https://launchpad.net/ubuntu/+source/r-base/3.6.2.20200221-1/+build/18748350 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lgw01-amd64-056 4.4.0-174-generic #204-Ubuntu SMP Wed Jan 29 06:41:01 UTC 2020 x86_64 Buildd toolchain package versions: launchpad-buildd_186 python-lpbuildd_186 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 22 Feb 23:14:18 ntpdate[1927]: adjust time server 10.211.37.1 offset -0.004805 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18748350 --image-type chroot /home/buildd/filecache-default/e96c25c651525abc9f0cabeb95ea71010abf4ecb Creating target for build PACKAGEBUILD-18748350 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18748350 Starting target for build PACKAGEBUILD-18748350 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18748350 'deb http://ftpmaster.internal/ubuntu focal main universe' 'deb http://ftpmaster.internal/ubuntu focal-security main universe' 'deb http://ftpmaster.internal/ubuntu focal-updates main universe' 'deb http://ftpmaster.internal/ubuntu focal-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-18748350 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18748350 Updating target for build PACKAGEBUILD-18748350 Get:1 http://ftpmaster.internal/ubuntu focal InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu focal-security InRelease [79.7 kB] Get:3 http://ftpmaster.internal/ubuntu focal-updates InRelease [79.7 kB] Get:4 http://ftpmaster.internal/ubuntu focal-proposed InRelease [255 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main amd64 Packages [982 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main Translation-en [505 kB] Get:7 http://ftpmaster.internal/ubuntu focal/universe amd64 Packages [8634 kB] Get:8 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5149 kB] Get:9 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 Packages [126 kB] Get:10 http://ftpmaster.internal/ubuntu focal-proposed/main Translation-en [55.1 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/universe amd64 Packages [508 kB] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/universe Translation-en [269 kB] Fetched 16.9 MB in 4s (4199 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libffi6 libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: gcc-10-base libctf-nobfd0 libctf0 libffi7 libgcc-s1 libhogweed5 libisl22 libnettle7 libperl5.30 libprocps8 perl-modules-5.30 The following packages will be upgraded: apt base-files base-passwd bash binutils binutils-common binutils-x86-64-linux-gnu bsdutils bzip2 cpp-9 debianutils e2fsprogs fdisk findutils g++-9 gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv grep gzip hostname libacl1 libapparmor1 libapt-pkg5.90 libasan5 libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcryptsetup12 libdebconfclient0 libdevmapper1.02.1 libext2fs2 libfdisk1 libgcc-9-dev libgcc1 libgcrypt20 libgmp10 libgnutls30 libgomp1 libgpg-error0 libip4tc2 libitm1 libjson-c4 libkmod2 liblockfile-bin liblockfile1 liblsan0 liblz4-1 libmount1 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpng16-16 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++-9-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login logsave lsb-base mount ncurses-base ncurses-bin openssl passwd perl perl-base procps sensible-utils systemd systemd-sysv sysvinit-utils ubuntu-keyring util-linux 112 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. Need to get 68.4 MB of archives. After this operation, 47.9 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main amd64 libc6-dev amd64 2.30-0ubuntu3 [2549 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main amd64 libc-dev-bin amd64 2.30-0ubuntu3 [71.8 kB] Get:3 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 linux-libc-dev amd64 5.4.0-15.18 [1146 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main amd64 gcc-10-base amd64 10-20200211-1ubuntu1 [18.8 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main amd64 libgcc-s1 amd64 10-20200211-1ubuntu1 [41.8 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main amd64 libgcc1 amd64 1:10-20200211-1ubuntu1 [41.7 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main amd64 libc6 amd64 2.30-0ubuntu3 [2725 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main amd64 base-files amd64 11ubuntu2 [60.1 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main amd64 debianutils amd64 4.9.1 [85.8 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main amd64 bash amd64 5.0-5ubuntu1 [639 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main amd64 bsdutils amd64 1:2.34-0.1ubuntu7 [63.3 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main amd64 findutils amd64 4.7.0-1ubuntu1 [329 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main amd64 grep amd64 3.4-1 [151 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main amd64 gzip amd64 1.10-0ubuntu4 [95.3 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main amd64 hostname amd64 3.23 [11.4 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main amd64 login amd64 1:4.8.1-1ubuntu1 [221 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main amd64 ncurses-bin amd64 6.1+20191019-1ubuntu1 [172 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main amd64 perl-modules-5.30 all 5.30.0-9 [2739 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main amd64 libperl5.30 amd64 5.30.0-9 [3950 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main amd64 perl amd64 5.30.0-9 [224 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main amd64 perl-base amd64 5.30.0-9 [1511 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main amd64 bzip2 amd64 1.0.8-2 [34.1 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main amd64 libbz2-1.0 amd64 1.0.8-2 [32.3 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main amd64 libblkid1 amd64 2.34-0.1ubuntu7 [137 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main amd64 libuuid1 amd64 2.34-0.1ubuntu7 [20.4 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main amd64 libfdisk1 amd64 2.34-0.1ubuntu7 [175 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main amd64 libpcre2-8-0 amd64 10.34-7 [197 kB] Get:28 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libselinux1 amd64 3.0-1build1 [68.8 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main amd64 libmount1 amd64 2.34-0.1ubuntu7 [149 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main amd64 libncurses6 amd64 6.1+20191019-1ubuntu1 [101 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main amd64 libtinfo6 amd64 6.1+20191019-1ubuntu1 [85.9 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main amd64 libncursesw6 amd64 6.1+20191019-1ubuntu1 [132 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main amd64 libsmartcols1 amd64 2.34-0.1ubuntu7 [101 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main amd64 fdisk amd64 2.34-0.1ubuntu7 [120 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main amd64 util-linux amd64 2.34-0.1ubuntu7 [1021 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main amd64 libdebconfclient0 amd64 0.251ubuntu1 [6160 B] Get:37 http://ftpmaster.internal/ubuntu focal/main amd64 base-passwd amd64 3.5.47 [47.7 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main amd64 libc-bin amd64 2.30-0ubuntu3 [625 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main amd64 ncurses-base all 6.1+20191019-1ubuntu1 [17.9 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main amd64 lsb-base all 11.1.0ubuntu2 [12.1 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main amd64 sysvinit-utils amd64 2.96-2.1ubuntu1 [20.6 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main amd64 libgpg-error0 amd64 1.37-1 [58.0 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main amd64 libgcrypt20 amd64 1.8.5-3ubuntu1 [419 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main amd64 liblz4-1 amd64 1.9.2-2 [55.9 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main amd64 libstdc++6 amd64 10-20200211-1ubuntu1 [502 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main amd64 systemd-sysv amd64 244.2-1ubuntu1 [9368 B] Get:47 http://ftpmaster.internal/ubuntu focal/main amd64 libacl1 amd64 2.2.53-5ubuntu1 [18.7 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main amd64 libapparmor1 amd64 2.13.3-7ubuntu2 [34.1 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main amd64 libaudit-common all 1:2.8.5-2ubuntu6 [3936 B] Get:50 http://ftpmaster.internal/ubuntu focal/main amd64 libcap-ng0 amd64 0.7.9-2.1build1 [11.1 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main amd64 libaudit1 amd64 1:2.8.5-2ubuntu6 [38.9 kB] Get:52 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libcap2 amd64 1:2.32-1 [15.9 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main amd64 libudev1 amd64 244.2-1ubuntu1 [77.1 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main amd64 libdevmapper1.02.1 amd64 2:1.02.167-1ubuntu1 [127 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main amd64 libjson-c4 amd64 0.13.1+dfsg-7 [29.2 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main amd64 libssl1.1 amd64 1.1.1d-2ubuntu3 [1316 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main amd64 libcryptsetup12 amd64 2:2.2.2-3ubuntu1 [182 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main amd64 libnettle7 amd64 3.5.1+really3.5.1-2 [114 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main amd64 libgmp10 amd64 2:6.2.0+dfsg-3 [240 kB] Get:60 http://ftpmaster.internal/ubuntu focal/main amd64 libhogweed5 amd64 3.5.1+really3.5.1-2 [138 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main amd64 libffi7 amd64 3.3-3 [19.6 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main amd64 libp11-kit0 amd64 0.23.20-1build1 [188 kB] Get:63 http://ftpmaster.internal/ubuntu focal/main amd64 libtasn1-6 amd64 4.16.0-2 [38.1 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main amd64 libgnutls30 amd64 3.6.11.1-2ubuntu2 [793 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main amd64 libip4tc2 amd64 1.8.4-3ubuntu1 [18.8 kB] Get:66 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libkmod2 amd64 27-1ubuntu1 [44.2 kB] Get:67 http://ftpmaster.internal/ubuntu focal/main amd64 libpam0g amd64 1.3.1-5ubuntu4 [55.4 kB] Get:68 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libseccomp2 amd64 2.4.2-2ubuntu3 [39.9 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main amd64 mount amd64 2.34-0.1ubuntu7 [115 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main amd64 systemd amd64 244.2-1ubuntu1 [3682 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main amd64 libsystemd0 amd64 244.2-1ubuntu1 [261 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main amd64 libzstd1 amd64 1.4.4+dfsg-3 [237 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main amd64 libapt-pkg5.90 amd64 1.9.10 [852 kB] Get:74 http://ftpmaster.internal/ubuntu focal/main amd64 gpgv amd64 2.2.17-3ubuntu1 [200 kB] Get:75 http://ftpmaster.internal/ubuntu focal/main amd64 ubuntu-keyring all 2020.02.11.1 [22.3 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main amd64 apt amd64 1.9.10 [1281 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main amd64 libpam-modules-bin amd64 1.3.1-5ubuntu4 [37.7 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main amd64 libpam-modules amd64 1.3.1-5ubuntu4 [250 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main amd64 logsave amd64 1.45.5-2ubuntu1 [10.2 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main amd64 libext2fs2 amd64 1.45.5-2ubuntu1 [183 kB] Get:81 http://ftpmaster.internal/ubuntu focal/main amd64 e2fsprogs amd64 1.45.5-2ubuntu1 [527 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main amd64 libattr1 amd64 1:2.4.48-5 [12.7 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main amd64 libpam-runtime all 1.3.1-5ubuntu4 [37.3 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main amd64 libsepol1 amd64 3.0-1 [252 kB] Get:85 http://ftpmaster.internal/ubuntu focal/main amd64 libsemanage-common all 3.0-1build1 [9876 B] Get:86 http://ftpmaster.internal/ubuntu focal/main amd64 libsemanage1 amd64 3.0-1build1 [85.9 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main amd64 passwd amd64 1:4.8.1-1ubuntu1 [797 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main amd64 libgomp1 amd64 10-20200211-1ubuntu1 [101 kB] Get:89 http://ftpmaster.internal/ubuntu focal/main amd64 libitm1 amd64 10-20200211-1ubuntu1 [26.3 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main amd64 libatomic1 amd64 10-20200211-1ubuntu1 [9308 B] Get:91 http://ftpmaster.internal/ubuntu focal/main amd64 libasan5 amd64 9.2.1-29ubuntu1 [395 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main amd64 liblsan0 amd64 10-20200211-1ubuntu1 [145 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main amd64 libtsan0 amd64 10-20200211-1ubuntu1 [320 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main amd64 libubsan1 amd64 10-20200211-1ubuntu1 [137 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main amd64 libquadmath0 amd64 10-20200211-1ubuntu1 [147 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main amd64 g++-9 amd64 9.2.1-29ubuntu1 [8395 kB] Get:97 http://ftpmaster.internal/ubuntu focal/main amd64 gcc-9 amd64 9.2.1-29ubuntu1 [8226 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main amd64 libstdc++-9-dev amd64 9.2.1-29ubuntu1 [1710 kB] Get:99 http://ftpmaster.internal/ubuntu focal/main amd64 libgcc-9-dev amd64 9.2.1-29ubuntu1 [2360 kB] Get:100 http://ftpmaster.internal/ubuntu focal/main amd64 libisl22 amd64 0.22.1-1 [592 kB] Get:101 http://ftpmaster.internal/ubuntu focal/main amd64 libcc1-0 amd64 10-20200211-1ubuntu1 [41.2 kB] Get:102 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.34-3ubuntu1 [1612 kB] Get:103 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libbinutils amd64 2.34-3ubuntu1 [475 kB] Get:104 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 binutils amd64 2.34-3ubuntu1 [3376 B] Get:105 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 binutils-common amd64 2.34-3ubuntu1 [207 kB] Get:106 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libctf-nobfd0 amd64 2.34-3ubuntu1 [46.9 kB] Get:107 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libctf0 amd64 2.34-3ubuntu1 [46.6 kB] Get:108 http://ftpmaster.internal/ubuntu focal/main amd64 cpp-9 amd64 9.2.1-29ubuntu1 [7491 kB] Get:109 http://ftpmaster.internal/ubuntu focal/main amd64 gcc-9-base amd64 9.2.1-29ubuntu1 [19.1 kB] Get:110 http://ftpmaster.internal/ubuntu focal/main amd64 libcom-err2 amd64 1.45.5-2ubuntu1 [9544 B] Get:111 http://ftpmaster.internal/ubuntu focal/main amd64 libss2 amd64 1.45.5-2ubuntu1 [11.3 kB] Get:112 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libprocps8 amd64 2:3.3.16-1ubuntu1 [33.3 kB] Get:113 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 procps amd64 2:3.3.16-1ubuntu1 [233 kB] Get:114 http://ftpmaster.internal/ubuntu focal/main amd64 sensible-utils all 0.0.12+nmu1 [15.0 kB] Get:115 http://ftpmaster.internal/ubuntu focal/main amd64 libsqlite3-0 amd64 3.31.1-1ubuntu1 [548 kB] Get:116 http://ftpmaster.internal/ubuntu focal/main amd64 openssl amd64 1.1.1d-2ubuntu3 [617 kB] Get:117 http://ftpmaster.internal/ubuntu focal/main amd64 libpng16-16 amd64 1.6.37-2 [179 kB] Get:118 http://ftpmaster.internal/ubuntu focal/main amd64 libassuan0 amd64 2.5.3-7ubuntu2 [35.7 kB] Get:119 http://ftpmaster.internal/ubuntu focal/main amd64 gpg amd64 2.2.17-3ubuntu1 [479 kB] Get:120 http://ftpmaster.internal/ubuntu focal/main amd64 gpgconf amd64 2.2.17-3ubuntu1 [124 kB] Get:121 http://ftpmaster.internal/ubuntu focal/main amd64 gpg-agent amd64 2.2.17-3ubuntu1 [232 kB] Get:122 http://ftpmaster.internal/ubuntu focal/main amd64 liblockfile-bin amd64 1.16-1.1 [11.7 kB] Get:123 http://ftpmaster.internal/ubuntu focal/main amd64 liblockfile1 amd64 1.16-1.1 [6680 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 68.4 MB in 9s (7248 kB/s) (Reading database ... 12741 files and directories currently installed.) Preparing to unpack .../libc6-dev_2.30-0ubuntu3_amd64.deb ... Unpacking libc6-dev:amd64 (2.30-0ubuntu3) over (2.30-0ubuntu2) ... Preparing to unpack .../libc-dev-bin_2.30-0ubuntu3_amd64.deb ... Unpacking libc-dev-bin (2.30-0ubuntu3) over (2.30-0ubuntu2) ... Preparing to unpack .../linux-libc-dev_5.4.0-15.18_amd64.deb ... Unpacking linux-libc-dev:amd64 (5.4.0-15.18) over (5.3.0-18.19) ... Selecting previously unselected package gcc-10-base:amd64. Preparing to unpack .../gcc-10-base_10-20200211-1ubuntu1_amd64.deb ... Unpacking gcc-10-base:amd64 (10-20200211-1ubuntu1) ... Setting up gcc-10-base:amd64 (10-20200211-1ubuntu1) ... Selecting previously unselected package libgcc-s1:amd64. (Reading database ... 12751 files and directories currently installed.) Preparing to unpack .../libgcc-s1_10-20200211-1ubuntu1_amd64.deb ... Unpacking libgcc-s1:amd64 (10-20200211-1ubuntu1) ... Replacing files in old package libgcc1:amd64 (1:9.2.1-9ubuntu2) ... 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Setting up libdevmapper1.02.1:amd64 (2:1.02.167-1ubuntu1) ... Setting up mount (2.34-0.1ubuntu7) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up gpgconf (2.2.17-3ubuntu1) ... Setting up libperl5.30:amd64 (5.30.0-9) ... Setting up libisl22:amd64 (0.22.1-1) ... Setting up liblockfile1:amd64 (1.16-1.1) ... Setting up libjson-c4:amd64 (0.13.1+dfsg-7) ... Setting up libbinutils:amd64 (2.34-3ubuntu1) ... Setting up libc-dev-bin (2.30-0ubuntu3) ... Setting up openssl (1.1.1d-2ubuntu3) ... Setting up libcc1-0:amd64 (10-20200211-1ubuntu1) ... Setting up gpg (2.2.17-3ubuntu1) ... Setting up liblsan0:amd64 (10-20200211-1ubuntu1) ... Setting up libprocps8:amd64 (2:3.3.16-1ubuntu1) ... Setting up libitm1:amd64 (10-20200211-1ubuntu1) ... Setting up libkmod2:amd64 (27-1ubuntu1) ... Setting up gcc-9-base:amd64 (9.2.1-29ubuntu1) ... Setting up libtsan0:amd64 (10-20200211-1ubuntu1) ... Setting up libctf0:amd64 (2.34-3ubuntu1) ... Setting up gpg-agent (2.2.17-3ubuntu1) ... Installing new version of config file /etc/logcheck/ignore.d.server/gpg-agent ... Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-browser.socket -> /usr/lib/systemd/user/gpg-agent-browser.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-extra.socket -> /usr/lib/systemd/user/gpg-agent-extra.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-ssh.socket -> /usr/lib/systemd/user/gpg-agent-ssh.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent.socket -> /usr/lib/systemd/user/gpg-agent.socket. Setting up e2fsprogs (1.45.5-2ubuntu1) ... Setting up libasan5:amd64 (9.2.1-29ubuntu1) ... Setting up perl (5.30.0-9) ... Setting up procps (2:3.3.16-1ubuntu1) ... Removing obsolete conffile /etc/sysctl.d/protect-links.conf ... Removing obsolete conffile /etc/sysctl.d/10-link-restrictions.conf ... Setting up cpp-9 (9.2.1-29ubuntu1) ... Setting up libc6-dev:amd64 (2.30-0ubuntu3) ... Setting up libcryptsetup12:amd64 (2:2.2.2-3ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.34-3ubuntu1) ... Setting up systemd (244.2-1ubuntu1) ... Installing new version of config file /etc/dhcp/dhclient-enter-hooks.d/resolved ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from KVM UUID. Setting up binutils (2.34-3ubuntu1) ... Setting up libgcc-9-dev:amd64 (9.2.1-29ubuntu1) ... Setting up gcc-9 (9.2.1-29ubuntu1) ... Setting up systemd-sysv (244.2-1ubuntu1) ... Setting up libstdc++-9-dev:amd64 (9.2.1-29ubuntu1) ... Setting up g++-9 (9.2.1-29ubuntu1) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-18748350 amd64 focal-proposed -c chroot:build-PACKAGEBUILD-18748350 --arch=amd64 --dist=focal-proposed --nolog -A r-base_3.6.2.20200221-1.dsc Initiating build PACKAGEBUILD-18748350 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-174-generic #204-Ubuntu SMP Wed Jan 29 06:41:01 UTC 2020 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-amd64-056.buildd +==============================================================================+ | r-base 3.6.2.20200221-1 (amd64) 22 Feb 2020 23:15 | +==============================================================================+ Package: r-base Version: 3.6.2.20200221-1 Source Version: 3.6.2.20200221-1 Distribution: focal-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/r-base-vY2pme/r-base-3.6.2.20200221' with '<>' I: NOTICE: Log filtering will replace 'build/r-base-vY2pme' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-18748350/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- r-base_3.6.2.20200221-1.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 '/<>/resolver-CzaTM_/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-CzaTM_/apt_archive ./ InRelease Get:2 copy:/<>/resolver-CzaTM_/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-CzaTM_/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-CzaTM_/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-CzaTM_/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (155 kB/s) Reading package lists... 