907] [908] [909] [910] [911] Underfull \hbox (badness 10000) in paragraph at lines 4729--4735 []\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 4729--4735 \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 [912] Underfull \hbox (badness 10000) in paragraph at lines 4860--4863 [913] [914 ] Underfull \hbox (badness 10000) in paragraph at lines 4921--4923 [915 ] [916] Underfull \hbox (badness 10000) in paragraph at lines 5111--5113 []\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 [917] [918] [919] [920] [921] Underfull \vbox (badness 10000) has occurred while \output is active [922] [923] [924] [925] [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6581--6582 [][] [941 ] [942] Underfull \vbox (badness 10000) has occurred while \output is active [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] Underfull \hbox (badness 1048) in paragraph at lines 7290--7295 \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 [953] Underfull \hbox (badness 1038) in paragraph at lines 7406--7409 []\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 [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] [971] [972] [973] [974] Underfull \hbox (badness 6691) in paragraph at lines 8625--8628 []\T1/ptm/m/n/10 The main ti-tle (on top) us-ing font and size (char-ac-ter ex- pan-sion) Underfull \hbox (badness 2799) in paragraph at lines 8628--8630 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font and size \T1/zi4/m/n/10 par ("font.sub") \T1/ptm/m/n/10 and color [975] [976]pdfTeX warning (ext4): destination with the same identifier (name{Rf n.units}) has been already used, duplicate ignored \relax l.8710 \HeaderA{units}{Graphical Units}{units} [977] [978] [979] [980]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [981] [982] [983] [984] [985] [986] 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 [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] 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 , [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [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] Underfull \vbox (badness 3803) has occurred while \output is active [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] 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 [1054] [1055] [1056] [1057] 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 [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] Underfull \hbox (badness 10000) in paragraph at lines 5854--5860 \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., [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] Underfull \hbox (badness 7649) in paragraph at lines 6324--6327 []\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 [1087] [1088] [1089] [1090]) (./methods-pkg.tex Chapter 7. [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] 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 [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] 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 [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] 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 [1128] [1129] 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 [1130] 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 [1131] [1132] [1133] [1134] [1135] [1136] [1137] 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 [1138] [1139] [1140] [1141] [1142] 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 [1143] [1144] [1145] [1146] [1147] [1148] Underfull \vbox (badness 10000) has occurred while \output is active [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156] 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 [1157] [1158] [1159] [1160] [1161] [1162] Underfull \vbox (badness 2452) has occurred while \output is active [1163] [1164] Underfull \vbox (badness 10000) has occurred while \output is active [1165] [1166] 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 [1167] [1168] [1169] [1170] [1171] 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 [1172] [1173] [1174] [1175] 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 [1176] [1177] [1178] [1179] [1180] Underfull \hbox (badness 1675) in paragraph at lines 6343--6349 \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 [1181] [1182] [1183] [1184] Underfull \vbox (badness 10000) has occurred while \output is active [1185] [1186]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4} ) has been already used, duplicate ignored \relax l.6820 \aliasA{S4}{S3Part}{S4} [1187] [1188] [1189] [1190]pdfTeX warning (ext4) : destination with the same identifier (name{Rfn.Complex}) has been already use d, duplicate ignored \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 \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 \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 \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 \relax l.7102 \aliasA{Summary}{S4groupGeneric}{Summary} [1191] 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 [1192] [1193] [1194] 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 [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] Underfull \hbox (badness 1852) in paragraph at lines 9759--9763 []\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., [1229] [1230] [1231] [1232]) (./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 [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] Underfull \hbox (badness 3386) in paragraph at lines 1246--1249 []\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 [1253] [1254]) (./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 \T1/ptm/ m/n/10 and William N. Ven-ables [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269]) (./stats-pkg.tex [1270] Chapter 10. [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] Underfull \hbox (badness 1412) in paragraph at lines 844--846 []\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 [1284] [1285] [1286] [1287] [1288] [1289] [1290] [1291] Underfull \hbox (badness 2503) in paragraph at lines 1325--1328 []\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 , [1292] [1293] [1294] Underfull \hbox (badness 10000) in paragraph at lines 1504--1508 []\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 [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] Underfull \hbox (badness 3965) in paragraph at lines 2164--2166 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1306] [1307] [1308] [1309] [1310] Underfull \hbox (badness 3965) in paragraph at lines 2506--2508 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] Underfull \hbox (badness 2503) in paragraph at lines 3323--3326 []\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 , [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 3989) in paragraph at lines 4548--4555 []\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 = [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] Underfull \hbox (badness 2556) in paragraph at lines 5149--5152 []\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 5166--5168 []\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 [1354] [1355] [1356] [1357] Underfull \hbox (badness 1142) in paragraph at lines 5407--5419 \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. [1358] [1359] Underfull \hbox (badness 2503) in paragraph at lines 5546--5550 []\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 , [1360] Underfull \hbox (badness 1168) in paragraph at lines 5607--5612 []\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 [1361] [1362] [1363] [1364] [1365] [1366] [1367] Underfull \hbox (badness 8132) in paragraph at lines 6049--6054 \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, [1368] [1369] [1370] [1371] [1372] Underfull \hbox (badness 7081) in paragraph at lines 6324--6327 []\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 6328--6330 []\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 [1373] [1374] [1375] [1376] [1377] Underfull \vbox (badness 3803) has occurred while \output is active [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] Underfull \hbox (badness 10000) in paragraph at lines 7136--7139 []\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 [1386] [1387] Underfull \hbox (badness 10000) in paragraph at lines 7273--7276 []\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 / [1388] [1389] [1390] [1391] Underfull \vbox (badness 3803) has occurred while \output is active [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] Underfull \hbox (badness 2626) in paragraph at lines 8771--8774 []\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 [1413] Underfull \hbox (badness 2503) in paragraph at lines 8871--8875 []\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 , [1414] [1415] [1416] [1417] [1418] Overfull \hbox (6.88992pt too wide) in paragraph at lines 9205--9207 []\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 . [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] Underfull \hbox (badness 4518) in paragraph at lines 10132--10137 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1434] [1435] [1436] [1437] Underfull \hbox (badness 2142) in paragraph at lines 10474--10477 []\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 ^^@ [1438] Underfull \hbox (badness 1253) in paragraph at lines 10493--10496 []\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, [1439] Underfull \hbox (badness 1708) in paragraph at lines 10555--10559 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1440] [1441] [1442] [1443] [1444] [1445] Underfull \hbox (badness 1694) in paragraph at lines 10951--10954 []\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 10970--10979 \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- [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453]pdfTeX warning (ext4): d estination with the same identifier (name{Rfn.hat}) has been already used, dupl icate ignored \relax l.11417 \aliasA{hat}{influence.measures}{hat} [1454] [1455] Underfull \hbox (badness 1484) in paragraph at lines 11540--11542 []\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 [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 4441) in paragraph at lines 12098--12100 []\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 12105--12107 []\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 [1465] [1466] [1467] [1468] [1469] [1470] Underfull \hbox (badness 2894) in paragraph at lines 12439--12443 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] Underfull \hbox (badness 4518) in paragraph at lines 13134--13139 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1482] [1483] [1484] [1485] [1486] [1487] [1488] [1489] [1490] [1491] Underfull \hbox (badness 4518) in paragraph at lines 13781--13786 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1492] [1493] Underfull \hbox (badness 10000) in paragraph at lines 13919--13923 []\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 13926--13928 []\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 [1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] [1509] [1510] [1511] Underfull \hbox (badness 2503) in paragraph at lines 14990--14994 []\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 , [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] Underfull \hbox (badness 1418) in paragraph at lines 15499--15505 []\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 [1520] [1521] [1522] [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] Underfull \hbox (badness 2359) in paragraph at lines 17123--17125 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1546] [1547] Underfull \vbox (badness 10000) has occurred while \output is active [1548] Underfull \vbox (badness 10000) has occurred while \output is active [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] Underfull \hbox (badness 1377) in paragraph at lines 18034--18039 []\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 18039--18042 []\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 18052--18056 \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 18060--18064 []\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 [1562] [1563] [1564] Underfull \vbox (badness 10000) has occurred while \output is active [1565] [1566] [1567] [1568] [1569] [1570] [1571] Underfull \hbox (badness 1337) in paragraph at lines 18676--18679 []\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 [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] Underfull \hbox (badness 5563) in paragraph at lines 19406--19408 []\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 19409--19412 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1585] [1586] [1587] [1588] [1589] [1590] Underfull \hbox (badness 2503) in paragraph at lines 19776--19779 []\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 , [1591] Underfull \hbox (badness 10000) in paragraph at lines 19803--19805 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602] [1603] [1604] [1605] [1606] [1607] Underfull \hbox (badness 10000) in paragraph at lines 20803--20809 []\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 , [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] Underfull \hbox (badness 1337) in paragraph at lines 22138--22144 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1631] [1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] Underfull \hbox (badness 10000) in paragraph at lines 22931--22934 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1643] [1644] [1645] [1646] [1647] [1648] [1649] [1650] [1651] Underfull \hbox (badness 10000) in paragraph at lines 23508--23511 []\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 [1652] Underfull \hbox (badness 3690) in paragraph at lines 23559--23563 [][][]\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 [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] Underfull \hbox (badness 3439) in paragraph at lines 24029--24035 [][]\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 , [1661] [1662] [1663] [1664] [1665] [1666] [1667] [1668] [1669] Underfull \hbox (badness 10000) in paragraph at lines 24577--24582 []\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 [1670] [1671] [1672] [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] Underfull \vbox (badness 3803) has occurred while \output is active [1685] [1686] Underfull \hbox (badness 3514) in paragraph at lines 25593--25598 []\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 [1687] Underfull \hbox (badness 3514) in paragraph at lines 25655--25660 []\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 [1688] Underfull \hbox (badness 3514) in paragraph at lines 25712--25717 []\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 [1689] Underfull \hbox (badness 3514) in paragraph at lines 25773--25779 []\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 [1690] [1691] [1692] [1693] Underfull \hbox (badness 3514) in paragraph at lines 25986--25991 []\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 Underfull \hbox (badness 3514) in paragraph at lines 26042--26047 []\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 [1694] Underfull \hbox (badness 3514) in paragraph at lines 26099--26104 []\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 [1695] Underfull \hbox (badness 3514) in paragraph at lines 26154--26159 []\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 [1696] [1697] Underfull \hbox (badness 6691) in paragraph at lines 26223--26228 []\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 [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] Underfull \hbox (badness 10000) in paragraph at lines 26747--26750 []\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 26747--26750 \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, [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] Underfull \hbox (badness 5431) in paragraph at lines 27353--27355 []\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 [1716] [1717] [1718] [1719] Underfull \hbox (badness 5431) in paragraph at lines 27563--27566 []\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 [1720] [1721] [1722] [1723] [1724] Underfull \hbox (badness 1337) in paragraph at lines 27875--27879 []\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 [1725] [1726] Underfull \hbox (badness 10000) in paragraph at lines 27992--27995 []\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 [1727] [1728] [1729] Underfull \hbox (badness 1616) in paragraph at lines 28175--28178 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] Underfull \hbox (badness 10000) in paragraph at lines 29302--29306 []\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 [1749] [1750] [1751] Underfull \vbox (badness 10000) has occurred while \output is active [1752] [1753] [1754] Underfull \hbox (badness 1337) in paragraph at lines 29666--29670 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] Underfull \hbox (badness 1337) in paragraph at lines 30150--30154 []\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 [1763] Underfull \hbox (badness 5161) in paragraph at lines 30243--30245 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1764] [1765] [1766] [1767] [1768] [1769] Underfull \hbox (badness 10000) in paragraph at lines 30607--30612 []\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 [1770] [1771] [1772]) (./stats4-pkg.tex Chapter 11. [1773] [1774] [1775] [1776] [1777] [1778]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1779] [1780] [1781] [1782]) (./tcltk-pkg.tex Chapter 12. [1783] [1784] [1785] [1786] [1787] [1788] [1789] Underfull \vbox (badness 10000) has occurred while \output is active [1790] Underfull \vbox (badness 10000) has occurred while \output is active [1791] 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 [1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] 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 [1803]) (./tools-pkg.tex [1804] Chapter 13. [1805] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1806] 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 [1807] [1808] 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 [1809] [1810] 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 [1811] [1812] [1813] [1814] [1815] [1816] [1817] [1818] [1819] [1820] [1821] 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 [1822] 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- [1823] 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 , [1824] [1825] [1826] 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 [1827] [1828] [1829] Underfull \hbox (badness 7981) in paragraph at lines 1518--1522 []\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 1524--1526 []\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 [1830] [1831] [1832] [1833]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1721 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1834] [1835] Underfull \hbox (badness 5726) in paragraph at lines 1847--1852 []\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 1847--1852 \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 [1836] [1837] [1838] [1839] [1840] [1841] [1842] [1843] Underfull \hbox (badness 7981) in paragraph at lines 2323--2329 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1844] [1845] [1846] [1847] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2607. [1848] [1849] [1850] [1851] Underfull \hbox (badness 1424) in paragraph at lines 2844--2846 []\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 [1852] [1853] [1854] [1855] [1856] [1857] [1858] [1859] [1860] [1861] [1862] Underfull \hbox (badness 10000) in paragraph at lines 3539--3541 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1863] [1864] [1865] [1866] [1867] [1868] Underfull \hbox (badness 1838) in paragraph at lines 3919--3925 []\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 3919--3925 \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 [1869] [1870] Underfull \hbox (badness 5726) in paragraph at lines 3999--4004 []\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 3999--4004 \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 [1871] [1872] Underfull \hbox (badness 1688) in paragraph at lines 4142--4154 []\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 [1873] [1874] [1875] [1876]) (./utils-pkg.tex Chapter 14. [1877] 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 ', [1878] [1879] 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 [1880] [1881] [1882] [1883] [1884] [1885] 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 [1886] Underfull \hbox (badness 5847) in paragraph at lines 656--662 []\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 656--662 \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 [1887] Underfull \hbox (badness 3861) in paragraph at lines 724--729 []\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 , [1888] [1889] [1890] [1891] [1892] Underfull \vbox (badness 10000) has occurred while \output is active [1893] [1894] [1895] [1896] [1897] Underfull \hbox (badness 1371) in paragraph at lines 1320--1322 []\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 [1898] [1899] [1900] [1901] [1902] [1903] [1904] Underfull \hbox (badness 2057) in paragraph at lines 1812--1814 []\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 [1905] [1906] Underfull \hbox (badness 10000) in paragraph at lines 1913--1915 []\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 [1907] Underfull \hbox (badness 5189) in paragraph at lines 2003--2005 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1908] [1909] [1910] [1911] Underfull \hbox (badness 1661) in paragraph at lines 2221--2228 []\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 2238--2241 []\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 [1912] [1913] [1914] [1915] [1916] [1917] [1918] [1919] [1920] [1921] [1922] [1923] [1924] [1925] [1926] Underfull \hbox (badness 1412) in paragraph at lines 3235--3239 []\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 [1927] Underfull \hbox (badness 1430) in paragraph at lines 3259--3267 []\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 3302--3308 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1928] [1929] [1930] [1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940] [1941]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4123 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4123 ...mat Unordered and Ordered Lists}{format} [1942] [1943] [1944] [1945] [1946] [1947] [1948] [1949] [1950] [1951] [1952] [1953] [1954] [1955] [1956] Underfull \hbox (badness 1371) in paragraph at lines 5073--5075 []\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 [1957] Underfull \hbox (badness 1502) in paragraph at lines 5162--5167 []\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 5162--5167 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1958] [1959] [1960] Underfull \hbox (badness 10000) in paragraph at lines 5335--5344 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [1961] Underfull \hbox (badness 2150) in paragraph at lines 5398--5401 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [1962] [1963] Underfull \hbox (badness 3118) in paragraph at lines 5535--5537 []\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 [1964] Underfull \hbox (badness 2409) in paragraph at lines 5568--5572 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [1965] Underfull \hbox (badness 1325) in paragraph at lines 5676--5680 []\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 [1966] Underfull \hbox (badness 10000) in paragraph at lines 5759--5762 []\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 5759--5762 \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., [1967] Underfull \hbox (badness 3219) in paragraph at lines 5832--5839 []\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 5832--5839 \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 5832--5839 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [1968] Underfull \hbox (badness 10000) in paragraph at lines 5912--5917 [][][]\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 , [1969] [1970] [1971] [1972] [1973] [1974] [1975] [1976] [1977] [1978] [1979] [1980] [1981] [1982] [1983] [1984] [1985] [1986] [1987] [1988] Underfull \hbox (badness 10000) in paragraph at lines 7124--7126 []\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 7129--7134 []\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, [1989] [1990] [1991] [1992] [1993] [1994] [1995] [1996] [1997] Underfull \hbox (badness 1789) in paragraph at lines 7679--7681 []\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 [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] Underfull \hbox (badness 1097) in paragraph at lines 8504--8507 []\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 [2010] [2011] Underfull \hbox (badness 3000) in paragraph at lines 8640--8645 [][][]\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 ; [2012] [2013] [2014] [2015] [2016] [2017] [2018] [2019] [2020] Underfull \hbox (badness 2134) in paragraph at lines 9222--9227 [][][]\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 ; [2021] [2022] [2023] [2024] [2025] [2026] [2027] Underfull \hbox (badness 2469) in paragraph at lines 9655--9659 []\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 9655--9659 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2028] [2029] [2030] [2031] [2032] [2033] Underfull \hbox (badness 10000) in paragraph at lines 9996--9998 []\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 [2034] [2035] Underfull \hbox (badness 2150) in paragraph at lines 10172--10174 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2036] [2037] [2038] Underfull \hbox (badness 10000) in paragraph at lines 10350--10354 []\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 [2039] Underfull \hbox (badness 10000) in paragraph at lines 10381--10387 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2040] Underfull \hbox (badness 2096) in paragraph at lines 10499--10502 []\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 10503--10506 []\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 [2041] Underfull \hbox (badness 1009) in paragraph at lines 10569--10580 []\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 [2042] [2043] [2044] [2045] [2046] Underfull \hbox (badness 3780) in paragraph at lines 10868--10872 []\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 10884--10887 []\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 [2047] [2048] [2049] [2050] [2051] [2052] Underfull \hbox (badness 5970) in paragraph at lines 11258--11261 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2053] [2054] [2055] Underfull \hbox (badness 10000) in paragraph at lines 11437--11439 []\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 [2056] [2057] [2058] [2059] [2060] [2061] Underfull \hbox (badness 10000) in paragraph at lines 11838--11841 [][][]$\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 11838--11841 \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 [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] [2070] Underfull \hbox (badness 10000) in paragraph at lines 12368--12370 []\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 12371--12373 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2071] Underfull \hbox (badness 10000) in paragraph at lines 12401--12406 []\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 12401--12406 [][]\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 12430--12433 [][][]\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 , [2072] [2073] [2074] [2075] Overfull \hbox (25.86961pt too wide) in paragraph at lines 12669--12672 [][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi -gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](, package = "") [2076] [2077] Underfull \hbox (badness 1454) in paragraph at lines 12747--12751 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, [2078] Underfull \hbox (badness 10000) in paragraph at lines 12817--12819 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion [2079] [2080] [2081]) [2082] (./fullrefman.ind [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] [2102] [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] Overfull \hbox (5.8567pt too wide) in paragraph at lines 11156--11158 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_depends Overfull \hbox (5.8567pt too wide) in paragraph at lines 11158--11160 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_results Overfull \hbox (5.8567pt too wide) in paragraph at lines 11160--11162 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_timings [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151]) (./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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name{Rfn.mosaic} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.levelplot} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.contourplot} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.assoc} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dpih} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.truehist} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.bkde2D} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.Surv} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.which.is.max} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.asNamespace} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getNamespace} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, replaced by a fixed one {/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/ texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dis t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}< /usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb> Output written on fullrefman.pdf (2182 pages, 5793327 bytes). 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 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 -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' 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 *** 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/bzip2' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/«PKGBUILDDIR»/src/extra/bzip2' make[4]: Entering directory '/«PKGBUILDDIR»/src/extra/pcre' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/«PKGBUILDDIR»/src/extra/pcre' 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/xz' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/«PKGBUILDDIR»/src/extra/xz' make[4]: Entering directory '/«PKGBUILDDIR»/src/extra/zlib' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/«PKGBUILDDIR»/src/extra/zlib' 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 -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 -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -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 -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: 67.0% -- 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: 68.3% -- 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: 66.9% -- 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: 68.0% -- 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: 70.1% -- 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 2748 -rw-rw-r-- 1 root root 1934370 Dec 4 12:07 libRmath.a -rwxrwxr-x 1 root root 871400 Dec 4 12:07 libRmath.so drwxr-xr-x 2 root root 4096 Dec 4 12:07 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 (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 amd64: 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: -is is deprecated; it is without effect dpkg-gencontrol: warning: -ip is deprecated; it is without effect 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: -is is deprecated; it is without effect dpkg-gencontrol: warning: -ip is deprecated; it is without effect 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 amd64: 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 'libtcl8.6.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 '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' 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 amd64: 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_3.2.2.20151203-1_amd64.ddeb dpkg-deb: building package 'r-base-core-dbgsym' in '../r-base-core-dbgsym_3.2.2.20151203-1_amd64.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile r-base-core-dbgsym_3.2.2.20151203-1_amd64.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_3.2.2.20151203-1_amd64.ddeb dpkg-deb: building package 'r-mathlib-dbgsym' in '../r-mathlib-dbgsym_3.2.2.20151203-1_amd64.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile r-mathlib-dbgsym_3.2.2.20151203-1_amd64.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 123 pkgstriptranslations: processing r-base-core (in debian/r-base-core); 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 " 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 Invalid PNG signature on usr/lib/R/library/graphics/help/figures/pch.png [at void throw_png_error():pngex.h:37] WARNING: advpng 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 Invalid PNG signature on usr/lib/R/library/graphics/help/figures/mai.png [at void throw_png_error():pngex.h:37] WARNING: advpng 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 Invalid PNG signature on usr/lib/R/library/graphics/help/figures/oma.png [at void throw_png_error():pngex.h:37] WARNING: advpng failed on usr/lib/R/library/graphics/help/figures/oma.png, ignoring oooo...ooo pkgstripfiles: PNG optimization (7/10) for package r-base-core took 6 s dpkg-deb: building package 'r-base-core' in '../r-base-core_3.2.2.20151203-1_amd64.deb'. INFO: pkgstriptranslations version 123 pkgstriptranslations: processing r-mathlib (in debian/r-mathlib); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " 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_3.2.2.20151203-1_amd64.deb'. INFO: pkgstriptranslations version 123 pkgstriptranslations: processing r-base-core-dbg (in debian/r-base-core-dbg); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " 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 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_3.2.2.20151203-1_amd64.deb'. *** binary-indep *** dh_testdir -i dh_testroot -i dh_link -i dh_installdocs -i dh_installdocs -v -pr-doc-html install -p -m0644 debian/copyright debian/r-doc-html/usr/share/doc/r-doc-html/copyright install -p -m0644 debian/r-doc-html.doc-base.faq debian/r-doc-html/usr/share/doc-base/r-faq install -p -m0644 debian/r-doc-html.doc-base.ints debian/r-doc-html/usr/share/doc-base/r-ints install -p -m0644 debian/r-doc-html.doc-base.data debian/r-doc-html/usr/share/doc-base/r-data install -p -m0644 debian/r-doc-html.doc-base.lang debian/r-doc-html/usr/share/doc-base/r-language install -p -m0644 debian/r-doc-html.doc-base.exts debian/r-doc-html/usr/share/doc-base/r-extensions install -p -m0644 debian/r-doc-html.doc-base.admin debian/r-doc-html/usr/share/doc-base/r-admin install -p -m0644 debian/r-doc-html.doc-base.intro debian/r-doc-html/usr/share/doc-base/r-intro dh_installchangelogs -i dh_installdirs -pr-base-dev usr/share/R/debian install -p -m 0755 debian/r-cran.mk \ /«PKGBUILDDIR»/debian/r-base-dev/usr/share/R/debian dh_compress -i dh_fixperms -i dh_installdeb -i dh_gencontrol -i 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 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 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 amd64: r-base-core r-mathlib r-base-core-dbg dh_gencontrol debug symbol wrapper: packages to act on: dh_gencontrol debug symbol wrapper: ignored packages: dh_md5sums -i dh_builddeb -i INFO: pkgstriptranslations version 123 pkgstriptranslations: processing r-base (in debian/r-base); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/r-base/DEBIAN/control, package r-base, directory debian/r-base Searching for duplicated docs in dependency r-base-core... symlinking changelog.Debian.gz in r-base to file in r-base-core Searching for duplicated docs in dependency r-recommended... pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-base ... pkgstripfiles: No PNG files. dpkg-deb: building package 'r-base' in '../r-base_3.2.2.20151203-1_all.deb'. INFO: pkgstriptranslations version 123 pkgstriptranslations: processing r-base-dev (in debian/r-base-dev); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/r-base-dev/DEBIAN/control, package r-base-dev, directory debian/r-base-dev pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-base-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'r-base-dev' in '../r-base-dev_3.2.2.20151203-1_all.deb'. INFO: pkgstriptranslations version 123 pkgstriptranslations: processing r-base-html (in debian/r-base-html); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/r-base-html/DEBIAN/control, package r-base-html, directory debian/r-base-html Searching for duplicated docs in dependency r-base-core... symlinking changelog.Debian.gz in r-base-html to file in r-base-core pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-base-html ... pkgstripfiles: No PNG files. dpkg-deb: building package 'r-base-html' in '../r-base-html_3.2.2.20151203-1_all.deb'. INFO: pkgstriptranslations version 123 pkgstriptranslations: processing r-doc-pdf (in debian/r-doc-pdf); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/r-doc-pdf/DEBIAN/control, package r-doc-pdf, directory debian/r-doc-pdf pkgstripfiles: Truncating usr/share/doc/r-doc-pdf/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-doc-pdf ... pkgstripfiles: No PNG files. dpkg-deb: building package 'r-doc-pdf' in '../r-doc-pdf_3.2.2.20151203-1_all.deb'. INFO: pkgstriptranslations version 123 pkgstriptranslations: processing r-doc-html (in debian/r-doc-html); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/r-doc-html/DEBIAN/control, package r-doc-html, directory debian/r-doc-html pkgstripfiles: Truncating usr/share/doc/r-doc-html/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-doc-html ... pkgstripfiles: No PNG files. dpkg-deb: building package 'r-doc-html' in '../r-doc-html_3.2.2.20151203-1_all.deb'. INFO: pkgstriptranslations version 123 pkgstriptranslations: processing r-doc-info (in debian/r-doc-info); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/r-doc-info/DEBIAN/control, package r-doc-info, directory debian/r-doc-info pkgstripfiles: Truncating usr/share/doc/r-doc-info/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-doc-info ... pkgstripfiles: No PNG files. dpkg-deb: building package 'r-doc-info' in '../r-doc-info_3.2.2.20151203-1_all.deb'. INFO: pkgstriptranslations version 123 pkgstriptranslations: processing r-recommended (in debian/r-recommended); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/r-recommended/DEBIAN/control, package r-recommended, directory debian/r-recommended pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-recommended ... pkgstripfiles: No PNG files. dpkg-deb: building package 'r-recommended' in '../r-recommended_3.2.2.20151203-1_all.deb'. dpkg-genchanges -b -mLaunchpad Build Daemon >../r-base_3.2.2.20151203-1_amd64.changes dpkg-genchanges: binary-only upload (no source code included) dpkg-source --after-build r-base-3.2.2.20151203 dpkg-buildpackage: binary-only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20151204-1208 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build Chroot │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ r-base_3.2.2.20151203-1_amd64.changes: ────────────────────────────────────── Format: 1.8 Date: Thu, 03 Dec 2015 22:08:11 -0600 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: amd64 all Version: 3.2.2.20151203-1 Distribution: xenial-proposed Urgency: low Maintainer: Launchpad Build Daemon Changed-By: Dirk Eddelbuettel 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 (3.2.2.20151203-1) unstable; urgency=low . * Initial rc build (r69731) of R 3.2.3 expected for December 10 . * debian/updated_x11_logo.patch: Applied again to src/modules/X11/ files devX11.c and rlogo_icon.h to provide the new R logo Checksums-Sha1: c333ea02302619017c20ee42511cca16aae02591 3023922 r-base-core-dbg_3.2.2.20151203-1_amd64.deb a391b6f72df19fb20df514ee1f46e249ab2bbd46 1508 r-base-core-dbgsym_3.2.2.20151203-1_amd64.ddeb 1fee9c8b418e6d80c7b10442b7a8c69825afe2da 20459028 r-base-core_3.2.2.20151203-1_amd64.deb f95cbdda4a2f5b7b4eb9c4d3237c653944a40537 4358 r-base-dev_3.2.2.20151203-1_all.deb 5190caef419d9359df217a9af1a18d35150a7a40 53902 r-base-html_3.2.2.20151203-1_all.deb 89cb9d8aa9f9c142d374ccdeb19dbdb7a943f341 9208 r-base_3.2.2.20151203-1_all.deb 7569e26a5dfaad070c24d88ba6310af5592e3c69 511040 r-doc-html_3.2.2.20151203-1_all.deb 69b49d52a9c119958404cdc0a4e0b0e08191b5a9 569994 r-doc-info_3.2.2.20151203-1_all.deb d6e81418077a1b76cbf54d5eb4e5f0772449cf0d 8950468 r-doc-pdf_3.2.2.20151203-1_all.deb 71b0340c206eac59e156a640e348581448c69629 1474 r-mathlib-dbgsym_3.2.2.20151203-1_amd64.ddeb fd69f0a6913dd2afe1c073ab65906d331474c89f 1331264 r-mathlib_3.2.2.20151203-1_amd64.deb 5ae7d22aaabd942cde3e31a9b8c54523e82e6b15 2782 r-recommended_3.2.2.20151203-1_all.deb Checksums-Sha256: cfbf20d72e2629615ada501eca015617f643bac15a29bd5b99bfd853ee553c18 3023922 r-base-core-dbg_3.2.2.20151203-1_amd64.deb 4cf05c9e1660596dda718807ce3a265bc50361686d6bc38fa63595c61a2abeed 1508 r-base-core-dbgsym_3.2.2.20151203-1_amd64.ddeb 711f41c5fb5e85db1f5530ace22f87ac2c96c9b2100d6af78dc2f5667d2b4ef7 20459028 r-base-core_3.2.2.20151203-1_amd64.deb c2d000eecc900a5e4c85ef3f91b47e4a67c1bf7b35fad8e8666ac6c40b010b22 4358 r-base-dev_3.2.2.20151203-1_all.deb 7dd4fc5799618aeecbb84886835ae2935fe0ffc4a50af2a22487dbcee683db1c 53902 r-base-html_3.2.2.20151203-1_all.deb 4a2237f1c3bef7b111c1099dee5e684a6bd0fd52c88de1989b5b8ed2e0a39810 9208 r-base_3.2.2.20151203-1_all.deb 5d5e3f6e130f5a67bebc3c6f6f45f58205899024a5da459e619b230a81fdc222 511040 r-doc-html_3.2.2.20151203-1_all.deb 7a27a079808de296038c006b3a7a443513011512ec24f1fe2f6d4b99a4c89dc6 569994 r-doc-info_3.2.2.20151203-1_all.deb 8560783e1980ee9cfff49b15556772fc3ef8b9ccf119e45b465479c9fd8f875c 8950468 r-doc-pdf_3.2.2.20151203-1_all.deb 2d253b7731cf1e22a42510045d281ec689b81dbd7e1cf27cb3e3e4c4a72827a1 1474 r-mathlib-dbgsym_3.2.2.20151203-1_amd64.ddeb b36c6e484e86f7edc4d18e06de5f4021fa15499fcc66f7ed0b7b53333e0db8c3 1331264 r-mathlib_3.2.2.20151203-1_amd64.deb 6fcf55ac8277c21b522498463e03f92c21de2b4c67bc2eb146b59baff892f76d 2782 r-recommended_3.2.2.20151203-1_all.deb Files: e98a00bfa476f4be99b1306f564dda3b 3023922 debug extra r-base-core-dbg_3.2.2.20151203-1_amd64.deb 12ce9c853444e48d6e30238dcacb57f9 1508 gnu-r extra r-base-core-dbgsym_3.2.2.20151203-1_amd64.ddeb 68d128f77829fe9c3d457fdee39671f6 20459028 gnu-r optional r-base-core_3.2.2.20151203-1_amd64.deb 978d7af4863f97aff36532115e293db3 4358 gnu-r optional r-base-dev_3.2.2.20151203-1_all.deb 2d7d89ac83d179266b642260c46ad809 53902 doc extra r-base-html_3.2.2.20151203-1_all.deb 9fa85ff8170ecae3d8936cc51d0e4790 9208 gnu-r optional r-base_3.2.2.20151203-1_all.deb e9bfd83c9d7c021619af24fc6de9c4f5 511040 doc optional r-doc-html_3.2.2.20151203-1_all.deb 759d1ad5953d70cbd7bb1e37f3e65cfc 569994 doc optional r-doc-info_3.2.2.20151203-1_all.deb 6c7983ea773cca8ed3ef27205fa1d5e1 8950468 doc optional r-doc-pdf_3.2.2.20151203-1_all.deb cb851999317a7bf29d5cd69ea289fdc3 1474 gnu-r extra r-mathlib-dbgsym_3.2.2.20151203-1_amd64.ddeb fc603504d7270abc071c7c9bb1408b44 1331264 gnu-r optional r-mathlib_3.2.2.20151203-1_amd64.deb 185a81c28d37d120c963c62121db7e69 2782 gnu-r optional r-recommended_3.2.2.20151203-1_all.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ r-base-core-dbg_3.2.2.20151203-1_amd64.deb ────────────────────────────────────────── new debian package, version 2.0. size 3023922 bytes: control archive=1845 bytes. 1871 bytes, 39 lines control 1700 bytes, 21 lines md5sums Package: r-base-core-dbg Source: r-base Version: 3.2.2.20151203-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Dirk Eddelbuettel Installed-Size: 12846 Depends: r-base-core (= 3.2.2.20151203-1), r-base-dev (= 3.2.2.20151203-1) 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-'. . This package contains debugging symbol tables for the binaries and dynamic libraries in the r-base-core package. drwxr-xr-x root/root 0 2015-12-04 12:07 ./ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/lib/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/lib/debug/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/lib/debug/usr/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/lib/debug/usr/bin/ -rw-r--r-- root/root 19264 2015-12-04 12:07 ./usr/lib/debug/usr/bin/Rscript drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/lib/debug/usr/lib/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/lib/debug/usr/lib/R/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/lib/debug/usr/lib/R/bin/ -rw-r--r-- root/root 19264 2015-12-04 12:07 ./usr/lib/debug/usr/lib/R/bin/Rscript drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/lib/debug/usr/lib/R/bin/exec/ -rw-r--r-- root/root 8392 2015-12-04 12:07 ./usr/lib/debug/usr/lib/R/bin/exec/R drwxr-xr-x root/root 0 2015-12-04 12:07 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20761 2015-12-04 11:54 ./usr/share/doc/r-base-core-dbg/copyright drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/share/lintian/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/share/lintian/overrides/ r-base-core_3.2.2.20151203-1_amd64.deb ────────────────────────────────────── new debian package, version 2.0. size 20459028 bytes: control archive=27440 bytes. 