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: libffi6 libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use '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 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-CzaTM_/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14676 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: 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, libpcre2-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-plain-generic, texlive-fonts-recommended, texlive-fonts-extra, texlive-extra-utils, texlive-latex-recommended, texlive-latex-extra, default-jdk | openjdk-10-jdk, mpack, bash-completion Filtered Build-Depends: 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, libpcre2-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-plain-generic, texlive-fonts-recommended, texlive-fonts-extra, texlive-extra-utils, texlive-latex-recommended, texlive-latex-extra, default-jdk | openjdk-10-jdk, mpack, bash-completion dpkg-deb: building package 'sbuild-build-depends-r-base-dummy' in '/<>/resolver-RwbMrK/apt_archive/sbuild-build-depends-r-base-dummy.deb'. Ign:1 copy:/<>/resolver-RwbMrK/apt_archive ./ InRelease Get:2 copy:/<>/resolver-RwbMrK/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-RwbMrK/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-RwbMrK/apt_archive ./ Sources [525 B] Get:5 copy:/<>/resolver-RwbMrK/apt_archive ./ Packages [812 B] Fetched 3456 B in 0s (203 kB/s) Reading package lists... 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: libffi6 libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bash-completion bison bsdmainutils ca-certificates-java debhelper default-jdk default-jdk-headless default-jre default-jre-headless dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core fonts-lmodern gettext gettext-base gfortran gfortran-9 gir1.2-freedesktop gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 gir1.2-pango-1.0 groff-base icu-devtools intltool-debian java-common libapache-pom-java libarchive-zip-perl libasn1-8-heimdal libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libblas-dev libblas3 libblkid-dev libbrotli1 libbsd0 libbz2-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev libcommons-logging-java libcommons-parent-java libcroco3 libcups2 libcurl4 libcurl4-openssl-dev libdatrie-dev libdatrie1 libdbus-1-3 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libexpat1 libexpat1-dev libffi-dev libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontconfig1-dev libfontenc1 libfreetype-dev libfreetype6 libfreetype6-dev libfribidi-dev libfribidi0 libgfortran-9-dev libgfortran5 libgif7 libgirepository-1.0-1 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libglvnd0 libglx-mesa0 libglx0 libgraphite2-3 libgraphite2-dev libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libice-dev libice6 libicu-dev libicu65 libjbig-dev libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libllvm9 liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libmime-charset-perl libmount-dev libmpdec2 libncurses-dev libncurses5-dev libnghttp2-14 libnspr4 libnss3 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 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix2 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpcsclite1 libpdfbox-java libpipeline1 libpixman-1-0 libpixman-1-dev libpng-dev libpsl5 libptexenc1 libpthread-stubs0-dev libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libreadline-dev libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libselinux1-dev libsensors-config libsensors5 libsepol1-dev libsigsegv2 libsm-dev libsm6 libsombok3 libssh-4 libsub-override-perl libsynctex2 libtcl8.6 libteckit0 libtexlua53 libtexluajit2 libtext-unidecode-perl libthai-data libthai-dev libthai0 libtiff-dev libtiff5 libtiff5-dev libtiffxx5 libtk8.6 libtool libuchardet0 libunicode-linebreak-perl libunwind8 libvulkan1 libwebp6 libwind0-heimdal libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-render0-dev libxcb-shm0 libxcb-shm0-dev libxcb-sync1 libxcb1 libxcb1-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes3 libxfont2 libxft-dev libxft2 libxi6 libxkbfile1 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml2 libxmu6 libxmuu1 libxpm4 libxrender-dev libxrender1 libxshmfence1 libxss-dev libxss1 libxt-dev libxt6 libxtst6 libxxf86vm1 libzzip-0-13 m4 man-db mime-support mpack openjdk-11-jdk openjdk-11-jdk-headless openjdk-11-jre openjdk-11-jre-headless pango1.0-tools pkg-config po-debconf preview-latex-style python3 python3-distutils python3-lib2to3 python3-minimal python3.8 python3.8-minimal t1utils tcl8.6 tcl8.6-dev tex-common texinfo texlive-base texlive-binaries texlive-extra-utils texlive-fonts-extra texlive-fonts-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures texlive-plain-generic tk8.6 tk8.6-dev ucf uuid-dev x11-common x11-xkb-utils x11proto-core-dev x11proto-dev x11proto-scrnsaver-dev x11proto-xext-dev xauth xdg-utils xfonts-base xfonts-encodings xfonts-utils xkb-data xorg-sgml-doctools xserver-common xtrans-dev xvfb zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc bison-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-multilib gfortran-doc gfortran-9-multilib gfortran-9-doc libcoarrays-dev groff libasound2-plugins alsa-utils liblapack-doc libcairo2-doc libavalon-framework-java libcommons-logging-java-doc libexcalibur-logkit-java liblog4j1.2-java cups-common libcurl4-doc libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev libssl-dev libdatrie-doc freetype2-doc libgirepository1.0-dev libglib2.0-doc libgdk-pixbuf2.0-bin | libgdk-pixbuf2.0-dev libxml2-utils libgraphite2-utils krb5-doc krb5-user libice-doc icu-doc liblcms2-utils liblzma-doc libencode-hanextra-perl libpod2-base-perl ncurses-doc imagemagick libpango1.0-doc pciutils pcscd readline-doc lm-sensors libsm-doc libthai-doc libtool-doc gcj-jdk libx11-doc libxcb-doc libxext-doc libxt-doc m4-doc apparmor less www-browser mail-transport-agent inews openjdk-11-demo openjdk-11-source visualvm libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic libmail-box-perl python3-doc python3-tk python3-venv python3.8-venv python3.8-doc binfmt-support tcl-tclreadline tcl8.6-doc ghostscript gv | postscript-viewer perl-tk xpdf | pdf-viewer xzdec chktex dvidvi dvipng fragmaster lacheck latexdiff latexmk purifyeps xindy cm-super texlive-fonts-extra-doc texlive-fonts-recommended-doc texlive-latex-base-doc python3-pygments icc-profiles libfile-which-perl libspreadsheet-parseexcel-perl texlive-latex-extra-doc texlive-latex-recommended-doc texlive-luatex texlive-pstricks dot2tex prerex ruby-tcltk | libtcltk-ruby texlive-pictures-doc vprerex tk8.6-doc Recommended packages: curl | wget | lynx alsa-ucm-conf alsa-topology-conf bzip2-doc dbus libarchive-cpio-perl shared-mime-info xdg-user-dirs krb5-locales libpng-tools publicsuffix libsasl2-modules libltdl-dev mesa-vulkan-drivers | vulkan-icd libwww-perl libxml-sax-expat-perl libatk-wrapper-java-jni fonts-dejavu-extra libmail-sendmail-perl lmodern dvisvgm ghostscript libfile-homedir-perl liblog-log4perl-perl libyaml-tiny-perl ruby | ruby-interpreter fonts-adf-accanthis fonts-adf-berenis fonts-adf-gillius fonts-adf-universalis fonts-cabin fonts-cantarell fonts-comfortaa fonts-croscore fonts-crosextra-caladea fonts-crosextra-carlito 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-go fonts-junicode fonts-lato fonts-linuxlibertine fonts-lobstertwo fonts-noto-core fonts-noto-mono fonts-oflb-asana-math fonts-open-sans fonts-roboto-unhinted fonts-sil-gentium fonts-sil-gentium-basic fonts-sil-gentiumplus fonts-sil-gentiumplus-compact fonts-stix texlive-fonts-extra-links tex-gyre tipa tk xterm | x-terminal-emulator libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bash-completion bison bsdmainutils ca-certificates-java debhelper default-jdk default-jdk-headless default-jre default-jre-headless dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core fonts-lmodern gettext gettext-base gfortran gfortran-9 gir1.2-freedesktop gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 gir1.2-pango-1.0 groff-base icu-devtools intltool-debian java-common libapache-pom-java libarchive-zip-perl libasn1-8-heimdal libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libblas-dev libblas3 libblkid-dev libbrotli1 libbsd0 libbz2-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev libcommons-logging-java libcommons-parent-java libcroco3 libcups2 libcurl4 libcurl4-openssl-dev libdatrie-dev libdatrie1 libdbus-1-3 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libexpat1 libexpat1-dev libffi-dev libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontconfig1-dev libfontenc1 libfreetype-dev libfreetype6 libfreetype6-dev libfribidi-dev libfribidi0 libgfortran-9-dev libgfortran5 libgif7 libgirepository-1.0-1 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libglvnd0 libglx-mesa0 libglx0 libgraphite2-3 libgraphite2-dev libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libice-dev libice6 libicu-dev libicu65 libjbig-dev libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libllvm9 liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libmime-charset-perl libmount-dev libmpdec2 libncurses-dev libncurses5-dev libnghttp2-14 libnspr4 libnss3 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 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix2 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpcsclite1 libpdfbox-java libpipeline1 libpixman-1-0 libpixman-1-dev libpng-dev libpsl5 libptexenc1 libpthread-stubs0-dev libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libreadline-dev libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libselinux1-dev libsensors-config libsensors5 libsepol1-dev libsigsegv2 libsm-dev libsm6 libsombok3 libssh-4 libsub-override-perl libsynctex2 libtcl8.6 libteckit0 libtexlua53 libtexluajit2 libtext-unidecode-perl libthai-data libthai-dev libthai0 libtiff-dev libtiff5 libtiff5-dev libtiffxx5 libtk8.6 libtool libuchardet0 libunicode-linebreak-perl libunwind8 libvulkan1 libwebp6 libwind0-heimdal libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-render0-dev libxcb-shm0 libxcb-shm0-dev libxcb-sync1 libxcb1 libxcb1-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes3 libxfont2 libxft-dev libxft2 libxi6 libxkbfile1 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml2 libxmu6 libxmuu1 libxpm4 libxrender-dev libxrender1 libxshmfence1 libxss-dev libxss1 libxt-dev libxt6 libxtst6 libxxf86vm1 libzzip-0-13 m4 man-db mime-support mpack openjdk-11-jdk openjdk-11-jdk-headless openjdk-11-jre openjdk-11-jre-headless pango1.0-tools pkg-config po-debconf preview-latex-style python3 python3-distutils python3-lib2to3 python3-minimal python3.8 python3.8-minimal sbuild-build-depends-r-base-dummy t1utils tcl8.6 tcl8.6-dev tex-common texinfo texlive-base texlive-binaries texlive-extra-utils texlive-fonts-extra texlive-fonts-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures texlive-plain-generic tk8.6 tk8.6-dev ucf uuid-dev x11-common x11-xkb-utils x11proto-core-dev x11proto-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, 310 newly installed, 0 to remove and 0 not upgraded. Need to get 975 MB of archives. After this operation, 2797 MB of additional disk space will be used. Get:1 copy:/<>/resolver-RwbMrK/apt_archive ./ sbuild-build-depends-r-base-dummy 0.invalid.0 [1140 B] Get:2 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libpython3.8-minimal amd64 3.8.2~rc2-2 [704 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main amd64 libexpat1 amd64 2.2.9-1 [73.3 kB] Get:4 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 python3.8-minimal amd64 3.8.2~rc2-2 [1894 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main amd64 python3-minimal amd64 3.8.0-3ubuntu1 [23.3 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main amd64 mime-support all 3.64ubuntu1 [30.6 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main amd64 libmpdec2 amd64 2.4.2-2 [84.1 kB] Get:8 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libpython3.8-stdlib amd64 3.8.2~rc2-2 [1665 kB] Get:9 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 python3.8 amd64 3.8.2~rc2-2 [363 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main amd64 libpython3-stdlib amd64 3.8.0-3ubuntu1 [6872 B] Get:11 http://ftpmaster.internal/ubuntu focal/main amd64 python3 amd64 3.8.0-3ubuntu1 [47.6 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main amd64 libbsd0 amd64 0.10.0-1 [45.4 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main amd64 bsdmainutils amd64 11.1.2ubuntu2 [181 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main amd64 groff-base amd64 1.22.4-4 [865 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main amd64 libpipeline1 amd64 1.5.2-2build1 [27.7 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main amd64 man-db amd64 2.9.0-2 [1114 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main amd64 ucf all 3.0038+nmu1 [51.6 kB] Get:19 http://ftpmaster.internal/ubuntu focal/universe amd64 tex-common all 6.13 [32.7 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main amd64 libmagic-mgc amd64 1:5.38-4 [218 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main amd64 libmagic1 amd64 1:5.38-4 [75.9 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main amd64 file amd64 1:5.38-4 [23.3 kB] Get:23 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libglib2.0-0 amd64 2.63.5-2 [1283 kB] Get:24 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libgirepository-1.0-1 amd64 1.63.2-1 [85.4 kB] Get:25 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 gir1.2-glib-2.0 amd64 1.63.2-1 [134 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main amd64 libdbus-1-3 amd64 1.12.16-2ubuntu2 [179 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main amd64 libelf1 amd64 0.176-1.1build1 [44.0 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main amd64 libfribidi0 amd64 1.0.8-2 [23.8 kB] Get:29 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libglib2.0-data all 2.63.5-2 [7080 B] Get:30 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libicu65 amd64 65.1-1ubuntu2 [8502 kB] Get:31 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libxml2 amd64 2.9.10+dfsg-1ubuntu2 [640 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main amd64 xkb-data all 2.26-2ubuntu4 [335 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main amd64 bash-completion all 1:2.10-1ubuntu1 [178 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main amd64 gettext-base amd64 0.19.8.1-10 [50.2 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main amd64 libdrm-common all 2.4.100-4 [5340 B] Get:36 http://ftpmaster.internal/ubuntu focal/main amd64 libdrm2 amd64 2.4.100-4 [31.8 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main amd64 libedit2 amd64 3.1-20191231-1 [87.0 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main amd64 libkrb5support0 amd64 1.17-6ubuntu4 [30.9 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main amd64 libk5crypto3 amd64 1.17-6ubuntu4 [80.2 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main amd64 libkeyutils1 amd64 1.6-6ubuntu1 [10.2 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main amd64 libkrb5-3 amd64 1.17-6ubuntu4 [330 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main amd64 libgssapi-krb5-2 amd64 1.17-6ubuntu4 [121 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main amd64 libpsl5 amd64 0.20.2-2 [50.0 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main amd64 libxau6 amd64 1:1.0.9-0ubuntu1 [7488 B] Get:45 http://ftpmaster.internal/ubuntu focal/main amd64 libxdmcp6 amd64 1:1.1.3-0ubuntu1 [10.6 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main amd64 libxcb1 amd64 1.13.1-5build1 [44.8 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main amd64 libx11-data all 2:1.6.8-1 [113 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main amd64 libx11-6 amd64 2:1.6.8-1 [573 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main amd64 libxext6 amd64 2:1.3.4-0ubuntu1 [29.1 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main amd64 libxmuu1 amd64 2:1.1.3-0ubuntu1 [9728 B] Get:51 http://ftpmaster.internal/ubuntu focal/main amd64 xauth amd64 1:1.1-0ubuntu1 [25.0 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main amd64 libsigsegv2 amd64 2.12-2 [13.9 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main amd64 m4 amd64 1.4.18-4 [199 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main amd64 autoconf all 2.69-11.1 [321 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main amd64 autotools-dev all 20180224.1 [39.6 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main amd64 automake all 1:1.16.1-4ubuntu6 [522 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main amd64 autopoint all 0.19.8.1-10 [412 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main amd64 bison amd64 2:3.5.1+dfsg-1 [657 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main amd64 java-common all 0.72 [6816 B] Get:60 http://ftpmaster.internal/ubuntu focal/main amd64 libavahi-common-data amd64 0.7-4ubuntu6 [21.3 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main amd64 libavahi-common3 amd64 0.7-4ubuntu6 [21.7 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main amd64 libavahi-client3 amd64 0.7-4ubuntu6 [25.5 kB] Get:63 http://ftpmaster.internal/ubuntu focal/main amd64 libcups2 amd64 2.3.1-7 [233 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main amd64 liblcms2-2 amd64 2.9-4 [140 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main amd64 libjpeg-turbo8 amd64 2.0.3-0ubuntu1 [118 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main amd64 libjpeg8 amd64 8c-2ubuntu8 [2194 B] Get:67 http://ftpmaster.internal/ubuntu focal/main amd64 libfreetype6 amd64 2.10.1-2 [341 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main amd64 fonts-dejavu-core all 2.37-1 [1041 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main amd64 fontconfig-config all 2.13.1-2ubuntu2 [28.9 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main amd64 libfontconfig1 amd64 2.13.1-2ubuntu2 [114 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main amd64 libnspr4 amd64 2:4.24-1 [107 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main amd64 libnss3 amd64 2:3.49.1-1ubuntu1 [1171 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main amd64 libasound2-data all 1.2.1.2-2ubuntu2 [18.9 kB] Get:74 http://ftpmaster.internal/ubuntu focal/main amd64 libasound2 amd64 1.2.1.2-2ubuntu2 [327 kB] Get:75 http://ftpmaster.internal/ubuntu focal/main amd64 libpcsclite1 amd64 1.8.26-3 [22.0 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main amd64 libxi6 amd64 2:1.7.10-0ubuntu1 [29.9 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main amd64 libxrender1 amd64 1:0.9.10-1 [18.7 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main amd64 x11-common all 1:7.7+19ubuntu14 [22.3 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main amd64 libxtst6 amd64 2:1.2.3-1 [12.8 kB] Get:80 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 openjdk-11-jre-headless amd64 11.0.6+10-2ubuntu2 [37.4 MB] Get:81 http://ftpmaster.internal/ubuntu focal/main amd64 default-jre-headless amd64 2:1.11-72 [3192 B] Get:82 http://ftpmaster.internal/ubuntu focal/main amd64 ca-certificates-java all 20190405ubuntu1 [12.2 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main amd64 libtool all 2.4.6-13 [161 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main amd64 dh-autoreconf all 19 [16.1 kB] Get:85 http://ftpmaster.internal/ubuntu focal/main amd64 libdebhelper-perl all 12.9ubuntu1 [62.0 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main amd64 libarchive-zip-perl all 1.67-1 [90.4 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main amd64 libsub-override-perl all 0.09-2 [9532 B] Get:88 http://ftpmaster.internal/ubuntu focal/main amd64 libfile-stripnondeterminism-perl all 1.6.3-2 [16.0 kB] Get:89 http://ftpmaster.internal/ubuntu focal/main amd64 dh-strip-nondeterminism all 1.6.3-2 [5228 B] Get:90 http://ftpmaster.internal/ubuntu focal/main amd64 dwz amd64 0.13-5 [151 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main amd64 libcroco3 amd64 0.6.13-1 [82.5 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main amd64 gettext amd64 0.19.8.1-10 [897 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main amd64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main amd64 po-debconf all 1.0.21 [233 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main amd64 debhelper all 12.9ubuntu1 [869 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main amd64 libglvnd0 amd64 1.3.1-1 [52.4 kB] Get:97 http://ftpmaster.internal/ubuntu focal/main amd64 libglapi-mesa amd64 20.0.0-1ubuntu1 [26.7 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main amd64 libx11-xcb1 amd64 2:1.6.8-1 [9236 B] Get:99 http://ftpmaster.internal/ubuntu focal/main amd64 libxcb-dri2-0 amd64 1.13.1-5build1 [6916 B] Get:100 http://ftpmaster.internal/ubuntu focal/main amd64 libxcb-dri3-0 amd64 1.13.1-5build1 [6556 B] Get:101 http://ftpmaster.internal/ubuntu focal/main amd64 libxcb-glx0 amd64 1.13.1-5build1 [22.0 kB] Get:102 http://ftpmaster.internal/ubuntu focal/main amd64 libxcb-present0 amd64 1.13.1-5build1 [5560 B] Get:103 http://ftpmaster.internal/ubuntu focal/main amd64 libxcb-sync1 amd64 1.13.1-5build1 [8892 B] Get:104 http://ftpmaster.internal/ubuntu focal/main amd64 libxdamage1 amd64 1:1.1.5-1 [7028 B] Get:105 http://ftpmaster.internal/ubuntu focal/main amd64 libxfixes3 amd64 1:5.0.3-1 [10.8 kB] Get:106 http://ftpmaster.internal/ubuntu focal/main amd64 libxshmfence1 amd64 1.3-1 [5028 B] Get:107 http://ftpmaster.internal/ubuntu focal/main amd64 libxxf86vm1 amd64 1:1.1.4-1build1 [10.2 kB] Get:108 http://ftpmaster.internal/ubuntu focal/main amd64 libdrm-amdgpu1 amd64 2.4.100-4 [18.4 kB] Get:109 http://ftpmaster.internal/ubuntu focal/main amd64 libpciaccess0 amd64 0.16-0ubuntu1 [17.9 kB] Get:110 http://ftpmaster.internal/ubuntu focal/main amd64 libdrm-intel1 amd64 2.4.100-4 [60.3 kB] Get:111 http://ftpmaster.internal/ubuntu focal/main amd64 libdrm-nouveau2 amd64 2.4.100-4 [16.4 kB] Get:112 http://ftpmaster.internal/ubuntu focal/main amd64 libdrm-radeon1 amd64 2.4.100-4 [19.7 kB] Get:113 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libllvm9 amd64 1:9.0.1-8build2 [14.8 MB] Get:114 http://ftpmaster.internal/ubuntu focal/main amd64 libsensors-config all 1:3.6.0-2ubuntu1 [6092 B] Get:115 http://ftpmaster.internal/ubuntu focal/main amd64 libsensors5 amd64 1:3.6.0-2ubuntu1 [27.4 kB] Get:116 http://ftpmaster.internal/ubuntu focal/main amd64 libvulkan1 amd64 1.2.131.2-1 [93.3 kB] Get:117 http://ftpmaster.internal/ubuntu focal/main amd64 libgl1-mesa-dri amd64 20.0.0-1ubuntu1 [9445 kB] Get:118 http://ftpmaster.internal/ubuntu focal/main amd64 libglx-mesa0 amd64 20.0.0-1ubuntu1 [139 kB] Get:119 http://ftpmaster.internal/ubuntu focal/main amd64 libglx0 amd64 1.3.1-1 [32.6 kB] Get:120 http://ftpmaster.internal/ubuntu focal/main amd64 libgl1 amd64 1.3.1-1 [87.5 kB] Get:121 http://ftpmaster.internal/ubuntu focal/main amd64 libgif7 amd64 5.1.9-1 [32.2 kB] Get:122 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 openjdk-11-jre amd64 11.0.6+10-2ubuntu2 [34.6 kB] Get:123 http://ftpmaster.internal/ubuntu focal/main amd64 default-jre amd64 2:1.11-72 [1084 B] Get:124 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 openjdk-11-jdk-headless amd64 11.0.6+10-2ubuntu2 [217 MB] Get:125 http://ftpmaster.internal/ubuntu focal/main amd64 default-jdk-headless amd64 2:1.11-72 [1140 B] Get:126 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 openjdk-11-jdk amd64 11.0.6+10-2ubuntu2 [4739 kB] Get:127 http://ftpmaster.internal/ubuntu focal/main amd64 default-jdk amd64 2:1.11-72 [1096 B] Get:128 http://ftpmaster.internal/ubuntu focal/main amd64 fontconfig amd64 2.13.1-2ubuntu2 [171 kB] Get:129 http://ftpmaster.internal/ubuntu focal/universe amd64 fonts-lmodern all 2.004.5-6 [4532 kB] Get:130 http://ftpmaster.internal/ubuntu focal/main amd64 libgfortran5 amd64 10-20200211-1ubuntu1 [728 kB] Get:131 http://ftpmaster.internal/ubuntu focal/main amd64 libgfortran-9-dev amd64 9.2.1-29ubuntu1 [685 kB] Get:132 http://ftpmaster.internal/ubuntu focal/main amd64 gfortran-9 amd64 9.2.1-29ubuntu1 [7910 kB] Get:133 http://ftpmaster.internal/ubuntu focal/main amd64 gfortran amd64 4:9.2.1-3.1ubuntu1 [1376 B] Get:134 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 gir1.2-freedesktop amd64 1.63.2-1 [19.2 kB] Get:135 http://ftpmaster.internal/ubuntu focal/main amd64 libgraphite2-3 amd64 1.3.13-11 [73.7 kB] Get:136 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libharfbuzz0b amd64 2.6.4-1ubuntu2 [391 kB] Get:137 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 gir1.2-harfbuzz-0.0 amd64 2.6.4-1ubuntu2 [26.4 kB] Get:138 http://ftpmaster.internal/ubuntu focal/main amd64 libthai-data all 0.1.28-3 [134 kB] Get:139 http://ftpmaster.internal/ubuntu focal/main amd64 libdatrie1 amd64 0.2.12-3 [18.7 kB] Get:140 http://ftpmaster.internal/ubuntu focal/main amd64 libthai0 amd64 0.1.28-3 [18.1 kB] Get:141 http://ftpmaster.internal/ubuntu focal/main amd64 libpango-1.0-0 amd64 1.44.7-1ubuntu2 [161 kB] Get:142 http://ftpmaster.internal/ubuntu focal/main amd64 libpixman-1-0 amd64 0.38.4-0ubuntu1 [227 kB] Get:143 http://ftpmaster.internal/ubuntu focal/main amd64 libxcb-render0 amd64 1.13.1-5build1 [14.9 kB] Get:144 http://ftpmaster.internal/ubuntu focal/main amd64 libxcb-shm0 amd64 1.13.1-5build1 [5588 B] Get:145 http://ftpmaster.internal/ubuntu focal/main amd64 libcairo2 amd64 1.16.0-4ubuntu1 [583 kB] Get:146 http://ftpmaster.internal/ubuntu focal/main amd64 libpangoft2-1.0-0 amd64 1.44.7-1ubuntu2 [35.1 kB] Get:147 http://ftpmaster.internal/ubuntu focal/main amd64 libpangocairo-1.0-0 amd64 1.44.7-1ubuntu2 [24.8 kB] Get:148 http://ftpmaster.internal/ubuntu focal/main amd64 libxft2 amd64 2.3.3-0ubuntu1 [39.2 kB] Get:149 http://ftpmaster.internal/ubuntu focal/main amd64 libpangoxft-1.0-0 amd64 1.44.7-1ubuntu2 [18.0 kB] Get:150 http://ftpmaster.internal/ubuntu focal/main amd64 gir1.2-pango-1.0 amd64 1.44.7-1ubuntu2 [26.6 kB] Get:151 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 icu-devtools amd64 65.1-1ubuntu2 [188 kB] Get:152 http://ftpmaster.internal/ubuntu focal/universe amd64 libapache-pom-java all 18-1 [4720 B] Get:153 http://ftpmaster.internal/ubuntu focal/main amd64 libroken18-heimdal amd64 7.7.0+dfsg-1 [41.9 kB] Get:154 http://ftpmaster.internal/ubuntu focal/main amd64 libasn1-8-heimdal amd64 7.7.0+dfsg-1 [181 kB] Get:155 http://ftpmaster.internal/ubuntu focal/main amd64 libblas3 amd64 3.9.0-1 [142 kB] Get:156 http://ftpmaster.internal/ubuntu focal/main amd64 libblas-dev amd64 3.9.0-1 [147 kB] Get:157 http://ftpmaster.internal/ubuntu focal/main amd64 libbrotli1 amd64 1.0.7-6build1 [270 kB] Get:158 http://ftpmaster.internal/ubuntu focal/main amd64 libbz2-dev amd64 1.0.8-2 [30.2 kB] Get:159 http://ftpmaster.internal/ubuntu focal/main amd64 libcairo-gobject2 amd64 1.16.0-4ubuntu1 [17.2 kB] Get:160 http://ftpmaster.internal/ubuntu focal/main amd64 liblzo2-2 amd64 2.10-2 [50.8 kB] Get:161 http://ftpmaster.internal/ubuntu focal/main amd64 libcairo-script-interpreter2 amd64 1.16.0-4ubuntu1 [54.2 kB] Get:162 http://ftpmaster.internal/ubuntu focal/main amd64 libexpat1-dev amd64 2.2.9-1 [116 kB] Get:163 http://ftpmaster.internal/ubuntu focal/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1ubuntu3 [172 kB] Get:164 http://ftpmaster.internal/ubuntu focal/main amd64 libpng-dev amd64 1.6.37-2 [175 kB] Get:165 http://ftpmaster.internal/ubuntu focal/main amd64 libfreetype-dev amd64 2.10.1-2 [493 kB] Get:166 http://ftpmaster.internal/ubuntu focal/main amd64 libfreetype6-dev amd64 2.10.1-2 [9792 B] Get:167 http://ftpmaster.internal/ubuntu focal/main amd64 uuid-dev amd64 2.34-0.1ubuntu7 [33.6 kB] Get:168 http://ftpmaster.internal/ubuntu focal/main amd64 pkg-config amd64 0.29.1-0ubuntu4 [45.5 kB] Get:169 http://ftpmaster.internal/ubuntu focal/main amd64 libfontconfig1-dev amd64 2.13.1-2ubuntu2 [732 kB] Get:170 http://ftpmaster.internal/ubuntu focal/main amd64 xorg-sgml-doctools all 1:1.11-1 [12.9 kB] Get:171 http://ftpmaster.internal/ubuntu focal/main amd64 x11proto-dev all 2018.4-4 [251 kB] Get:172 http://ftpmaster.internal/ubuntu focal/main amd64 x11proto-core-dev all 2018.4-4 [2620 B] Get:173 http://ftpmaster.internal/ubuntu focal/main amd64 libxau-dev amd64 1:1.0.9-0ubuntu1 [9552 B] Get:174 http://ftpmaster.internal/ubuntu focal/main amd64 libxdmcp-dev amd64 1:1.1.3-0ubuntu1 [25.3 kB] Get:175 http://ftpmaster.internal/ubuntu focal/main amd64 xtrans-dev all 1.3.5-1build1 [70.7 kB] Get:176 http://ftpmaster.internal/ubuntu focal/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5384 B] Get:177 http://ftpmaster.internal/ubuntu focal/main amd64 libxcb1-dev amd64 1.13.1-5build1 [80.6 kB] Get:178 http://ftpmaster.internal/ubuntu focal/main amd64 libx11-dev amd64 2:1.6.8-1 [645 kB] Get:179 http://ftpmaster.internal/ubuntu focal/main amd64 libxrender-dev amd64 1:0.9.10-1 [24.9 kB] Get:180 http://ftpmaster.internal/ubuntu focal/main amd64 x11proto-xext-dev all 2018.4-4 [2620 B] Get:181 http://ftpmaster.internal/ubuntu focal/main amd64 libxext-dev amd64 2:1.3.4-0ubuntu1 [82.2 kB] Get:182 http://ftpmaster.internal/ubuntu focal/main amd64 libice6 amd64 2:1.0.10-0ubuntu1 [41.0 kB] Get:183 http://ftpmaster.internal/ubuntu focal/main amd64 libsm6 amd64 2:1.2.3-1 [16.1 kB] Get:184 http://ftpmaster.internal/ubuntu focal/main amd64 libice-dev amd64 2:1.0.10-0ubuntu1 [47.8 kB] Get:185 http://ftpmaster.internal/ubuntu focal/main amd64 libsm-dev amd64 2:1.2.3-1 [17.0 kB] Get:186 http://ftpmaster.internal/ubuntu focal/main amd64 libpixman-1-dev amd64 0.38.4-0ubuntu1 [243 kB] Get:187 http://ftpmaster.internal/ubuntu focal/main amd64 libxcb-render0-dev amd64 1.13.1-5build1 [18.5 kB] Get:188 http://ftpmaster.internal/ubuntu focal/main amd64 libxcb-shm0-dev amd64 1.13.1-5build1 [6728 B] Get:189 http://ftpmaster.internal/ubuntu focal/main amd64 libffi-dev amd64 3.3-3 [56.9 kB] Get:190 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libglib2.0-bin amd64 2.63.5-2 [72.5 kB] Get:191 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 python3-lib2to3 all 3.8.0-1ubuntu1 [74.1 kB] Get:192 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 python3-distutils all 3.8.0-1ubuntu1 [140 kB] Get:193 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libglib2.0-dev-bin amd64 2.63.5-2 [107 kB] Get:194 http://ftpmaster.internal/ubuntu focal/main amd64 libblkid-dev amd64 2.34-0.1ubuntu7 [167 kB] Get:195 http://ftpmaster.internal/ubuntu focal/main amd64 libmount-dev amd64 2.34-0.1ubuntu7 [176 kB] Get:196 http://ftpmaster.internal/ubuntu focal/main amd64 libpcre16-3 amd64 2:8.39-12 [149 kB] Get:197 http://ftpmaster.internal/ubuntu focal/main amd64 libpcre32-3 amd64 2:8.39-12 [140 kB] Get:198 http://ftpmaster.internal/ubuntu focal/main amd64 libpcrecpp0v5 amd64 2:8.39-12 [15.4 kB] Get:199 http://ftpmaster.internal/ubuntu focal/main amd64 libpcre3-dev amd64 2:8.39-12 [542 kB] Get:200 http://ftpmaster.internal/ubuntu focal/main amd64 libsepol1-dev amd64 3.0-1 [325 kB] Get:201 http://ftpmaster.internal/ubuntu focal/main amd64 libpcre2-16-0 amd64 10.34-7 [181 kB] Get:202 http://ftpmaster.internal/ubuntu focal/main amd64 libpcre2-32-0 amd64 10.34-7 [169 kB] Get:203 http://ftpmaster.internal/ubuntu focal/main amd64 libpcre2-posix2 amd64 10.34-7 [5992 B] Get:204 http://ftpmaster.internal/ubuntu focal/main amd64 libpcre2-dev amd64 10.34-7 [670 kB] Get:205 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libselinux1-dev amd64 3.0-1build1 [151 kB] Get:206 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libglib2.0-dev amd64 2.63.5-2 [1501 kB] Get:207 http://ftpmaster.internal/ubuntu focal/main amd64 libcairo2-dev amd64 1.16.0-4ubuntu1 [627 kB] Get:208 http://ftpmaster.internal/ubuntu focal/universe amd64 libcommons-parent-java all 43-1 [10.8 kB] Get:209 http://ftpmaster.internal/ubuntu focal/universe amd64 libcommons-logging-java all 1.2-2 [60.3 kB] Get:210 http://ftpmaster.internal/ubuntu focal/main amd64 libheimbase1-heimdal amd64 7.7.0+dfsg-1 [29.7 kB] Get:211 http://ftpmaster.internal/ubuntu focal/main amd64 libhcrypto4-heimdal amd64 7.7.0+dfsg-1 [87.8 kB] Get:212 http://ftpmaster.internal/ubuntu focal/main amd64 libwind0-heimdal amd64 7.7.0+dfsg-1 [47.9 kB] Get:213 http://ftpmaster.internal/ubuntu focal/main amd64 libhx509-5-heimdal amd64 7.7.0+dfsg-1 [107 kB] Get:214 http://ftpmaster.internal/ubuntu focal/main amd64 libkrb5-26-heimdal amd64 7.7.0+dfsg-1 [207 kB] Get:215 http://ftpmaster.internal/ubuntu focal/main amd64 libheimntlm0-heimdal amd64 7.7.0+dfsg-1 [15.1 kB] Get:216 http://ftpmaster.internal/ubuntu focal/main amd64 libgssapi3-heimdal amd64 7.7.0+dfsg-1 [96.6 kB] Get:217 http://ftpmaster.internal/ubuntu focal/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2 [14.9 kB] Get:218 http://ftpmaster.internal/ubuntu focal/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2 [49.3 kB] Get:219 http://ftpmaster.internal/ubuntu focal/main amd64 libldap-common all 2.4.49+dfsg-1ubuntu1 [17.2 kB] Get:220 http://ftpmaster.internal/ubuntu focal/main amd64 libldap-2.4-2 amd64 2.4.49+dfsg-1ubuntu1 [155 kB] Get:221 http://ftpmaster.internal/ubuntu focal/main amd64 libnghttp2-14 amd64 1.40.0-1 [78.1 kB] Get:222 http://ftpmaster.internal/ubuntu focal/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build1 [54.9 kB] Get:223 http://ftpmaster.internal/ubuntu focal/main amd64 libssh-4 amd64 0.9.3-2ubuntu1 [170 kB] Get:224 http://ftpmaster.internal/ubuntu focal/main amd64 libcurl4 amd64 7.67.0-2ubuntu1 [232 kB] Get:225 http://ftpmaster.internal/ubuntu focal/main amd64 libcurl4-openssl-dev amd64 7.67.0-2ubuntu1 [319 kB] Get:226 http://ftpmaster.internal/ubuntu focal/main amd64 libdatrie-dev amd64 0.2.12-3 [17.6 kB] Get:227 http://ftpmaster.internal/ubuntu focal/main amd64 libfontenc1 amd64 1:1.1.4-0ubuntu1 [14.0 kB] Get:228 http://ftpmaster.internal/ubuntu focal/main amd64 libfribidi-dev amd64 1.0.8-2 [62.3 kB] Get:229 http://ftpmaster.internal/ubuntu focal/main amd64 libgraphite2-dev amd64 1.3.13-11 [14.7 kB] Get:230 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libharfbuzz-icu0 amd64 2.6.4-1ubuntu2 [5584 B] Get:231 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libharfbuzz-gobject0 amd64 2.6.4-1ubuntu2 [20.4 kB] Get:232 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libicu-dev amd64 65.1-1ubuntu2 [9434 kB] Get:233 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libharfbuzz-dev amd64 2.6.4-1ubuntu2 [526 kB] Get:234 http://ftpmaster.internal/ubuntu focal/main amd64 libjpeg-turbo8-dev amd64 2.0.3-0ubuntu1 [238 kB] Get:235 http://ftpmaster.internal/ubuntu focal/main amd64 libjpeg8-dev amd64 8c-2ubuntu8 [1552 B] Get:236 http://ftpmaster.internal/ubuntu focal/main amd64 libjpeg-dev amd64 8c-2ubuntu8 [1546 B] Get:237 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libkpathsea6 amd64 2019.20190605.51237-3build1 [57.1 kB] Get:238 http://ftpmaster.internal/ubuntu focal/main amd64 liblapack3 amd64 3.9.0-1 [2155 kB] Get:239 http://ftpmaster.internal/ubuntu focal/main amd64 liblapack-dev amd64 3.9.0-1 [4243 kB] Get:240 http://ftpmaster.internal/ubuntu focal/universe amd64 libmime-charset-perl all 1.012.2-1 [30.9 kB] Get:241 http://ftpmaster.internal/ubuntu focal/main amd64 libncurses-dev amd64 6.1+20191019-1ubuntu1 [339 kB] Get:242 http://ftpmaster.internal/ubuntu focal/main amd64 libncurses5-dev amd64 6.1+20191019-1ubuntu1 [992 B] Get:243 http://ftpmaster.internal/ubuntu focal/main amd64 libthai-dev amd64 0.1.28-3 [24.5 kB] Get:244 http://ftpmaster.internal/ubuntu focal/main amd64 libxft-dev amd64 2.3.3-0ubuntu1 [49.1 kB] Get:245 http://ftpmaster.internal/ubuntu focal/main amd64 pango1.0-tools amd64 1.44.7-1ubuntu2 [26.2 kB] Get:246 http://ftpmaster.internal/ubuntu focal/main amd64 libpango1.0-dev amd64 1.44.7-1ubuntu2 [132 kB] Get:247 http://ftpmaster.internal/ubuntu focal/main amd64 libpaper1 amd64 1.1.28 [13.0 kB] Get:248 http://ftpmaster.internal/ubuntu focal/main amd64 libpaper-utils amd64 1.1.28 [8400 B] Get:249 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libptexenc1 amd64 2019.20190605.51237-3build1 [35.5 kB] Get:250 http://ftpmaster.internal/ubuntu focal/main amd64 libreadline-dev amd64 8.0-3 [141 kB] Get:251 http://ftpmaster.internal/ubuntu focal/universe amd64 libsombok3 amd64 2.4.0-2 [26.9 kB] Get:252 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libsynctex2 amd64 2019.20190605.51237-3build1 [54.9 kB] Get:253 http://ftpmaster.internal/ubuntu focal/main amd64 libtcl8.6 amd64 8.6.10+dfsg-1 [902 kB] Get:254 http://ftpmaster.internal/ubuntu focal/universe amd64 libteckit0 amd64 2.5.8+ds2-5ubuntu1 [317 kB] Get:255 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libtexlua53 amd64 2019.20190605.51237-3build1 [105 kB] Get:256 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libtexluajit2 amd64 2019.20190605.51237-3build1 [235 kB] Get:257 http://ftpmaster.internal/ubuntu focal/universe amd64 libtext-unidecode-perl all 1.30-1 [99.0 kB] Get:258 http://ftpmaster.internal/ubuntu focal/main amd64 libjbig0 amd64 2.1-3.1build1 [26.7 kB] Get:259 http://ftpmaster.internal/ubuntu focal/main amd64 libjbig-dev amd64 2.1-3.1build1 [25.2 kB] Get:260 http://ftpmaster.internal/ubuntu focal/main amd64 liblzma-dev amd64 5.2.4-1 [145 kB] Get:261 http://ftpmaster.internal/ubuntu focal/main amd64 libwebp6 amd64 0.6.1-2 [185 kB] Get:262 http://ftpmaster.internal/ubuntu focal/main amd64 libtiff5 amd64 4.1.0+git191117-2 [162 kB] Get:263 http://ftpmaster.internal/ubuntu focal/main amd64 libtiffxx5 amd64 4.1.0+git191117-2 [5944 B] Get:264 http://ftpmaster.internal/ubuntu focal/main amd64 libtiff-dev amd64 4.1.0+git191117-2 [284 kB] Get:265 http://ftpmaster.internal/ubuntu focal/main amd64 libtiff5-dev amd64 4.1.0+git191117-2 [2256 B] Get:266 http://ftpmaster.internal/ubuntu focal/main amd64 libxss1 amd64 1:1.2.3-1 [8140 B] Get:267 http://ftpmaster.internal/ubuntu focal/main amd64 libtk8.6 amd64 8.6.10-1 [714 kB] Get:268 http://ftpmaster.internal/ubuntu focal/universe amd64 libunicode-linebreak-perl amd64 0.0.20190101-1build1 [96.9 kB] Get:269 http://ftpmaster.internal/ubuntu focal/main amd64 libunwind8 amd64 1.2.1-9 [47.0 kB] Get:270 http://ftpmaster.internal/ubuntu focal/main amd64 libxt6 amd64 1:1.1.5-1 [160 kB] Get:271 http://ftpmaster.internal/ubuntu focal/main amd64 libxmu6 amd64 2:1.1.3-0ubuntu1 [45.8 kB] Get:272 http://ftpmaster.internal/ubuntu focal/main amd64 libxpm4 amd64 1:3.5.12-1 [34.0 kB] Get:273 http://ftpmaster.internal/ubuntu focal/main amd64 libxaw7 amd64 2:1.0.13-1 [173 kB] Get:274 http://ftpmaster.internal/ubuntu focal/main amd64 libxfont2 amd64 1:2.0.3-1 [91.7 kB] Get:275 http://ftpmaster.internal/ubuntu focal/main amd64 libxkbfile1 amd64 1:1.1.0-0ubuntu1 [65.1 kB] Get:276 http://ftpmaster.internal/ubuntu focal/main amd64 libxml-namespacesupport-perl all 1.12-1 [13.2 kB] Get:277 http://ftpmaster.internal/ubuntu focal/main amd64 libxml-sax-base-perl all 1.09-1 [18.8 kB] Get:278 http://ftpmaster.internal/ubuntu focal/main amd64 libxml-sax-perl all 1.02+dfsg-1 [56.2 kB] Get:279 http://ftpmaster.internal/ubuntu focal/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1build1 [320 kB] Get:280 http://ftpmaster.internal/ubuntu focal/main amd64 x11proto-scrnsaver-dev all 2018.4-4 [2628 B] Get:281 http://ftpmaster.internal/ubuntu focal/main amd64 libxss-dev amd64 1:1.2.3-1 [11.9 kB] Get:282 http://ftpmaster.internal/ubuntu focal/main amd64 libxt-dev amd64 1:1.1.5-1 [395 kB] Get:283 http://ftpmaster.internal/ubuntu focal/universe amd64 libzzip-0-13 amd64 0.13.62-3.2 [25.8 kB] Get:284 http://ftpmaster.internal/ubuntu focal/universe amd64 mpack amd64 1.6-8.2 [35.5 kB] Get:285 http://ftpmaster.internal/ubuntu focal/universe amd64 preview-latex-style all 11.91-2ubuntu1 [185 kB] Get:286 http://ftpmaster.internal/ubuntu focal/main amd64 t1utils amd64 1.41-3 [56.1 kB] Get:287 http://ftpmaster.internal/ubuntu focal/main amd64 tcl8.6 amd64 8.6.10+dfsg-1 [14.8 kB] Get:288 http://ftpmaster.internal/ubuntu focal/main amd64 tcl8.6-dev amd64 8.6.10+dfsg-1 [905 kB] Get:289 http://ftpmaster.internal/ubuntu focal/universe amd64 texinfo amd64 6.7.0.dfsg.2-5 [1375 kB] Get:290 http://ftpmaster.internal/ubuntu focal-proposed/universe amd64 texlive-binaries amd64 2019.20190605.51237-3build1 [8038 kB] Get:291 http://ftpmaster.internal/ubuntu focal/main amd64 xdg-utils all 1.1.3-1ubuntu2 [60.5 kB] Get:292 http://ftpmaster.internal/ubuntu focal/universe amd64 texlive-base all 2019.20200218-1 [20.8 MB] Get:293 http://ftpmaster.internal/ubuntu focal/universe amd64 texlive-latex-base all 2019.20200218-1 [990 kB] Get:294 http://ftpmaster.internal/ubuntu focal/universe amd64 texlive-extra-utils all 2019.202000218-1 [43.6 MB] Get:295 http://ftpmaster.internal/ubuntu focal/universe amd64 texlive-fonts-extra all 2019.202000218-1 [460 MB] Get:296 http://ftpmaster.internal/ubuntu focal/universe amd64 texlive-fonts-recommended all 2019.20200218-1 [4972 kB] Get:297 http://ftpmaster.internal/ubuntu focal/universe amd64 libfontbox-java all 1:1.8.16-2 [207 kB] Get:298 http://ftpmaster.internal/ubuntu focal/universe amd64 libpdfbox-java all 1:1.8.16-2 [5199 kB] Get:299 http://ftpmaster.internal/ubuntu focal/universe amd64 texlive-latex-recommended all 2019.20200218-1 [15.7 MB] Get:300 http://ftpmaster.internal/ubuntu focal/universe amd64 texlive-pictures all 2019.20200218-1 [4492 kB] Get:301 http://ftpmaster.internal/ubuntu focal/universe amd64 texlive-latex-extra all 2019.202000218-1 [12.5 MB] Get:302 http://ftpmaster.internal/ubuntu focal/universe amd64 texlive-plain-generic all 2019.202000218-1 [24.6 MB] Get:303 http://ftpmaster.internal/ubuntu focal/main amd64 tk8.6 amd64 8.6.10-1 [12.5 kB] Get:304 http://ftpmaster.internal/ubuntu focal/main amd64 tk8.6-dev amd64 8.6.10-1 [711 kB] Get:305 http://ftpmaster.internal/ubuntu focal/main amd64 x11-xkb-utils amd64 7.7+4 [160 kB] Get:306 http://ftpmaster.internal/ubuntu focal/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu1 [573 kB] Get:307 http://ftpmaster.internal/ubuntu focal/main amd64 xfonts-utils amd64 1:7.7+6 [91.5 kB] Get:308 http://ftpmaster.internal/ubuntu focal/main amd64 xfonts-base all 1:1.0.5 [5896 kB] Get:309 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 xserver-common all 2:1.20.7-2ubuntu2 [27.0 kB] Get:310 http://ftpmaster.internal/ubuntu focal-proposed/universe amd64 xvfb amd64 2:1.20.7-2ubuntu2 [778 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 975 MB in 17s (58.2 MB/s) Selecting previously unselected package libpython3.8-minimal:amd64. (Reading database ... 