93 bytes, 5 lines conffiles 2765 bytes, 45 lines control 72128 bytes, 915 lines md5sums 2396 bytes, 70 lines * postinst #!/bin/sh 160 bytes, 5 lines * postrm #!/bin/sh 667 bytes, 34 lines * preinst #!/bin/sh 689 bytes, 26 lines * prerm #!/bin/sh 30 bytes, 1 lines shlibs Package: r-base-core Source: r-base Version: 3.2.2.20151203-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Dirk Eddelbuettel Installed-Size: 33305 Depends: zip, unzip, libpaper-utils, xdg-utils, libblas3 | libblas.so.3, libbz2-1.0, libc6 (>= 2.16), libcairo2 (>= 1.6.0), libcurl3 (>= 7.28.0), libglib2.0-0 (>= 2.12.0), libgomp1 (>= 4.9), 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, libpng12-0 (>= 1.2.13-4), 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-'. . 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 2015-12-04 12:07 ./ drwxr-xr-x root/root 0 2015-12-04 12:07 ./etc/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./etc/R/ -rw-r--r-- root/root 6275 2015-12-04 12:07 ./etc/R/Makeconf -rw-r--r-- root/root 608 2015-12-04 12:07 ./etc/R/Renviron.site -rw-r--r-- root/root 792 2015-12-04 12:07 ./etc/R/Rprofile.site -rw-r--r-- root/root 628 2015-12-04 12:07 ./etc/R/ldpaths -rw-r--r-- root/root 1424 2015-12-04 12:07 ./etc/R/repositories drwxr-xr-x root/root 0 2015-12-04 12:07 ./etc/bash_completion.d/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./etc/ld.so.conf.d/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/bin/ -rwxr-xr-x root/root 8712 2015-12-04 12:07 ./usr/bin/R -rwxr-xr-x root/root 10488 2015-12-04 12:07 ./usr/bin/Rscript 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lrwxrwxrwx root/root 0 2015-12-04 12:07 ./usr/share/texmf/tex/latex/R -> ../../../R/share/texmf r-base-dev_3.2.2.20151203-1_all.deb ─────────────────────────────────── new debian package, version 2.0. size 4358 bytes: control archive=1593 bytes. 2245 bytes, 40 lines control 63 bytes, 1 lines md5sums 425 bytes, 26 lines * preinst #!/bin/sh Package: r-base-dev Source: r-base Version: 3.2.2.20151203-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Dirk Eddelbuettel Installed-Size: 15 Depends: r-base-core (>= 3.2.2.20151203-1), build-essential, gcc, g++, gfortran, libblas-dev | libatlas-base-dev, liblapack-dev | libatlas-base-dev, libncurses5-dev, libreadline-dev, libjpeg-dev, libpcre3-dev, libpng-dev, zlib1g-dev, libbz2-dev, liblzma-dev, cdbs Suggests: debhelper, texlive-base, texlive-latex-base, texlive-generic-recommended, texlive-fonts-recommended, texlive-fonts-extra, texlive-extra-utils, texlive-latex-recommended, texlive-latex-extra, texinfo Section: gnu-r Priority: optional Homepage: http://www.r-project.org/ Description: GNU R installation of auxiliary GNU R packages 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-'. . This package ensures that other Debian packages needed for installation of some auxiliary R packages are installed. drwxr-xr-x root/root 0 2015-12-04 12:08 ./ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/ drwxr-xr-x root/root 0 2015-12-04 12:08 ./usr/share/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/share/R/ drwxr-xr-x root/root 0 2015-12-04 12:08 ./usr/share/R/debian/ -rwxr-xr-x root/root 5826 2015-12-04 11:54 ./usr/share/R/debian/r-cran.mk drwxr-xr-x root/root 0 2015-12-04 12:08 ./usr/share/doc/ lrwxrwxrwx root/root 0 2015-12-04 12:08 ./usr/share/doc/r-base-dev -> r-base-core r-base-html_3.2.2.20151203-1_all.deb ──────────────────────────────────── new debian package, version 2.0. size 53902 bytes: control archive=1822 bytes. 2017 bytes, 43 lines control 2138 bytes, 29 lines md5sums Package: r-base-html Source: r-base Version: 3.2.2.20151203-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Dirk Eddelbuettel Installed-Size: 539 Depends: r-base-core Suggests: r-doc-html, mozilla | www-browser Replaces: r-base (<= 1.4.1-1), r-recommended (<< 1.9.0) Section: doc Priority: extra Homepage: http://www.r-project.org/ Description: GNU R html docs for statistical computing system functions 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-'. . This package provides html documentation suitable for browsing with a web-browser for the libraries included in the r-base package. 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./usr/share/doc/r-base-html/changelog.Debian.gz -> ../r-base-core/changelog.Debian.gz -rw-r--r-- root/root 20761 2015-12-04 11:54 ./usr/share/doc/r-base-html/copyright r-base_3.2.2.20151203-1_all.deb ─────────────────────────────── new debian package, version 2.0. size 9208 bytes: control archive=1376 bytes. 2134 bytes, 43 lines control 134 bytes, 2 lines md5sums Package: r-base Version: 3.2.2.20151203-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Dirk Eddelbuettel Installed-Size: 57 Depends: r-base-core (>= 3.2.2.20151203-1), r-recommended (= 3.2.2.20151203-1) Recommends: r-base-html, r-doc-html Suggests: ess, r-doc-info | r-doc-pdf Section: gnu-r Priority: optional Homepage: http://www.r-project.org/ Description: GNU R 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-'. . This package is a metapackage which eases the transition from the pre-1.5.0 package setup with its larger r-base package. Once installed, it can be safely removed and apt-get will automatically upgrade its components during future upgrades. 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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-'. . This package provides the R manuals in html format. 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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. 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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. 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The sibling packages r-doc-html and r-doc-info provides the same manuals. drwxr-xr-x root/root 0 2015-12-04 12:08 ./ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/ drwxr-xr-x root/root 0 2015-12-04 12:08 ./usr/share/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/share/R/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/share/R/doc/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/share/R/doc/manual/ -rw-r--r-- root/root 380786 2015-12-04 12:07 ./usr/share/R/doc/manual/R-FAQ.pdf -rw-r--r-- root/root 506143 2015-12-04 12:07 ./usr/share/R/doc/manual/R-admin.pdf -rw-r--r-- root/root 315451 2015-12-04 12:07 ./usr/share/R/doc/manual/R-data.pdf -rw-r--r-- root/root 901172 2015-12-04 12:07 ./usr/share/R/doc/manual/R-exts.pdf -rw-r--r-- root/root 633814 2015-12-04 12:07 ./usr/share/R/doc/manual/R-intro.pdf -rw-r--r-- root/root 431143 2015-12-04 12:07 ./usr/share/R/doc/manual/R-ints.pdf -rw-r--r-- root/root 379659 2015-12-04 12:07 ./usr/share/R/doc/manual/R-lang.pdf -rw-r--r-- root/root 5793327 2015-12-04 12:07 ./usr/share/R/doc/manual/fullrefman.pdf -rw-r--r-- root/root 5793327 2015-12-04 12:07 ./usr/share/R/doc/manual/refman.pdf drwxr-xr-x root/root 0 2015-12-04 12:08 ./usr/share/doc/ drwxr-xr-x root/root 0 2015-12-04 12:08 ./usr/share/doc/r-doc-pdf/ -rw-r--r-- root/root 951 