14676 files and directories currently installed.) Preparing to unpack .../libpython3.8-minimal_3.8.2~rc2-2_amd64.deb ... Unpacking libpython3.8-minimal:amd64 (3.8.2~rc2-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.2.9-1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.9-1) ... Selecting previously unselected package python3.8-minimal. Preparing to unpack .../python3.8-minimal_3.8.2~rc2-2_amd64.deb ... Unpacking python3.8-minimal (3.8.2~rc2-2) ... Setting up libpython3.8-minimal:amd64 (3.8.2~rc2-2) ... Setting up libexpat1:amd64 (2.2.9-1) ... Setting up python3.8-minimal (3.8.2~rc2-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 14967 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.8.0-3ubuntu1_amd64.deb ... Unpacking python3-minimal (3.8.0-3ubuntu1) ... Selecting previously unselected package mime-support. 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Setting up python3-minimal (3.8.0-3ubuntu1) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Selecting previously unselected package python3. (Reading database ... 15369 files and directories currently installed.) Preparing to unpack .../000-python3_3.8.0-3ubuntu1_amd64.deb ... Unpacking python3 (3.8.0-3ubuntu1) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../001-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../002-bsdmainutils_11.1.2ubuntu2_amd64.deb ... Unpacking bsdmainutils (11.1.2ubuntu2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../003-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... 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Setting up libsensors-config (1:3.6.0-2ubuntu1) ... Setting up libicu65:amd64 (65.1-1ubuntu2) ... Setting up libnghttp2-14:amd64 (1.40.0-1) ... Setting up libmagic1:amd64 (1:5.38-4) ... Setting up libsepol1-dev:amd64 (3.0-1) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up gettext-base (0.19.8.1-10) ... Setting up xkb-data (2.26-2ubuntu4) ... Setting up liblzo2-2:amd64 (2.10-2) ... Setting up libzzip-0-13:amd64 (0.13.62-3.2) ... Setting up file (1:5.38-4) ... Setting up libreadline-dev:amd64 (8.0-3) ... Setting up libffi-dev:amd64 (3.3-3) ... Setting up libldap-common (2.4.49+dfsg-1ubuntu1) ... Setting up libunwind8:amd64 (1.2.1-9) ... Setting up libpthread-stubs0-dev:amd64 (0.4-1) ... Setting up libjbig0:amd64 (2.1-3.1build1) ... Setting up libpcre2-16-0:amd64 (10.34-7) ... Setting up libkrb5support0:amd64 (1.17-6ubuntu4) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2) ... Setting up libasound2-data (1.2.1.2-2ubuntu2) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up xtrans-dev (1.3.5-1build1) ... Setting up libgraphite2-dev:amd64 (1.3.13-11) ... Setting up libfontenc1:amd64 (1:1.1.4-0ubuntu1) ... Setting up autotools-dev (20180224.1) ... Setting up libpcre2-32-0:amd64 (10.34-7) ... Setting up libblas3:amd64 (3.9.0-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libglib2.0-data (2.63.5-2) ... Setting up libexpat1-dev:amd64 (2.2.9-1) ... Setting up libfreetype6:amd64 (2.10.1-2) ... Setting up libx11-data (2:1.6.8-1) ... Setting up libnspr4:amd64 (2:4.24-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build1) ... Setting up libteckit0:amd64 (2.5.8+ds2-5ubuntu1) ... Setting up bash-completion (1:2.10-1ubuntu1) ... Setting up uuid-dev:amd64 (2.34-0.1ubuntu7) ... Setting up libapache-pom-java (18-1) ... Setting up libavahi-common-data:amd64 (0.7-4ubuntu6) ... Setting up libdbus-1-3:amd64 (1.12.16-2ubuntu2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up xfonts-encodings (1:1.0.5-0ubuntu1) ... Setting up libfribidi0:amd64 (1.0.8-2) ... Setting up t1utils (1.41-3) ... Setting up libpcre32-3:amd64 (2:8.39-12) ... Setting up libtcl8.6:amd64 (8.6.10+dfsg-1) ... Setting up autopoint (0.19.8.1-10) ... Setting up libwebp6:amd64 (0.6.1-2) ... Setting up icu-devtools (65.1-1ubuntu2) ... Setting up pkg-config (0.29.1-0ubuntu4) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libpcsclite1:amd64 (1.8.26-3) ... Setting up ucf (3.0038+nmu1) ... Setting up libpcre2-posix2:amd64 (10.34-7) ... Setting up libsensors5:amd64 (1:3.6.0-2ubuntu1) ... Setting up libk5crypto3:amd64 (1.17-6ubuntu4) ... Setting up libjpeg-turbo8:amd64 (2.0.3-0ubuntu1) ... Setting up libglapi-mesa:amd64 (20.0.0-1ubuntu1) ... Setting up libkpathsea6:amd64 (2019.20190605.51237-3build1) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2) ... Setting up libgfortran5:amd64 (10-20200211-1ubuntu1) ... Setting up libvulkan1:amd64 (1.2.131.2-1) ... Setting up libroken18-heimdal:amd64 (7.7.0+dfsg-1) ... Setting up liblzma-dev:amd64 (5.2.4-1) ... Setting up libgif7:amd64 (5.1.9-1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-1ubuntu3) ... Setting up libdatrie-dev:amd64 (0.2.12-3) ... Setting up libxshmfence1:amd64 (1.3-1) ... Setting up libmime-charset-perl (1.012.2-1) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libasound2:amd64 (1.2.1.2-2ubuntu2) ... Setting up libncurses5-dev:amd64 (6.1+20191019-1ubuntu1) ... Setting up fonts-lmodern (2.004.5-6) ... Setting up libsub-override-perl (0.09-2) ... Setting up libharfbuzz0b:amd64 (2.6.4-1ubuntu2) ... Setting up libthai-data (0.1.28-3) ... Setting up libgirepository-1.0-1:amd64 (1.63.2-1) ... Setting up xorg-sgml-doctools (1:1.11-1) ... Setting up libkrb5-3:amd64 (1.17-6ubuntu4) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up libpython3.8-stdlib:amd64 (3.8.2~rc2-2) ... Setting up libtext-unidecode-perl (1.30-1) ... Setting up python3.8 (3.8.2~rc2-2) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up libdrm-common (2.4.100-4) ... Setting up libelf1:amd64 (0.176-1.1build1) ... Setting up libxfont2:amd64 (1:2.0.3-1) ... Setting up libicu-dev:amd64 (65.1-1ubuntu2) ... Setting up libxml2:amd64 (2.9.10+dfsg-1ubuntu2) ... Setting up xdg-utils (1.1.3-1ubuntu2) ... Setting up libblas-dev:amd64 (3.9.0-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libsynctex2:amd64 (2019.20190605.51237-3build1) ... Setting up libpython3-stdlib:amd64 (3.8.0-3ubuntu1) ... Setting up libheimbase1-heimdal:amd64 (7.7.0+dfsg-1) ... Setting up libbz2-dev:amd64 (1.0.8-2) ... Setting up libjpeg8:amd64 (8c-2ubuntu8) ... Setting up x11proto-dev (2018.4-4) ... Setting up libfile-stripnondeterminism-perl (1.6.3-2) ... Setting up libblkid-dev:amd64 (2.34-0.1ubuntu7) ... Setting up libpaper1:amd64 (1.1.28) ... Creating config file /etc/papersize with new version Setting up libice6:amd64 (2:1.0.10-0ubuntu1) ... Setting up libjpeg-turbo8-dev:amd64 (2.0.3-0ubuntu1) ... Setting up libxdmcp6:amd64 (1:1.1.3-0ubuntu1) ... Setting up tcl8.6 (8.6.10+dfsg-1) ... Setting up liblapack3:amd64 (3.9.0-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.13.1-5build1) ... Setting up libharfbuzz-icu0:amd64 (2.6.4-1ubuntu2) ... Setting up libpdfbox-java (1:1.8.16-2) ... Setting up libxau-dev:amd64 (1:1.0.9-0ubuntu1) ... Setting up libpcre2-dev:amd64 (10.34-7) ... Setting up libice-dev:amd64 (2:1.0.10-0ubuntu1) ... Setting up libtool (2.4.6-13) ... Setting up libxcb-render0:amd64 (1.13.1-5build1) ... Setting up libselinux1-dev:amd64 (3.0-1build1) ... Setting up libpcre3-dev:amd64 (2:8.39-12) ... Setting up fontconfig-config (2.13.1-2ubuntu2) ... Setting up libfribidi-dev:amd64 (1.0.8-2) ... Setting up libxcb-glx0:amd64 (1.13.1-5build1) ... Setting up libasn1-8-heimdal:amd64 (7.7.0+dfsg-1) ... Setting up tcl8.6-dev:amd64 (8.6.10+dfsg-1) ... Setting up libedit2:amd64 (3.1-20191231-1) ... Setting up libpng-dev:amd64 (1.6.37-2) ... Setting up libcommons-parent-java (43-1) ... Setting up libavahi-common3:amd64 (0.7-4ubuntu6) ... Setting up libjbig-dev:amd64 (2.1-3.1build1) ... Setting up libcommons-logging-java (1.2-2) ... Setting up libgfortran-9-dev:amd64 (9.2.1-29ubuntu1) ... Setting up libglib2.0-bin (2.63.5-2) ... Setting up m4 (1.4.18-4) ... Setting up python3 (3.8.0-3ubuntu1) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up libnss3:amd64 (2:3.49.1-1ubuntu1) ... Setting up libxcb-shm0:amd64 (1.13.1-5build1) ... Setting up libharfbuzz-gobject0:amd64 (2.6.4-1ubuntu2) ... Setting up libpaper-utils (1.1.28) ... Setting up xfonts-utils (1:7.7+6) ... Setting up libxml-sax-perl (1.02+dfsg-1) ... 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 libhcrypto4-heimdal:amd64 (7.7.0+dfsg-1) ... Setting up libfreetype-dev:amd64 (2.10.1-2) ... Setting up libxcb-present0:amd64 (1.13.1-5build1) ... Setting up tex-common (6.13) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libthai0:amd64 (0.1.28-3) ... Setting up libxdmcp-dev:amd64 (1:1.1.3-0ubuntu1) ... Setting up libwind0-heimdal:amd64 (7.7.0+dfsg-1) ... Setting up xfonts-base (1:1.0.5) ... Setting up libptexenc1:amd64 (2019.20190605.51237-3build1) ... Setting up libxcb-sync1:amd64 (1.13.1-5build1) ... Setting up x11proto-core-dev (2018.4-4) ... Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up liblapack-dev:amd64 (3.9.0-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-6ubuntu4) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up gir1.2-glib-2.0:amd64 (1.63.2-1) ... Setting up libssh-4:amd64 (0.9.3-2ubuntu1) ... Setting up autoconf (2.69-11.1) ... Setting up libthai-dev:amd64 (0.1.28-3) ... Setting up libxml-libxml-perl (2.0134+dfsg-1build1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxcb-dri2-0:amd64 (1.13.1-5build1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up x11proto-xext-dev (2018.4-4) ... Setting up libdrm2:amd64 (2.4.100-4) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up bison (2:3.5.1+dfsg-1) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up libx11-6:amd64 (2:1.6.8-1) ... Setting up libtiff5:amd64 (4.1.0+git191117-2) ... Setting up libfontconfig1:amd64 (2.13.1-2ubuntu2) ... Setting up libxkbfile1:amd64 (1:1.1.0-0ubuntu1) ... Setting up libjpeg8-dev:amd64 (8c-2ubuntu8) ... Setting up x11proto-scrnsaver-dev (2018.4-4) ... Setting up python3-lib2to3 (3.8.0-1ubuntu1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libavahi-client3:amd64 (0.7-4ubuntu6) ... Setting up libmount-dev:amd64 (2.34-0.1ubuntu7) ... Setting up libllvm9:amd64 (1:9.0.1-8build2) ... Setting up libxmuu1:amd64 (2:1.1.3-0ubuntu1) ... Setting up libtiffxx5:amd64 (4.1.0+git191117-2) ... Setting up libdrm-amdgpu1:amd64 (2.4.100-4) ... Setting up automake (1:1.16.1-4ubuntu6) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3-distutils (3.8.0-1ubuntu1) ... Setting up libxcb-dri3-0:amd64 (1.13.1-5build1) ... Setting up libglib2.0-dev-bin (2.63.5-2) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up fontconfig (2.13.1-2ubuntu2) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:amd64 (2.4.100-4) ... Setting up gettext (0.19.8.1-10) ... Setting up gir1.2-freedesktop:amd64 (1.63.2-1) ... Setting up libxdamage1:amd64 (1:1.1.5-1) ... Setting up libxcb1-dev:amd64 (1.13.1-5build1) ... Setting up libxpm4:amd64 (1:3.5.12-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up gfortran-9 (9.2.1-29ubuntu1) ... Setting up libsombok3:amd64 (2.4.0-2) ... Setting up libsm-dev:amd64 (2:1.2.3-1) ... Setting up libdrm-radeon1:amd64 (2.4.100-4) ... Setting up libhx509-5-heimdal:amd64 (7.7.0+dfsg-1) ... Setting up preview-latex-style (11.91-2ubuntu1) ... Setting up libpango-1.0-0:amd64 (1.44.7-1ubuntu2) ... Setting up libdrm-intel1:amd64 (2.4.100-4) ... Setting up libgl1-mesa-dri:amd64 (20.0.0-1ubuntu1) ... Setting up libjpeg-dev:amd64 (8c-2ubuntu8) ... Setting up libx11-dev:amd64 (2:1.6.8-1) ... Setting up libxext6:amd64 (2:1.3.4-0ubuntu1) ... Setting up man-db (2.9.0-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up gir1.2-harfbuzz-0.0:amd64 (2.6.4-1ubuntu2) ... Setting up gfortran (4:9.2.1-3.1ubuntu1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libcairo2:amd64 (1.16.0-4ubuntu1) ... Setting up libfreetype6-dev:amd64 (2.10.1-2) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1build1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxcb-shm0-dev:amd64 (1.13.1-5build1) ... Setting up libglib2.0-dev:amd64 (2.63.5-2) ... Setting up libtiff-dev:amd64 (4.1.0+git191117-2) ... Setting up libxfixes3:amd64 (1:5.0.3-1) ... Setting up libunicode-linebreak-perl (0.0.20190101-1build1) ... Setting up libxcb-render0-dev:amd64 (1.13.1-5build1) ... Setting up libxt6:amd64 (1:1.1.5-1) ... Setting up texinfo (6.7.0.dfsg.2-5) ... Running mktexlsr. This may take some time. ... done. Setting up libxext-dev:amd64 (2:1.3.4-0ubuntu1) ... Setting up libcups2:amd64 (2.3.1-7) ... Setting up xauth (1:1.1-0ubuntu1) ... Setting up libcairo-gobject2:amd64 (1.16.0-4ubuntu1) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libpangoft2-1.0-0:amd64 (1.44.7-1ubuntu2) ... Setting up libxrender-dev:amd64 (1:0.9.10-1) ... Setting up libpangocairo-1.0-0:amd64 (1.44.7-1ubuntu2) ... Setting up libkrb5-26-heimdal:amd64 (7.7.0+dfsg-1) ... Setting up libcairo-script-interpreter2:amd64 (1.16.0-4ubuntu1) ... Setting up libharfbuzz-dev:amd64 (2.6.4-1ubuntu2) ... Setting up libxft2:amd64 (2.3.3-0ubuntu1) ... Setting up libxmu6:amd64 (2:1.1.3-0ubuntu1) ... Setting up libfontconfig1-dev:amd64 (2.13.1-2ubuntu2) ... Setting up libglx-mesa0:amd64 (20.0.0-1ubuntu1) ... Setting up libpangoxft-1.0-0:amd64 (1.44.7-1ubuntu2) ... Setting up libxi6:amd64 (2:1.7.10-0ubuntu1) ... Setting up libglx0:amd64 (1.3.1-1) ... Setting up libxtst6:amd64 (2:1.2.3-1) ... Setting up po-debconf (1.0.21) ... Setting up libtk8.6:amd64 (8.6.10-1) ... Setting up pango1.0-tools (1.44.7-1ubuntu2) ... Setting up libtiff5-dev (4.1.0+git191117-2) ... Setting up libxaw7:amd64 (2:1.0.13-1) ... Setting up libxss-dev:amd64 (1:1.2.3-1) ... Setting up libheimntlm0-heimdal:amd64 (7.7.0+dfsg-1) ... Setting up gir1.2-pango-1.0:amd64 (1.44.7-1ubuntu2) ... Setting up libgl1:amd64 (1.3.1-1) ... Setting up libgssapi3-heimdal:amd64 (7.7.0+dfsg-1) ... Setting up libxt-dev:amd64 (1:1.1.5-1) ... Setting up texlive-binaries (2019.20190605.51237-3build1) ... 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 libcairo2-dev:amd64 (1.16.0-4ubuntu1) ... Setting up texlive-base (2019.20200218-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/config/pdftexconfig.tex Setting up libxft-dev:amd64 (2.3.3-0ubuntu1) ... Setting up tk8.6 (8.6.10-1) ... Setting up x11-xkb-utils (7.7+4) ... Setting up texlive-plain-generic (2019.202000218-1) ... Setting up libldap-2.4-2:amd64 (2.4.49+dfsg-1ubuntu1) ... Setting up texlive-latex-base (2019.20200218-1) ... Setting up texlive-extra-utils (2019.202000218-1) ... Setting up texlive-fonts-extra (2019.202000218-1) ... Setting up libpango1.0-dev:amd64 (1.44.7-1ubuntu2) ... Setting up texlive-latex-recommended (2019.20200218-1) ... Setting up texlive-pictures (2019.20200218-1) ... Setting up tk8.6-dev:amd64 (8.6.10-1) ... Setting up texlive-fonts-recommended (2019.20200218-1) ... Setting up libcurl4:amd64 (7.67.0-2ubuntu1) ... Setting up xserver-common (2:1.20.7-2ubuntu2) ... Setting up xvfb (2:1.20.7-2ubuntu2) ... Setting up texlive-latex-extra (2019.202000218-1) ... Setting up libcurl4-openssl-dev:amd64 (7.67.0-2ubuntu1) ... Setting up default-jre-headless (2:1.11-72) ... Setting up openjdk-11-jre-headless:amd64 (11.0.6+10-2ubuntu2) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up openjdk-11-jre:amd64 (11.0.6+10-2ubuntu2) ... Setting up openjdk-11-jdk-headless:amd64 (11.0.6+10-2ubuntu2) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jaotc to provide /usr/bin/jaotc (jaotc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre (2:1.11-72) ... Setting up dh-autoreconf (19) ... Setting up default-jdk-headless (2:1.11-72) ... Setting up openjdk-11-jdk:amd64 (11.0.6+10-2ubuntu2) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up ca-certificates-java (20190405ubuntu1) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:AddTrust_External_Root.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:DST_Root_CA_X3.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:TrustCor_ECA-1.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:SecureTrust_CA.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:AffirmTrust_Premium.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Certinomis_-_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:EC-ACC.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:ISRG_Root_X1.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Secure_Global_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:Taiwan_GRCA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Certigna.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:ACCVRAIZ1.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:SecureSign_RootCA11.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:AffirmTrust_Networking.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:LuxTrust_Global_Root_2.pem Adding debian:Izenpe.com.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:DigiCert_Global_Root_G3.pem done. Setting up debhelper (12.9ubuntu1) ... Setting up default-jdk (2:1.11-72) ... Setting up sbuild-build-depends-r-base-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... Processing triggers for systemd (244.2-1ubuntu1) ... Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. Processing triggers for tex-common (6.13) ... 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. +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-174-generic amd64 (x86_64) Toolchain package versions: binutils_2.34-3ubuntu1 dpkg-dev_1.19.7ubuntu2 g++-9_9.2.1-29ubuntu1 gcc-9_9.2.1-29ubuntu1 libc6-dev_2.30-0ubuntu3 libstdc++-9-dev_9.2.1-29ubuntu1 libstdc++6_10-20200211-1ubuntu1 linux-libc-dev_5.4.0-15.18 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1 apt_1.9.10 autoconf_2.69-11.1 automake_1:1.16.1-4ubuntu6 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11ubuntu2 base-passwd_3.5.47 bash_5.0-5ubuntu1 bash-completion_1:2.10-1ubuntu1 binutils_2.34-3ubuntu1 binutils-common_2.34-3ubuntu1 binutils-x86-64-linux-gnu_2.34-3ubuntu1 bison_2:3.5.1+dfsg-1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.34-0.1ubuntu7 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110 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libexpat1-dev_2.2.9-1 libext2fs2_1.45.5-2ubuntu1 libfakeroot_1.24-1 libfdisk1_2.34-0.1ubuntu7 libffi-dev_3.3-3 libffi6_3.2.1-9 libffi7_3.3-3 libfile-stripnondeterminism-perl_1.6.3-2 libfontbox-java_1:1.8.16-2 libfontconfig1_2.13.1-2ubuntu2 libfontconfig1-dev_2.13.1-2ubuntu2 libfontenc1_1:1.1.4-0ubuntu1 libfreetype-dev_2.10.1-2 libfreetype6_2.10.1-2 libfreetype6-dev_2.10.1-2 libfribidi-dev_1.0.8-2 libfribidi0_1.0.8-2 libgcc-9-dev_9.2.1-29ubuntu1 libgcc-s1_10-20200211-1ubuntu1 libgcc1_1:10-20200211-1ubuntu1 libgcrypt20_1.8.5-3ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran-9-dev_9.2.1-29ubuntu1 libgfortran5_10-20200211-1ubuntu1 libgif7_5.1.9-1 libgirepository-1.0-1_1.63.2-1 libgl1_1.3.1-1 libgl1-mesa-dri_20.0.0-1ubuntu1 libglapi-mesa_20.0.0-1ubuntu1 libglib2.0-0_2.63.5-2 libglib2.0-bin_2.63.5-2 libglib2.0-data_2.63.5-2 libglib2.0-dev_2.63.5-2 libglib2.0-dev-bin_2.63.5-2 libglvnd0_1.3.1-1 libglx-mesa0_20.0.0-1ubuntu1 libglx0_1.3.1-1 libgmp10_2:6.2.0+dfsg-3 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systemd-sysv_244.2-1ubuntu1 sysvinit-utils_2.96-2.1ubuntu1 t1utils_1.41-3 tar_1.30+dfsg-6 tcl8.6_8.6.10+dfsg-1 tcl8.6-dev_8.6.10+dfsg-1 tex-common_6.13 texinfo_6.7.0.dfsg.2-5 texlive-base_2019.20200218-1 texlive-binaries_2019.20190605.51237-3build1 texlive-extra-utils_2019.202000218-1 texlive-fonts-extra_2019.202000218-1 texlive-fonts-recommended_2019.20200218-1 texlive-latex-base_2019.20200218-1 texlive-latex-extra_2019.202000218-1 texlive-latex-recommended_2019.20200218-1 texlive-pictures_2019.20200218-1 texlive-plain-generic_2019.202000218-1 tk8.6_8.6.10-1 tk8.6-dev_8.6.10-1 tzdata_2019c-3 ubuntu-keyring_2020.02.11.1 ucf_3.0038+nmu1 util-linux_2.34-0.1ubuntu7 uuid-dev_2.34-0.1ubuntu7 x11-common_1:7.7+19ubuntu14 x11-xkb-utils_7.7+4 x11proto-core-dev_2018.4-4 x11proto-dev_2018.4-4 x11proto-scrnsaver-dev_2018.4-4 x11proto-xext-dev_2018.4-4 xauth_1:1.1-0ubuntu1 xdg-utils_1.1.3-1ubuntu2 xfonts-base_1:1.0.5 xfonts-encodings_1:1.0.5-0ubuntu1 xfonts-utils_1:7.7+6 xkb-data_2.26-2ubuntu4 xorg-sgml-doctools_1:1.11-1 xserver-common_2:1.20.7-2ubuntu2 xtrans-dev_1.3.5-1build1 xvfb_2:1.20.7-2ubuntu2 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu3 zlib1g-dev_1:1.2.11.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sat Feb 22 13:39:08 2020 UTC gpgv: using RSA key A1489FE2AB99A21A gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./r-base_3.6.2.20200221-1.dsc dpkg-source: info: extracting r-base in r-base-3.6.2.20200221 dpkg-source: info: unpacking r-base_3.6.2.20200221.orig.tar.gz dpkg-source: info: unpacking r-base_3.6.2.20200221-1.debian.tar.xz Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-18748350 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-18748350 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-18748350 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package r-base dpkg-buildpackage: info: source version 3.6.2.20200221-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: 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_SHELL=/bin/bash \ mkdir_p="/bin/mkdir -p" \ MKDIR_P="/bin/mkdir -p" \ R_TEXI2DVICMD=emulation \ R_PAPERSIZE=letter \ R_BROWSER=xdg-open \ R_BZIPCMD=/bin/bzip2 \ R_GZIPCMD="/bin/gzip -n" \ PAGER=/usr/bin/pager \ PERL=/usr/bin/perl \ JAVA_HOME=/usr/lib/jvm/default-java \ R_UNZIPCMD=/usr/bin/unzip \ R_ZIPCMD=/usr/bin/zip \ R_PRINTCMD=/usr/bin/lpr \ TAR=/bin/tar \ LIBnn=lib \ AWK=/usr/bin/awk \ DD=/bin/dd \ GREP=/bin/grep \ FGREP="/bin/grep -F" \ EGREP="/bin/grep -E" \ SED=/bin/sed \ GETWD="/bin/pwd" \ CC="gcc -std=gnu99" \ CXX=g++ \ F77=gfortran \ FC=gfortran \ CFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \ CXXFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \ FFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong" \ FCFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -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 configure: WARNING: unrecognized options: --with-system-bzlib, --with-system-pcre, --with-system-zlib 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 whether ln -s works... yes checking for ar... ar checking for a BSD-compatible install... /usr/bin/install -c checking for sed... /bin/sed checking for which... /usr/bin/which checking for /usr/bin/pager... /usr/bin/pager checking for /bin/tar... /bin/tar checking for tex... /usr/bin/tex checking for pdftex... /usr/bin/pdftex checking for pdflatex... /usr/bin/pdflatex checking for makeindex... /usr/bin/makeindex checking for texi2any... /usr/bin/texi2any checking whether texi2any version is at least 5.1... yes checking for ginstall-info... no checking for install-info... no checking for texi2dvi... /usr/bin/texi2dvi checking for kpsewhich... /usr/bin/kpsewhich checking for latex inconsolata package... found zi4.sty checking for unzip... /usr/bin/unzip checking for zip... /usr/bin/zip checking for gzip... /bin/gzip -n checking for bzip2... /bin/bzip2 using default browser ... xdg-open checking for acroread... no checking for acroread4... no checking for xdg-open... /usr/bin/xdg-open checking for working aclocal... found checking for working autoconf... found checking for working autoheader... found checking for bison... bison -y checking for notangle... false checking for realpath... /usr/bin/realpath checking for pkg-config... /usr/bin/pkg-config checking for gcc... gcc -std=gnu99 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -std=gnu99 -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether gcc -std=gnu99 needs -traditional... no checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking how to run the C preprocessor... gcc -std=gnu99 -E looking for a modern Fortran compiler checking whether we are using the GNU Fortran compiler... yes checking whether gfortran accepts -g... yes checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g can compile C++ code... yes checking how to run the C++ preprocessor... g++ -E checking whether __attribute__((visibility())) is supported... yes checking whether gcc -std=gnu99 accepts -fvisibility... yes checking whether g++ accepts -fvisibility... yes checking whether gfortran accepts -fvisibility... yes checking for gcc... gcc checking whether we are using the GNU Objective C compiler... no checking whether gcc accepts -g... no checking whether g++ can compile ObjC++... no checking whether can compile ObjC++... no checking for Objective C++ compiler... no working ObjC++ compiler found checking how to print strings... printf checking for a sed that does not truncate output... (cached) /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc -std=gnu99... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking for gawk... /usr/bin/awk checking command to parse /usr/bin/nm -B output from gcc -std=gnu99 object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes checking if gcc -std=gnu99 static flag -static works... yes checking if gcc -std=gnu99 supports -c -o file.o... yes checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes checking whether the gcc -std=gnu99 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for gfortran option to produce PIC... -fPIC checking if gfortran PIC flag -fPIC works... yes checking if gfortran static flag -static works... yes checking if gfortran supports -c -o file.o... yes checking if gfortran supports -c -o file.o... (cached) yes checking whether the gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for cos in -lm... yes checking for sin in -lm... yes checking for dlopen in -ldl... yes checking readline/history.h usability... yes checking readline/history.h presence... yes checking for readline/history.h... yes checking readline/readline.h usability... yes checking readline/readline.h presence... yes checking for readline/readline.h... yes checking for rl_callback_read_char in -lreadline... yes checking for history_truncate_file... yes checking for tilde_expand_word... yes checking whether rl_callback_sigcleanup exists and is declared... yes checking whether rl_completion_matches exists and is declared... yes checking whether rl_resize_terminal exists and is declared... yes checking whether rl_sort_completion_matches exists and is declared... yes checking for ANSI C header files... (cached) yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for sys/wait.h that is POSIX.1 compatible... yes checking for dlfcn.h... (cached) yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking glob.h usability... yes checking glob.h presence... yes checking for glob.h... yes checking grp.h usability... yes checking grp.h presence... yes checking for grp.h... yes checking pwd.h usability... yes checking pwd.h presence... yes checking for pwd.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for strings.h... 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(cached) yes checking utime.h usability... yes checking utime.h presence... yes checking for utime.h... yes checking arpa/inet.h usability... yes checking arpa/inet.h presence... yes checking for arpa/inet.h... yes checking elf.h usability... yes checking elf.h presence... yes checking for elf.h... yes checking features.h usability... yes checking features.h presence... yes checking for features.h... yes checking floatingpoint.h usability... no checking floatingpoint.h presence... no checking for floatingpoint.h... no checking langinfo.h usability... yes checking langinfo.h presence... yes checking for langinfo.h... yes checking netdb.h usability... yes checking netdb.h presence... yes checking for netdb.h... yes checking netinet/in.h usability... yes checking netinet/in.h presence... yes checking for netinet/in.h... yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking stdalign.h usability... yes checking stdalign.h presence... yes checking for stdalign.h... yes checking errno.h usability... yes checking errno.h presence... yes checking for errno.h... yes checking for inttypes.h... (cached) yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking locale.h usability... yes checking locale.h presence... yes checking for locale.h... yes checking stdarg.h usability... yes checking stdarg.h presence... yes checking for stdarg.h... yes checking stdbool.h usability... yes checking stdbool.h presence... yes checking for stdbool.h... yes checking for stdint.h... (cached) yes checking for string.h... (cached) yes checking whether setjmp.h is POSIX.1 compatible... yes checking whether sigsetjmp is declared... yes checking whether siglongjmp is declared... yes checking for GNU C library with version >= 2... yes checking return type of signal handlers... void checking for uint64_t... yes checking for int64_t... yes checking for int_fast64_t... yes checking for pid_t... yes checking for size_t... yes checking whether SIZE_MAX is declared... yes checking for blkcnt_t... yes checking for type of socket length... socklen_t * checking for stack_t... yes checking for intptr_t... yes checking for uintptr_t... yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for gcc -std=gnu99 option to accept ISO C99... none needed checking for gcc -std=gnu99 option to accept ISO Standard C... (cached) none needed checking for inline... inline checking size of int... 4 checking size of long... 8 checking size of long long... 8 checking size of double... 8 checking size of size_t... 8 checking for C stack direction... down checking size of long double... 16 checking whether we can compute C Make dependencies... yes, using $(CC) -MM checking whether gcc -std=gnu99 supports -c -o FILE.lo... yes checking for gcc -std=gnu99 option to support OpenMP... -fopenmp checking how to get verbose linking output from gfortran... -v checking for Fortran libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lgfortran -lm -lquadmath checking how to get verbose linking output from gcc -std=gnu99... -v checking for C libraries of gcc -std=gnu99... -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lgcc_s checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore checking whether gfortran appends underscores to external names... yes checking whether gfortran appends extra underscores to external names... no checking whether mixed C/Fortran code can be run... yes checking whether gfortran and gcc -std=gnu99 agree on int and double... yes checking whether gfortran and gcc -std=gnu99 agree on double complex... yes checking for gfortran option to support OpenMP... -fopenmp checking whether g++ accepts -M for generating dependencies... yes checking whether we can compute ObjC Make dependencies... no checking if need 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checking whether log10 exists and is declared... yes checking whether nearbyint exists and is declared... yes checking whether nearbyintl exists and is declared... yes checking whether powl exists and is declared... yes checking whether rintl exists and is declared... yes checking whether va_copy exists and is declared... yes checking for isblank... yes checking sunmath.h usability... no checking sunmath.h presence... no checking for sunmath.h... no checking for cospi in -lsunmath... no checking for atanpi... no checking for atan2pi... no checking for cospi... no checking for exp10... yes checking for pown... no checking for sinpi... no checking for tanpi... no checking for __cospi... no checking for __sinpi... no checking for __tanpi... no checking for fseeko... yes checking for ftello... yes checking for matherr... no checking whether fcntl exists and is declared... yes checking whether getgrgid exists and is declared... yes checking whether getpwuid exists and is declared... yes checking whether kill exists and is declared... yes checking whether sigaction exists and is declared... yes checking whether sigaltstack exists and is declared... yes checking whether sigemptyset exists and is declared... yes checking whether fdopen exists and is declared... yes checking whether popen exists and is declared... yes checking whether getline exists and is declared... yes checking whether select exists and is declared... yes checking whether setenv exists and is declared... yes checking whether unsetenv exists and is declared... yes checking whether getrlimit exists and is declared... yes checking whether setrlimit exists and is declared... yes checking whether getrusage exists and is declared... yes checking whether getpriority exists and is declared... yes checking whether chmod exists and is declared... yes checking whether mkfifo exists and is declared... yes checking whether stat exists and is declared... yes checking whether umask exists and is declared... yes checking whether gettimeofday exists and is declared... yes checking whether utimes exists and is declared... yes checking whether times exists and is declared... yes checking whether gmtime_r exists and is declared... yes checking whether localtime_r exists and is declared... yes checking whether nl_langinfo exists and is declared... yes checking whether access exists and is declared... yes checking whether chdir exists and is declared... yes checking whether execv exists and is declared... yes checking whether ftruncate exists and is declared... yes checking whether getcwd exists and is declared... yes checking whether geteuid exists and is declared... yes checking whether getuid exists and is declared... yes checking whether link exists and is declared... yes checking whether readlink exists and is declared... yes checking whether symlink exists and is declared... yes checking whether sysconf exists and is declared... yes checking whether sched_setaffinity exists and is declared... yes checking whether sched_getaffinity exists and is declared... yes checking whether utime exists and is declared... yes checking whether utimensat exists and is declared... yes checking for clock_gettime in -lrt... yes checking whether clock_gettime exists and is declared... yes checking whether timespec_get exists and is declared... yes checking for putenv... yes checking whether putenv is declared... yes checking for vasprintf... yes checking whether vasprintf is declared... yes checking for mempcpy... yes checking for realpath... yes checking whether realpath is declared... yes checking whether glob exists and is declared... yes checking for dladdr... yes checking for dlsym... yes checking whether dladdr is declared... yes checking whether dlsym is declared... yes checking whether RTLD_DEFAULT is declared... yes checking whether RTLD_NEXT is declared... yes checking thread.h usability... no checking thread.h presence... no checking for thread.h... no checking whether thr_stksegment exists and is declared... no checking for isnan... yes checking whether isfinite is declared... yes checking whether isnan is declared... yes checking whether you have IEEE 754 floating-point arithmetic... yes checking whether putenv("FOO") can unset an environment variable... yes checking whether putenv("FOO=") can unset an environment variable... no checking for nl_langinfo and CODESET... yes checking for mkdtemp... yes checking for strdup... yes checking for strncasecmp... yes checking whether mkdtemp is declared... yes checking whether strdup is declared... yes checking whether strncasecmp is declared... yes checking for library containing connect... none required checking for library containing gethostbyname... none required checking for library containing xdr_string... none required checking for working calloc... yes checking for working isfinite... yes checking for working log1p... yes checking whether ftell works correctly on files opened for append... yes checking for working sigaction... yes checking whether mktime sets errno... no checking whether mktime works correctly outside 1902-2037... yes checking complex.h usability... yes checking complex.h presence... yes checking for complex.h... yes checking for double complex... yes checking whether C99 double complex is supported... yes checking whether cabs exists and is declared... yes checking whether carg exists and is declared... yes checking whether cexp exists and is declared... yes checking whether clog exists and is declared... yes checking whether csqrt exists and is declared... yes checking whether cpow exists and is declared... yes checking whether ccos exists and is declared... yes checking whether csin exists and is declared... yes checking whether ctan exists and is declared... yes checking whether cacos exists and is declared... yes checking whether casin exists and is declared... yes checking whether catan exists and is declared... yes checking whether ccosh exists and is declared... yes checking whether csinh exists and is declared... yes checking whether ctanh exists and is declared... yes checking for working ctanh... yes checking whether 'struct tm' includes tm_zone... yes checking whether 'struct tm' includes tm_gmtoff... yes checking for dgemm_... no checking for sgemm_ in -lopenblas... no checking for ATL_xerbla in -latlas... no checking for dgemm_ in -lblas... yes checking for dgemm_ in -ldgemm... no checking for dgemm_ in -lblas... 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(cached) -fopenmp checking whether NLS is requested... yes Configuring src/extra/intl directory checking for a thread-safe mkdir -p... /bin/mkdir -p checking whether we are using the GNU C Library 2 or newer... yes checking for ranlib... (cached) ranlib checking for simple visibility declarations... yes checking for stdint.h... yes checking for getpagesize... yes checking for working mmap... yes checking whether integer division by zero raises SIGFPE... yes checking for inttypes.h... yes checking for unsigned long long int... yes checking for inttypes.h... (cached) yes checking whether the inttypes.h PRIxNN macros are broken... no checking for ld used by gcc -std=gnu99... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking for shared library run path origin... done checking whether imported symbols can be declared weak... yes checking for multithread API to use... none checking argz.h usability... yes checking argz.h presence... yes checking for argz.h... yes checking for inttypes.h... (cached) yes checking for limits.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... (cached) yes checking for getcwd... yes checking for getegid... yes checking for geteuid... yes checking for getgid... yes checking for getuid... yes checking for mempcpy... (cached) yes checking for munmap... yes checking for stpcpy... yes checking for strcasecmp... yes checking for strdup... (cached) yes checking for strtoul... yes checking for tsearch... yes checking for argz_count... yes checking for argz_stringify... yes checking for argz_next... yes checking for __fsetlocking... yes checking whether feof_unlocked is declared... yes checking whether fgets_unlocked is declared... yes checking for iconv... (cached) yes checking for iconv declaration... (cached) extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft); checking for NL_LOCALE_NAME macro... yes checking for bison... bison checking version of bison... 3.5.1, 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... 