2015-12-04 12:08 ./usr/share/doc/r-doc-pdf/changelog.Debian.gz -rw-r--r-- root/root 20761 2015-12-04 11:54 ./usr/share/doc/r-doc-pdf/copyright drwxr-xr-x root/root 0 2015-12-04 12:08 ./usr/share/doc/r-doc-pdf/manual/ lrwxrwxrwx root/root 0 2015-12-04 12:08 ./usr/share/doc/r-doc-pdf/manual/R-FAQ.pdf -> ../../../R/doc/manual/R-FAQ.pdf lrwxrwxrwx root/root 0 2015-12-04 12:08 ./usr/share/doc/r-doc-pdf/manual/R-admin.pdf -> ../../../R/doc/manual/R-admin.pdf lrwxrwxrwx root/root 0 2015-12-04 12:08 ./usr/share/doc/r-doc-pdf/manual/R-data.pdf -> ../../../R/doc/manual/R-data.pdf lrwxrwxrwx root/root 0 2015-12-04 12:08 ./usr/share/doc/r-doc-pdf/manual/R-exts.pdf -> ../../../R/doc/manual/R-exts.pdf lrwxrwxrwx root/root 0 2015-12-04 12:08 ./usr/share/doc/r-doc-pdf/manual/R-intro.pdf -> ../../../R/doc/manual/R-intro.pdf lrwxrwxrwx root/root 0 2015-12-04 12:08 ./usr/share/doc/r-doc-pdf/manual/R-ints.pdf -> ../../../R/doc/manual/R-ints.pdf lrwxrwxrwx root/root 0 2015-12-04 12:08 ./usr/share/doc/r-doc-pdf/manual/R-lang.pdf -> ../../../R/doc/manual/R-lang.pdf lrwxrwxrwx root/root 0 2015-12-04 12:08 ./usr/share/doc/r-doc-pdf/manual/refman.pdf -> ../../../R/doc/manual/refman.pdf r-mathlib_3.2.2.20151203-1_amd64.deb ──────────────────────────────────── new debian package, version 2.0. size 1331264 bytes: control archive=2047 bytes. 1865 bytes, 40 lines control 1148 bytes, 17 lines md5sums 370 bytes, 27 lines * postinst 30 bytes, 1 lines shlibs 60 bytes, 2 lines triggers Package: r-mathlib Source: r-base Version: 3.2.2.20151203-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Dirk Eddelbuettel Installed-Size: 2053 Depends: libc6 (>= 2.4) Recommends: r-base-core (= 3.2.2.20151203-1), r-base-dev (= 3.2.2.20151203-1) Section: gnu-r Priority: optional Homepage: http://www.r-project.org/ Description: GNU R standalone mathematics library 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-'. . 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 2015-12-04 12:07 ./ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/include/ -rw-r--r-- root/root 17620 2015-12-04 12:07 ./usr/include/Rmath.h drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/lib/ -rw-r--r-- root/root 564234 2015-12-04 12:07 ./usr/lib/libRmath.a lrwxrwxrwx root/root 0 2015-12-04 12:07 ./usr/lib/libRmath.so -> libRmath.so.1 lrwxrwxrwx root/root 0 2015-12-04 12:07 ./usr/lib/libRmath.so.1 -> libRmath.so.1.0.0 -rw-r--r-- root/root 207168 2015-12-04 12:07 ./usr/lib/libRmath.so.1.0.0 drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/lib/pkgconfig/ -rw-r--r-- root/root 173 2015-12-04 12:07 ./usr/lib/pkgconfig/libRmath.pc drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/share/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/share/doc/ drwxr-xr-x root/root 0 2015-12-04 12:08 ./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 96602 2015-03-18 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 61976 2015-11-27 23:15 ./usr/share/doc/r-mathlib/NEWS.Rd.gz lrwxrwxrwx root/root 0 2015-12-04 12:07 ./usr/share/doc/r-mathlib/NEWS.gz -> changelog.gz -rw-r--r-- root/root 376629 2015-12-04 12:01 ./usr/share/doc/r-mathlib/NEWS.pdf.gz -rw-r--r-- root/root 259190 2015-12-04 12:01 ./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 2015-12-04 11:54 ./usr/share/doc/r-mathlib/README.mathlib -rw-r--r-- root/root 951 2015-12-04 12:08 ./usr/share/doc/r-mathlib/changelog.Debian.gz -rw-r--r-- root/root 20761 2015-12-04 11:54 ./usr/share/doc/r-mathlib/copyright drwxr-xr-x root/root 0 2015-12-04 12:07 ./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 2015-12-04 12:07 ./usr/share/lintian/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 231 2015-12-04 11:54 ./usr/share/lintian/overrides/r-mathlib r-recommended_3.2.2.20151203-1_all.deb ────────────────────────────────────── new debian package, version 2.0. size 2782 bytes: control archive=2114 bytes. 3305 bytes, 57 lines control 76 bytes, 1 lines md5sums 434 bytes, 26 lines * preinst #!/bin/sh Package: r-recommended Source: r-base Version: 3.2.2.20151203-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Dirk Eddelbuettel Installed-Size: 13 Depends: r-base-core (>= 3.2.2.20151203-1), r-cran-boot (>= 1.2.19), r-cran-cluster (>= 1.9.6-2), r-cran-foreign (>= 0.7-2), r-cran-kernsmooth (>= 2.2.14), r-cran-lattice (>= 0.10.11), r-cran-mgcv (>= 1.1.5), r-cran-nlme (>= 3.1.52), r-cran-rpart (>= 3.1.20), r-cran-survival (>= 2.13.2-1), r-cran-mass, r-cran-class, r-cran-nnet, r-cran-spatial, r-cran-codetools, r-cran-matrix Section: gnu-r Priority: optional Homepage: http://www.r-project.org/ Description: GNU R collection of recommended packages [metapackage] 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-'. . This Debian package is now a metapackage that depends on a set of packages that are recommended by the upstream R core team as part of a complete R distribution, and distributed along with the source of R itself, as well as directly via the CRAN network of mirrors. This set comprises the following packages (listed in their upstream names): - KernSmooth: Functions for kernel smoothing for Wand & Jones (1995) - Matrix: Classes and methods for dense and sparse matrices and operations on them using Lapack and SuiteSparse - MASS, class, nnet and spatial: packages from Venables and Ripley, `Modern Applied Statistics with S' (4th edition). - boot: Bootstrap R (S-Plus) Functions from the book "Bootstrap Methods and Their Applications" by A.C. Davison and D.V. Hinkley (1997). - cluster: Functions for clustering (by Rousseeuw et al.) - codetools: Code analysis tools for R - foreign: Read data stored by Minitab, S, SAS, SPSS, Stata, ... - lattice: Implementation of Trellis (R) graphics - mgcv: Multiple smoothing parameter estimation and GAMs by GCV - nlme: Linear and nonlinear mixed effects models - rpart: Recursive partitioning and regression trees - survival: Survival analysis, including penalised likelihood. drwxr-xr-x root/root 0 2015-12-04 12:08 ./ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/lib/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/lib/R/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/lib/R/library/ drwxr-xr-x root/root 0 2015-12-04 12:08 ./usr/share/ drwxr-xr-x root/root 0 2015-12-04 12:08 ./usr/share/doc/ lrwxrwxrwx root/root 0 2015-12-04 12:08 ./usr/share/doc/r-recommended -> r-base-core drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/share/lintian/ drwxr-xr-x root/root 0 2015-12-04 12:07 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 542 2015-12-04 11:54 ./usr/share/lintian/overrides/r-recommended ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Not removing build depends: as requested Keeping session: ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: amd64 Build-Space: 354760 Build-Time: 823 Distribution: xenial-proposed Host Architecture: amd64 Install-Time: 285 Job: r-base_3.2.2.20151203-1.dsc Machine Architecture: amd64 Package: r-base Package-Time: 1110 Source-Version: 3.2.2.20151203-1 Space: 354760 Status: successful Version: 3.2.2.20151203-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20151204-1208 Build needed 00:18:30, 354760k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-8391953'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-8391953/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-8391953'] Unmounting chroot for build PACKAGEBUILD-8391953... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-8391953'] Removing build PACKAGEBUILD-8391953