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(cached) no checking whether included gettext is requested... no checking for GNU gettext in libc... yes checking whether to use NLS... yes checking where the gettext function comes from... libc Finished configuring src/extra/intl directory checking whether OpenMP SIMD reduction is supported... yes using as R_SHELL for scripts ... /bin/bash configure: creating ./config.status config.status: creating Makeconf config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/html/Makefile config.status: creating doc/manual/Makefile config.status: creating etc/Makefile config.status: creating etc/Makeconf config.status: creating etc/Renviron config.status: creating etc/javaconf config.status: creating etc/ldpaths config.status: creating m4/Makefile config.status: creating po/Makefile config.status: creating share/Makefile config.status: creating src/Makefile config.status: creating src/appl/Makefile config.status: creating src/extra/Makefile config.status: creating src/extra/blas/Makefile config.status: creating src/extra/intl/Makefile config.status: creating src/extra/tre/Makefile config.status: creating src/extra/tzone/Makefile config.status: creating src/extra/xdr/Makefile config.status: creating src/include/Makefile config.status: creating src/include/Rmath.h0 config.status: creating src/include/R_ext/Makefile config.status: creating src/library/Recommended/Makefile config.status: creating src/library/Makefile config.status: creating src/library/base/DESCRIPTION config.status: creating src/library/base/Makefile config.status: creating src/library/compiler/DESCRIPTION config.status: creating src/library/compiler/Makefile config.status: creating src/library/datasets/DESCRIPTION config.status: creating src/library/datasets/Makefile config.status: creating src/library/graphics/DESCRIPTION config.status: creating src/library/graphics/Makefile config.status: creating src/library/graphics/src/Makefile config.status: creating src/library/grDevices/DESCRIPTION config.status: creating src/library/grDevices/Makefile config.status: creating src/library/grDevices/src/Makefile config.status: creating src/library/grDevices/src/cairo/Makefile config.status: creating src/library/grid/DESCRIPTION config.status: creating src/library/grid/Makefile config.status: creating src/library/grid/src/Makefile config.status: creating src/library/methods/DESCRIPTION config.status: creating src/library/methods/Makefile config.status: creating src/library/methods/src/Makefile config.status: creating src/library/parallel/DESCRIPTION config.status: creating src/library/parallel/Makefile config.status: creating src/library/parallel/src/Makefile config.status: creating src/library/profile/Makefile config.status: creating src/library/stats/DESCRIPTION config.status: creating src/library/stats/Makefile config.status: creating src/library/stats/src/Makefile config.status: creating src/library/stats4/DESCRIPTION config.status: creating src/library/stats4/Makefile config.status: creating src/library/splines/DESCRIPTION config.status: creating src/library/splines/Makefile config.status: creating src/library/splines/src/Makefile config.status: creating src/library/tcltk/DESCRIPTION config.status: creating src/library/tcltk/Makefile config.status: creating src/library/tcltk/src/Makefile config.status: creating src/library/tools/DESCRIPTION config.status: creating src/library/tools/Makefile config.status: creating src/library/tools/src/Makefile config.status: creating src/library/translations/DESCRIPTION config.status: creating src/library/translations/Makefile config.status: creating src/library/utils/DESCRIPTION config.status: creating src/library/utils/Makefile config.status: creating src/library/utils/src/Makefile config.status: creating src/main/Makefile config.status: creating src/modules/Makefile config.status: creating src/modules/X11/Makefile config.status: creating src/modules/internet/Makefile config.status: creating src/modules/lapack/Makefile config.status: creating src/nmath/Makefile config.status: creating src/nmath/standalone/Makefile config.status: creating src/scripts/Makefile config.status: creating src/scripts/R.sh config.status: creating src/scripts/Rcmd config.status: creating src/scripts/javareconf config.status: creating src/scripts/mkinstalldirs config.status: creating src/scripts/pager config.status: creating src/scripts/rtags config.status: creating src/unix/Makefile config.status: creating tests/Makefile config.status: creating tests/Embedding/Makefile config.status: creating tests/Examples/Makefile config.status: creating tools/Makefile config.status: creating src/include/config.h config.status: executing libtool commands config.status: executing stamp-h commands configure: WARNING: unrecognized options: --with-system-bzlib, --with-system-pcre, --with-system-zlib R is now configured for x86_64-pc-linux-gnu Source directory: . Installation directory: /usr C compiler: gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g Fortran fixed-form compiler: gfortran -fno-optimize-sibling-calls -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong Default C++ compiler: g++ -std=gnu++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g C++98 compiler: g++ -std=gnu++98 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g C++11 compiler: g++ -std=gnu++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g C++14 compiler: g++ -std=gnu++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g C++17 compiler: g++ -std=gnu++17 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g Fortran free-form compiler: gfortran -fno-optimize-sibling-calls -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong Obj-C compiler: Interfaces supported: X11, tcltk External libraries: readline, BLAS(generic), LAPACK(generic), curl Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU Options enabled: shared R library, R profiling, memory profiling Capabilities skipped: Options not enabled: shared BLAS Recommended packages: no touch configure-stamp *** make-arch *** /usr/bin/make CFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \ CXXFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \ FFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong" \ FCFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong" \ CC="gcc -std=gnu99" \ CXX=g++ \ F77=gfortran \ LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro" \ PKG_BUILT_STAMP="""" \ R_GZIPCMD="/bin/gzip -n" \ R make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/m4' make[2]: Entering directory '/<>/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/tools' make[2]: Entering directory '/<>/doc' make[3]: Entering directory '/<>/doc/html' make[3]: Leaving directory '/<>/doc/html' make[3]: Entering directory '/<>/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/<>/doc/manual' make[2]: Leaving directory '/<>/doc' make[2]: Entering directory '/<>/etc' make[2]: Leaving directory '/<>/etc' make[2]: Entering directory '/<>/share' make[2]: Leaving directory '/<>/share' make[2]: Entering directory '/<>/src' make[3]: Entering directory '/<>/src/scripts' creating src/scripts/R.fe make[4]: Entering directory '/<>/src/scripts' mkdir -p -- ../../bin make[4]: Leaving directory '/<>/src/scripts' make[3]: Leaving directory '/<>/src/scripts' make[3]: Entering directory '/<>/src/include' mkdir -p -- ../../include make[4]: Entering directory '/<>/src/include/R_ext' mkdir -p -- ../../../include/R_ext make[4]: Leaving directory '/<>/src/include/R_ext' make[3]: Leaving directory '/<>/src/include' make[3]: Entering directory '/<>/src/extra' make[4]: Entering directory '/<>/src/extra/tre' make[5]: Entering directory '/<>/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 '/<>/src/extra/tre' make[5]: Entering directory '/<>/src/extra/tre' gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c regcomp.c -o regcomp.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c regerror.c -o regerror.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c regexec.c -o regexec.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-ast.c -o tre-ast.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-compile.c -o tre-compile.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-mem.c -o tre-mem.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-parse.c -o tre-parse.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-stack.c -o tre-stack.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c xmalloc.c -o xmalloc.o ar -cr libtre.a regcomp.o regerror.o regexec.o tre-ast.o tre-compile.o tre-match-approx.o tre-match-backtrack.o tre-match-parallel.o tre-mem.o tre-parse.o tre-stack.o xmalloc.o ranlib libtre.a make[5]: Leaving directory '/<>/src/extra/tre' make[4]: Leaving directory '/<>/src/extra/tre' make[3]: Leaving directory '/<>/src/extra' make[3]: Entering directory '/<>/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 '/<>/src/appl' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c integrate.c -o integrate.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c interv.c -o interv.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c maxcol.c -o maxcol.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c optim.c -o optim.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pretty.c -o pretty.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c uncmin.c -o uncmin.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dchdc.f -o dchdc.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dpbfa.f -o dpbfa.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dpbsl.f -o dpbsl.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dpoco.f -o dpoco.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dpodi.f -o dpodi.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dpofa.f -o dpofa.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dposl.f -o dposl.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dqrdc.f -o dqrdc.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dqrdc2.f -o dqrdc2.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dqrls.f -o dqrls.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dqrsl.f -o dqrsl.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dqrutl.f -o dqrutl.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dsvdc.f -o dsvdc.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dtrco.f -o dtrco.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dtrsl.f -o dtrsl.o ar -cr libappl.a integrate.o interv.o maxcol.o optim.o pretty.o uncmin.o dchdc.o dpbfa.o dpbsl.o dpoco.o dpodi.o dpofa.o dposl.o dqrdc.o dqrdc2.o dqrls.o dqrsl.o dqrutl.o dsvdc.o dtrco.o dtrsl.o ranlib libappl.a make[4]: Leaving directory '/<>/src/appl' make[3]: Leaving directory '/<>/src/appl' make[3]: Entering directory '/<>/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 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 '/<>/src/nmath' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mlutils.c -o mlutils.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c d1mach.c -o d1mach.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c i1mach.c -o i1mach.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fmax2.c -o fmax2.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fmin2.c -o fmin2.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fprec.c -o fprec.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fround.c -o fround.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ftrunc.c -o ftrunc.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sign.c -o sign.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fsign.c -o fsign.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c imax2.c -o imax2.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c imin2.c -o imin2.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chebyshev.c -o chebyshev.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c log1p.c -o log1p.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lgammacor.c -o lgammacor.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gammalims.c -o gammalims.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stirlerr.c -o stirlerr.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bd0.c -o bd0.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gamma.c -o gamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lgamma.c -o lgamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gamma_cody.c -o gamma_cody.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c beta.c -o beta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lbeta.c -o lbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c polygamma.c -o polygamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cospi.c -o cospi.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bessel_i.c -o bessel_i.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bessel_j.c -o bessel_j.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bessel_k.c -o bessel_k.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bessel_y.c -o bessel_y.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c choose.c -o choose.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c snorm.c -o snorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sexp.c -o sexp.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dgamma.c -o dgamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pgamma.c -o pgamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qgamma.c -o qgamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rgamma.c -o rgamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dbeta.c -o dbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pbeta.c -o pbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qbeta.c -o qbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rbeta.c -o rbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dunif.c -o dunif.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c punif.c -o punif.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qunif.c -o qunif.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c runif.c -o runif.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnorm.c -o dnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnorm.c -o pnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnorm.c -o qnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rnorm.c -o rnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dlnorm.c -o dlnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plnorm.c -o plnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qlnorm.c -o qlnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rlnorm.c -o rlnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c df.c -o df.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pf.c -o pf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qf.c -o qf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rf.c -o rf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnf.c -o dnf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dt.c -o dt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pt.c -o pt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qt.c -o qt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rt.c -o rt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnt.c -o dnt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dchisq.c -o dchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pchisq.c -o pchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qchisq.c -o qchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rchisq.c -o rchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rnchisq.c -o rnchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dbinom.c -o dbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pbinom.c -o pbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qbinom.c -o qbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rbinom.c -o rbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rmultinom.c -o rmultinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dcauchy.c -o dcauchy.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pcauchy.c -o pcauchy.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qcauchy.c -o qcauchy.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rcauchy.c -o rcauchy.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dexp.c -o dexp.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pexp.c -o pexp.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qexp.c -o qexp.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rexp.c -o rexp.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dgeom.c -o dgeom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pgeom.c -o pgeom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qhyper.c -o qhyper.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rhyper.c -o rhyper.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnbinom.c -o dnbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnbinom.c -o pnbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnbinom.c -o qnbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rnbinom.c -o rnbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dpois.c -o dpois.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ppois.c -o ppois.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qpois.c -o qpois.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rpois.c -o rpois.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dweibull.c -o dweibull.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pweibull.c -o pweibull.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qweibull.c -o qweibull.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rweibull.c -o rweibull.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dlogis.c -o dlogis.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plogis.c -o plogis.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qlogis.c -o qlogis.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rlogis.c -o rlogis.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnchisq.c -o dnchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnchisq.c -o pnchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnchisq.c -o qnchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnbeta.c -o dnbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnbeta.c -o pnbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnbeta.c -o qnbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnf.c -o pnf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnt.c -o pnt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnf.c -o qnf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnt.c -o qnt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ptukey.c -o ptukey.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qtukey.c -o qtukey.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c toms708.c -o toms708.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c wilcox.c -o wilcox.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c signrank.c -o signrank.o ar -cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o 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 '/<>/src/nmath' make[3]: Leaving directory '/<>/src/nmath' make[3]: Entering directory '/<>/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 '/<>/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rembedded.c -o Rembedded.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dynload.c -o dynload.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c system.c -o system.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sys-unix.c -o sys-unix.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sys-std.c -o sys-std.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c X11.c -o X11.o ar -cr libunix.a Rembedded.o dynload.o system.o sys-unix.o sys-std.o X11.o ranlib libunix.a make[4]: Leaving directory '/<>/src/unix' make[4]: Entering directory '/<>/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/<>"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/<>/src/unix' make[3]: Leaving directory '/<>/src/unix' make[3]: Entering directory '/<>/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 altclasses.d from altclasses.c making altrep.d from altrep.c making apply.d from apply.c making arithmetic.d from arithmetic.c making array.d from array.c making attrib.d from attrib.c making bind.d from bind.c making builtin.d from builtin.c making character.d from character.c making coerce.d from coerce.c making colors.d from colors.c making complex.d from complex.c making connections.d from connections.c making context.d from context.c making cum.d from cum.c making dcf.d from dcf.c making datetime.d from datetime.c making debug.d from debug.c making deparse.d from deparse.c making devices.d from devices.c making dotcode.d from dotcode.c making dounzip.d from dounzip.c making dstruct.d from dstruct.c making duplicate.d from duplicate.c making edit.d from edit.c making engine.d from engine.c making envir.d from envir.c making errors.d from errors.c making eval.d from eval.c making format.d from format.c making gevents.d from gevents.c making gram.d from gram.c making gram-ex.d from gram-ex.c making graphics.d from graphics.c making grep.d from grep.c making identical.d from identical.c making inlined.d from inlined.c making inspect.d from inspect.c making internet.d from internet.c making iosupport.d from iosupport.c making lapack.d from lapack.c making list.d from list.c making localecharset.d from localecharset.c making logic.d from logic.c making main.d from main.c making mapply.d from mapply.c making match.d from match.c making memory.d from memory.c making names.d from names.c making objects.d from objects.c making options.d from options.c making paste.d from paste.c making platform.d from platform.c making plot.d from plot.c making plot3d.d from plot3d.c making plotmath.d from plotmath.c making print.d from print.c making printarray.d from printarray.c making printvector.d from printvector.c making printutils.d from printutils.c making qsort.d from qsort.c making radixsort.d from radixsort.c making random.d from random.c making raw.d from raw.c making registration.d from registration.c making relop.d from relop.c making rlocale.d from rlocale.c making saveload.d from saveload.c making scan.d from scan.c making seq.d from seq.c making serialize.d from serialize.c making sort.d from sort.c making source.d from source.c making split.d from split.c making sprintf.d from sprintf.c making startup.d from startup.c making subassign.d from subassign.c making subscript.d from subscript.c making subset.d from subset.c making summary.d from summary.c making sysutils.d from sysutils.c making times.d from times.c making unique.d from unique.c making util.d from util.c making version.d from version.c making g_alab_her.d from g_alab_her.c making g_cntrlify.d from g_cntrlify.c making g_fontdb.d from g_fontdb.c making g_her_glyph.d from g_her_glyph.c making Rmain.d from Rmain.c making alloca.d from alloca.c making mkdtemp.d from mkdtemp.c making strdup.d from strdup.c making strncasecmp.d from strncasecmp.c make[4]: Entering directory '/<>/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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c CommandLineArgs.c -o CommandLineArgs.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rdynload.c -o Rdynload.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Renviron.c -o Renviron.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RNG.c -o RNG.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c agrep.c -o agrep.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c altclasses.c -o altclasses.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c altrep.c -o altrep.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c apply.c -o apply.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c arithmetic.c -o arithmetic.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c array.c -o array.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c attrib.c -o attrib.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bind.c -o bind.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c builtin.c -o builtin.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c character.c -o character.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c coerce.c -o coerce.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c colors.c -o colors.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c complex.c -o complex.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c connections.c -o connections.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c context.c -o context.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cum.c -o cum.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dcf.c -o dcf.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c datetime.c -o datetime.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c debug.c -o debug.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c deparse.c -o deparse.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devices.c -o devices.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dotcode.c -o dotcode.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dounzip.c -o dounzip.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dstruct.c -o dstruct.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c duplicate.c -o duplicate.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c edit.c -o edit.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c engine.c -o engine.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c envir.c -o envir.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c errors.c -o errors.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c eval.c -o eval.o In file included from /usr/include/string.h:494, from ../../src/include/Rinlinedfuns.h:73, from ../../src/include/Rinternals.h:1552, from ../../src/include/Defn.h:81, from eval.c:27: In function ‘strncpy’, inlined from ‘inflateAssignmentCall’ at eval.c:6083:5, inlined from ‘R_getBCInterpreterExpression’ at eval.c:6136:8: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eval.c: In function ‘R_getBCInterpreterExpression’: eval.c:6076:19: note: length computed here 6076 | size_t slen = strlen(name); | ^~~~~~~~~~~~ gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c format.c -o format.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gevents.c -o gevents.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gram.c -o gram.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gram-ex.c -o gram-ex.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c graphics.c -o graphics.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c grep.c -o grep.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c identical.c -o identical.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c inlined.c -o inlined.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c inspect.c -o inspect.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c internet.c -o internet.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c iosupport.c -o iosupport.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lapack.c -o lapack.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c list.c -o list.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c localecharset.c -o localecharset.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c logic.c -o logic.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c main.c -o main.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mapply.c -o mapply.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c match.c -o match.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c memory.c -o memory.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c names.c -o names.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c objects.c -o objects.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c options.c -o options.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c paste.c -o paste.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c platform.c -o platform.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plot.c -o plot.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plot3d.c -o plot3d.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plotmath.c -o plotmath.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c print.c -o print.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c printarray.c -o printarray.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c printvector.c -o printvector.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c printutils.c -o printutils.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qsort.c -o qsort.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c radixsort.c -o radixsort.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c random.c -o random.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c raw.c -o raw.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c registration.c -o registration.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c relop.c -o relop.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rlocale.c -o rlocale.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c saveload.c -o saveload.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c scan.c -o scan.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c seq.c -o seq.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c serialize.c -o serialize.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sort.c -o sort.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c source.c -o source.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c split.c -o split.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sprintf.c -o sprintf.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c startup.c -o startup.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c subassign.c -o subassign.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c subscript.c -o subscript.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c subset.c -o subset.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c summary.c -o summary.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sysutils.c -o sysutils.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c times.c -o times.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unique.c -o unique.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c util.c -o util.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c version.c -o version.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c g_alab_her.c -o g_alab_her.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c g_cntrlify.c -o g_cntrlify.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c g_fontdb.c -o g_fontdb.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c g_her_glyph.c -o g_her_glyph.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/<>=. -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 altclasses.o altrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o radixsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/tre/libtre.a -lblas -lgfortran -lm -lquadmath -lreadline -lpcre2-8 -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n make[5]: Entering directory '/<>/src/main' mkdir -p -- /<>/bin/exec mkdir -p -- /<>/lib make[5]: Leaving directory '/<>/src/main' make[4]: Leaving directory '/<>/src/main' make[4]: Entering directory '/<>/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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rmain.c -o Rmain.o gcc -std=gnu99 -Wl,--export-dynamic -fopenmp -L"../../lib" -Wl,-Bsymbolic-functions -Wl,-z,relro -o R.bin Rmain.o -lR make[5]: Entering directory '/<>/src/main' make[5]: Leaving directory '/<>/src/main' make[4]: Leaving directory '/<>/src/main' make[3]: Leaving directory '/<>/src/main' make[3]: Entering directory '/<>/src/modules' make[4]: Entering directory '/<>/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 '/<>/src/modules/internet' gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c Rsock.c -o Rsock.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c internet.c -o internet.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c libcurl.c -o libcurl.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c nanoftp.c -o nanoftp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c nanohttp.c -o nanohttp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c sock.c -o sock.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c sockconn.c -o sockconn.o gcc -std=gnu99 -shared -L"../../../lib" -Wl,-Bsymbolic-functions -Wl,-z,relro -o internet.so Rhttpd.o Rsock.o internet.o libcurl.o nanoftp.o nanohttp.o sock.o sockconn.o -lcurl -lR make[6]: Entering directory '/<>/src/modules/internet' mkdir -p -- /<>/modules make[6]: Leaving directory '/<>/src/modules/internet' make[5]: Leaving directory '/<>/src/modules/internet' make[4]: Leaving directory '/<>/src/modules/internet' make[4]: Entering directory '/<>/src/modules/lapack' making Lapack.d from Lapack.c make[5]: Entering directory '/<>/src/modules/lapack' gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Lapack.c -o Lapack.o gcc -std=gnu99 -shared -L"../../../lib" -Wl,-Bsymbolic-functions -Wl,-z,relro -o lapack.so Lapack.o -lR -llapack -lblas -lgfortran -lm -lquadmath make[6]: Entering directory '/<>/src/modules/lapack' make[6]: Leaving directory '/<>/src/modules/lapack' make[5]: Leaving directory '/<>/src/modules/lapack' make[4]: Leaving directory '/<>/src/modules/lapack' make[4]: Entering directory '/<>/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 '/<>/src/modules/X11' gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/harfbuzz -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/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devX11.c -o devX11.o gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/harfbuzz -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/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rotated.c -o rotated.o gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/harfbuzz -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/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rbitmap.c -o rbitmap.o gcc -std=gnu99 -shared -L"../../../lib" -Wl,-Bsymbolic-functions -Wl,-z,relro -o R_X11.so devX11.o rotated.o rbitmap.o -ltiff -L/build/libjpeg-turbo-ff4xqQ/libjpeg-turbo-2.0.3/obj-x86_64-linux-gnu/lib/x86_64-linux-gnu -ljpeg -lpng16 -lz -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt -lR -lm gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/harfbuzz -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/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dataentry.c -o dataentry.o gcc -std=gnu99 -shared -L"../../../lib" -Wl,-Bsymbolic-functions -Wl,-z,relro -o R_de.so dataentry.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt -lR -lm make[5]: Leaving directory '/<>/src/modules/X11' make[5]: Entering directory '/<>/src/modules/X11' make[5]: Leaving directory '/<>/src/modules/X11' make[4]: Leaving directory '/<>/src/modules/X11' make[3]: Leaving directory '/<>/src/modules' make[3]: Entering directory '/<>/src/library' mkdir -p -- ../../library make[4]: Entering directory '/<>/src/library/profile' building system startup profile mkdir -p -- ../../../library/base/R make[4]: Leaving directory '/<>/src/library/profile' make[4]: Entering directory '/<>/src/library/translations' building package 'translations' mkdir -p -- ../../../library/translations make[5]: Entering directory '/<>/src/library/translations' make[5]: Leaving directory '/<>/src/library/translations' make[4]: Leaving directory '/<>/src/library/translations' make[4]: Entering directory '/<>/src/library/base' building package 'base' make[5]: Entering directory '/<>/src/library/base' mkdir -p -- ../../../library/base/demo make[5]: Leaving directory '/<>/src/library/base' make[4]: Leaving directory '/<>/src/library/base' make[4]: Entering directory '/<>/src/library/tools' building package 'tools' mkdir -p -- ../../../library/tools make[5]: Entering directory '/<>/src/library/tools' mkdir -p -- ../../../library/tools/R make[5]: Leaving directory '/<>/src/library/tools' make[5]: Entering directory '/<>/src/library/tools' make[6]: Entering directory '/<>/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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c text.c -o text.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rmd5.c -o Rmd5.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c md5.c -o md5.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c signals.c -o signals.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c install.c -o install.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c getfmts.c -o getfmts.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c http.c -o http.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gramLatex.c -o gramLatex.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gramRd.c -o gramRd.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o -L../../../../lib -lR make[7]: Entering directory '/<>/src/library/tools/src' mkdir -p -- ../../../../library/tools/libs make[7]: Leaving directory '/<>/src/library/tools/src' make[6]: Leaving directory '/<>/src/library/tools/src' make[5]: Leaving directory '/<>/src/library/tools' make[5]: Entering directory '/<>/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/<>/src/library/tools' make[4]: Leaving directory '/<>/src/library/tools' make[4]: Entering directory '/<>/src/library/compiler' building package 'compiler' mkdir -p -- ../../../library/compiler make[5]: Entering directory '/<>/src/library/compiler' mkdir -p -- ../../../library/compiler/R make[5]: Leaving directory '/<>/src/library/compiler' make[5]: Entering directory '/<>/src/library/compiler' byte-compiling package 'compiler' make[5]: Leaving directory '/<>/src/library/compiler' make[4]: Leaving directory '/<>/src/library/compiler' make[4]: Entering directory '/<>/src/library/base' byte-compiling package 'base' make[4]: Leaving directory '/<>/src/library/base' make[4]: Entering directory '/<>/src/library/tools' byte-compiling package 'tools' make[4]: Leaving directory '/<>/src/library/tools' make[4]: Entering directory '/<>/src/library/utils' building package 'utils' mkdir -p -- ../../../library/utils mkdir -p -- ../../../library/utils/doc make[5]: Entering directory '/<>/src/library/utils' mkdir -p -- ../../../library/utils/R mkdir -p -- ../../../library/utils/Sweave mkdir -p -- ../../../library/utils/misc make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' make[6]: Entering directory '/<>/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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io.c -o io.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c size.c -o size.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sock.c -o sock.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stubs.c -o stubs.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o utils.so init.o io.o size.o sock.o stubs.o utils.o -L../../../../lib -lR make[7]: Entering directory '/<>/src/library/utils/src' mkdir -p -- ../../../../library/utils/libs make[7]: Leaving directory '/<>/src/library/utils/src' make[6]: Leaving directory '/<>/src/library/utils/src' make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' byte-compiling package 'utils' make[5]: Leaving directory '/<>/src/library/utils' make[4]: Leaving directory '/<>/src/library/utils' make[4]: Entering directory '/<>/src/library/grDevices' building package 'grDevices' mkdir -p -- ../../../library/grDevices make[5]: Entering directory '/<>/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 '/<>/src/library/grDevices' make[5]: Entering directory '/<>/src/library/grDevices' make[6]: Entering directory '/<>/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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c axis_scales.c -o axis_scales.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chull.c -o chull.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devices.c -o devices.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stubs.c -o stubs.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c colors.c -o colors.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devCairo.c -o devCairo.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devPicTeX.c -o devPicTeX.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devPS.c -o devPS.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devQuartz.c -o devQuartz.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR make[7]: Entering directory '/<>/src/library/grDevices/src' mkdir -p -- ../../../../library/grDevices/libs make[8]: Entering directory '/<>/src/library/grDevices/src/cairo' making cairoBM.d from cairoBM.c make[9]: Entering directory '/<>/src/library/grDevices/src/cairo' make[10]: Entering directory '/<>/src/library/grDevices/src/cairo' gcc -std=gnu99 -I. -I../../../../../src/include -I../../../../../src/include -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/harfbuzz -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/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../../../src/modules/X11 -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cairoBM.c -o cairoBM.o gcc -std=gnu99 -shared -L"../../../../../lib" -Wl,-Bsymbolic-functions -Wl,-z,relro -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -ltiff -L/build/libjpeg-turbo-ff4xqQ/libjpeg-turbo-2.0.3/obj-x86_64-linux-gnu/lib/x86_64-linux-gnu -ljpeg -lpng16 -lz -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lpng16 -lz -lcairo -L"../../../../../lib" -lR -lm make[10]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[9]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[8]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[7]: Leaving directory '/<>/src/library/grDevices/src' make[6]: Leaving directory '/<>/src/library/grDevices/src' make[5]: Leaving directory '/<>/src/library/grDevices' make[5]: Entering directory '/<>/src/library/grDevices' byte-compiling package 'grDevices' make[5]: Leaving directory '/<>/src/library/grDevices' make[4]: Leaving directory '/<>/src/library/grDevices' make[4]: Entering directory '/<>/src/library/graphics' building package 'graphics' mkdir -p -- ../../../library/graphics make[5]: Entering directory '/<>/src/library/graphics' mkdir -p -- ../../../library/graphics/R make[5]: Leaving directory '/<>/src/library/graphics' make[5]: Entering directory '/<>/src/library/graphics' make[6]: Entering directory '/<>/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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c base.c -o base.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c graphics.c -o graphics.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c par.c -o par.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plot.c -o plot.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plot3d.c -o plot3d.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stem.c -o stem.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR make[7]: Entering directory '/<>/src/library/graphics/src' mkdir -p -- ../../../../library/graphics/libs make[7]: Leaving directory '/<>/src/library/graphics/src' make[6]: Leaving directory '/<>/src/library/graphics/src' make[5]: Leaving directory '/<>/src/library/graphics' make[5]: Entering directory '/<>/src/library/graphics' byte-compiling package 'graphics' make[5]: Leaving directory '/<>/src/library/graphics' make[4]: Leaving directory '/<>/src/library/graphics' make[4]: Entering directory '/<>/src/library/stats' building package 'stats' mkdir -p -- ../../../library/stats make[5]: Entering directory '/<>/src/library/stats' mkdir -p -- ../../../library/stats/R make[5]: Leaving directory '/<>/src/library/stats' make[5]: Entering directory '/<>/src/library/stats' make[6]: Entering directory '/<>/src/library/stats/src' making init.d from init.c making kmeans.d from kmeans.c making ansari.d from ansari.c making bandwidths.d from bandwidths.c making chisqsim.d from chisqsim.c making d2x2xk.d from d2x2xk.c making fexact.d from fexact.c making kendall.d from kendall.c making ks.d from ks.c making line.d from line.c making smooth.d from smooth.c making prho.d from prho.c making swilk.d from swilk.c making ksmooth.d from ksmooth.c making loessc.d from loessc.c making monoSpl.d from monoSpl.c making isoreg.d from isoreg.c making Srunmed.d from Srunmed.c making dblcen.d from dblcen.c making distance.d from distance.c making hclust-utils.d from hclust-utils.c making nls.d from nls.c making rWishart.d from rWishart.c making HoltWinters.d from HoltWinters.c making PPsum.d from PPsum.c making arima.d from arima.c making burg.d from burg.c making filter.d from filter.c making mAR.d from mAR.c making pacf.d from pacf.c making starma.d from starma.c making port.d from port.c making family.d from family.c making sbart.d from sbart.c making approx.d from approx.c making loglin.d from loglin.c making lowess.d from lowess.c making massdist.d from massdist.c making splines.d from splines.c making lm.d from lm.c making complete_cases.d from complete_cases.c making cov.d from cov.c making deriv.d from deriv.c making fft.d from fft.c making fourier.d from fourier.c making model.d from model.c making optim.d from optim.c making optimize.d from optimize.c making integrate.d from integrate.c making random.d from random.c making distn.d from distn.c making zeroin.d from zeroin.c making rcont.d from rcont.c making influence.d from influence.c gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c kmeans.c -o kmeans.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ansari.c -o ansari.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bandwidths.c -o bandwidths.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chisqsim.c -o chisqsim.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c d2x2xk.c -o d2x2xk.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fexact.c -o fexact.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c kendall.c -o kendall.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ks.c -o ks.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c line.c -o line.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c smooth.c -o smooth.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c prho.c -o prho.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c swilk.c -o swilk.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ksmooth.c -o ksmooth.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c loessc.c -o loessc.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c monoSpl.c -o monoSpl.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c isoreg.c -o isoreg.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Srunmed.c -o Srunmed.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dblcen.c -o dblcen.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c distance.c -o distance.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c hclust-utils.c -o hclust-utils.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nls.c -o nls.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rWishart.c -o rWishart.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c HoltWinters.c -o HoltWinters.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c PPsum.c -o PPsum.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c arima.c -o arima.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c burg.c -o burg.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c filter.c -o filter.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mAR.c -o mAR.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pacf.c -o pacf.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c starma.c -o starma.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c port.c -o port.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c family.c -o family.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sbart.c -o sbart.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c approx.c -o approx.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c loglin.c -o loglin.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lowess.c -o lowess.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c massdist.c -o massdist.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c splines.c -o splines.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lm.c -o lm.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c complete_cases.c -o complete_cases.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cov.c -o cov.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c deriv.c -o deriv.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fft.c -o fft.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fourier.c -o fourier.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c model.c -o model.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c optim.c -o optim.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c optimize.c -o optimize.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c integrate.c -o integrate.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c random.c -o random.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c distn.c -o distn.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c zeroin.c -o zeroin.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rcont.c -o rcont.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c influence.c -o influence.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c bsplvd.f -o bsplvd.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c bvalue.f -o bvalue.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c bvalus.f -o bvalus.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c loessf.f -o loessf.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c ppr.f -o ppr.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c qsbart.f -o qsbart.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c sgram.f -o sgram.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c sinerp.f -o sinerp.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c sslvrg.f -o sslvrg.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c stxwx.f -o stxwx.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c hclust.f -o hclust.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c kmns.f -o kmns.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c eureka.f -o eureka.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c stl.f -o stl.o gfortran -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -msse2 -mfpmath=sse -c portsrc.f -o portsrc.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -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 '/<>/src/library/stats/src' mkdir -p -- ../../../../library/stats/libs make[7]: Leaving directory '/<>/src/library/stats/src' make[6]: Leaving directory '/<>/src/library/stats/src' make[5]: Leaving directory '/<>/src/library/stats' make[5]: Entering directory '/<>/src/library/stats' byte-compiling package 'stats' make[5]: Leaving directory '/<>/src/library/stats' make[4]: Leaving directory '/<>/src/library/stats' make[4]: Entering directory '/<>/src/library/datasets' building package 'datasets' mkdir -p -- ../../../library/datasets make[5]: Entering directory '/<>/src/library/datasets' make[5]: Leaving directory '/<>/src/library/datasets' mkdir -p -- ../../../library/datasets/data make[4]: Leaving directory '/<>/src/library/datasets' make[4]: Entering directory '/<>/src/library/methods' building package 'methods' mkdir -p -- ../../../library/methods make[5]: Entering directory '/<>/src/library/methods' mkdir -p -- ../../../library/methods/R make[5]: Leaving directory '/<>/src/library/methods' make[5]: Entering directory '/<>/src/library/methods' make[6]: Entering directory '/<>/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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c do_substitute_direct.c -o do_substitute_direct.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c methods_list_dispatch.c -o methods_list_dispatch.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c slot.c -o slot.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c class_support.c -o class_support.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tests.c -o tests.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o -L../../../../lib -lR make[7]: Entering directory '/<>/src/library/methods/src' mkdir -p -- ../../../../library/methods/libs make[7]: Leaving directory '/<>/src/library/methods/src' make[6]: Leaving directory '/<>/src/library/methods/src' make[5]: Leaving directory '/<>/src/library/methods' make[5]: Entering directory '/<>/src/library/methods' byte-compiling 'methods' initializing class and method definitions ... done make[5]: Leaving directory '/<>/src/library/methods' make[4]: Leaving directory '/<>/src/library/methods' make[4]: Entering directory '/<>/src/library/grid' building package 'grid' mkdir -p -- ../../../library/grid mkdir -p -- ../../../library/grid/doc make[5]: Entering directory '/<>/src/library/grid' mkdir -p -- ../../../library/grid/R make[5]: Leaving directory '/<>/src/library/grid' make[5]: Entering directory '/<>/src/library/grid' make[6]: Entering directory '/<>/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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gpar.c -o gpar.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c grid.c -o grid.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c just.c -o just.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c layout.c -o layout.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c matrix.c -o matrix.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c register.c -o register.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c state.c -o state.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unit.c -o unit.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c util.c -o util.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c viewport.c -o viewport.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o grid.so gpar.o grid.o just.o layout.o matrix.o register.o state.o unit.o util.o viewport.o -L../../../../lib -lR make[7]: Entering directory '/<>/src/library/grid/src' mkdir -p -- ../../../../library/grid/libs make[7]: Leaving directory '/<>/src/library/grid/src' make[6]: Leaving directory '/<>/src/library/grid/src' make[5]: Leaving directory '/<>/src/library/grid' make[5]: Entering directory '/<>/src/library/grid' byte-compiling package 'grid' make[5]: Leaving directory '/<>/src/library/grid' make[4]: Leaving directory '/<>/src/library/grid' make[4]: Entering directory '/<>/src/library/splines' building package 'splines' mkdir -p -- ../../../library/splines make[5]: Entering directory '/<>/src/library/splines' mkdir -p -- ../../../library/splines/R make[5]: Leaving directory '/<>/src/library/splines' make[5]: Entering directory '/<>/src/library/splines' make[6]: Entering directory '/<>/src/library/splines/src' making splines.d from splines.c gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c splines.c -o splines.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o splines.so splines.o -L../../../../lib -lR make[7]: Entering directory '/<>/src/library/splines/src' mkdir -p -- ../../../../library/splines/libs make[7]: Leaving directory '/<>/src/library/splines/src' make[6]: Leaving directory '/<>/src/library/splines/src' make[5]: Leaving directory '/<>/src/library/splines' make[5]: Entering directory '/<>/src/library/splines' byte-compiling package 'splines' make[5]: Leaving directory '/<>/src/library/splines' make[4]: Leaving directory '/<>/src/library/splines' make[4]: Entering directory '/<>/src/library/stats4' building package 'stats4' mkdir -p -- ../../../library/stats4 make[5]: Entering directory '/<>/src/library/stats4' mkdir -p -- ../../../library/stats4/R make[5]: Leaving directory '/<>/src/library/stats4' make[5]: Entering directory '/<>/src/library/stats4' byte-compiling package 'stats4' make[5]: Leaving directory '/<>/src/library/stats4' make[4]: Leaving directory '/<>/src/library/stats4' make[4]: Entering directory '/<>/src/library/tcltk' building package 'tcltk' mkdir -p -- ../../../library/tcltk/R make[5]: Entering directory '/<>/src/library/tcltk' mkdir -p -- ../../../library/tcltk/exec make[5]: Leaving directory '/<>/src/library/tcltk' make[5]: Entering directory '/<>/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 -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include/tcl8.6 -I/usr/include/tcl8.6 -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tcltk.c -o tcltk.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include/tcl8.6 -I/usr/include/tcl8.6 -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tcltk_unix.c -o tcltk_unix.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib/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 '/<>/src/library/tcltk/src' mkdir -p -- ../../../../library/tcltk/libs make[6]: Leaving directory '/<>/src/library/tcltk/src' make[5]: Leaving directory '/<>/src/library/tcltk/src' make[5]: Entering directory '/<>/src/library/tcltk' byte-compiling package 'tcltk' make[5]: Leaving directory '/<>/src/library/tcltk' make[4]: Leaving directory '/<>/src/library/tcltk' make[4]: Entering directory '/<>/src/library/parallel' building package 'parallel' mkdir -p -- ../../../library/parallel mkdir -p -- ../../../library/parallel/doc make[5]: Entering directory '/<>/src/library/parallel' mkdir -p -- ../../../library/parallel/R make[5]: Leaving directory '/<>/src/library/parallel' make[5]: Entering directory '/<>/src/library/parallel' make[6]: Entering directory '/<>/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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rngstream.c -o rngstream.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fork.c -o fork.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR make[7]: Entering directory '/<>/src/library/parallel/src' mkdir -p -- ../../../../library/parallel/libs make[7]: Leaving directory '/<>/src/library/parallel/src' make[6]: Leaving directory '/<>/src/library/parallel/src' make[5]: Leaving directory '/<>/src/library/parallel' make[5]: Entering directory '/<>/src/library/parallel' byte-compiling package 'parallel' make[5]: Leaving directory '/<>/src/library/parallel' make[4]: Leaving directory '/<>/src/library/parallel' make[4]: Entering directory '/<>/src/library/base' make[4]: Leaving directory '/<>/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/<>/src/library' make[2]: Leaving directory '/<>/src' make[2]: Entering directory '/<>/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/tests' you should 'make docs' now ... make[1]: Leaving directory '/<>' (cd src/nmath/standalone; \ /usr/bin/make CFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ CXXFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ FFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -D_REENTRANT" \ CC="gcc -std=gnu99" \ CXX=g++ \ F77=gfortran \ R_GZIPCMD="/bin/gzip -n" \ libRmath_la_LDFLAGS=-Wl,-soname,libRmath.so.1 \ shared static ) make[1]: Entering directory '/<>/src/nmath/standalone' (cd ../../include; /usr/bin/make Rmath.h) make[2]: Entering directory '/<>/src/include' make[2]: 'Rmath.h' is up to date. make[2]: Leaving directory '/<>/src/include' Copying source files make[2]: Entering directory '/<>/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 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 '/<>/src/nmath/standalone' make[2]: Entering directory '/<>/src/nmath/standalone' gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c mlutils.c -o mlutils.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c d1mach.c -o d1mach.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c i1mach.c -o i1mach.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fmax2.c -o fmax2.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fmin2.c -o fmin2.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fprec.c -o fprec.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fround.c -o fround.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ftrunc.c -o ftrunc.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c sign.c -o sign.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fsign.c -o fsign.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c imax2.c -o imax2.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c imin2.c -o imin2.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c chebyshev.c -o chebyshev.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c log1p.c -o log1p.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lgammacor.c -o lgammacor.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gammalims.c -o gammalims.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c stirlerr.c -o stirlerr.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bd0.c -o bd0.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gamma.c -o gamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lgamma.c -o lgamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gamma_cody.c -o gamma_cody.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c beta.c -o beta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lbeta.c -o lbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c polygamma.c -o polygamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c cospi.c -o cospi.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_i.c -o bessel_i.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_j.c -o bessel_j.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_k.c -o bessel_k.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_y.c -o bessel_y.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c choose.c -o choose.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c snorm.c -o snorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c sexp.c -o sexp.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dgamma.c -o dgamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pgamma.c -o pgamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qgamma.c -o qgamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rgamma.c -o rgamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dbeta.c -o dbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pbeta.c -o pbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbeta.c -o qbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rbeta.c -o rbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dunif.c -o dunif.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c punif.c -o punif.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qunif.c -o qunif.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c runif.c -o runif.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnorm.c -o dnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnorm.c -o pnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnorm.c -o qnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnorm.c -o rnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dlnorm.c -o dlnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c plnorm.c -o plnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qlnorm.c -o qlnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rlnorm.c -o rlnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c df.c -o df.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pf.c -o pf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qf.c -o qf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rf.c -o rf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnf.c -o dnf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dt.c -o dt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pt.c -o pt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qt.c -o qt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rt.c -o rt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnt.c -o dnt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dchisq.c -o dchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pchisq.c -o pchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qchisq.c -o qchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rchisq.c -o rchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnchisq.c -o rnchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dbinom.c -o dbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pbinom.c -o pbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbinom.c -o qbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rbinom.c -o rbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rmultinom.c -o rmultinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dcauchy.c -o dcauchy.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pcauchy.c -o pcauchy.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qcauchy.c -o qcauchy.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rcauchy.c -o rcauchy.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dexp.c -o dexp.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pexp.c -o pexp.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qexp.c -o qexp.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rexp.c -o rexp.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dgeom.c -o dgeom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pgeom.c -o pgeom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qgeom.c -o qgeom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rgeom.c -o rgeom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dhyper.c -o dhyper.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c phyper.c -o phyper.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qhyper.c -o qhyper.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rhyper.c -o rhyper.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnbinom.c -o dnbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnbinom.c -o pnbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnbinom.c -o qnbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnbinom.c -o rnbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dpois.c -o dpois.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ppois.c -o ppois.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qpois.c -o qpois.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rpois.c -o rpois.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dweibull.c -o dweibull.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pweibull.c -o pweibull.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qweibull.c -o qweibull.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rweibull.c -o rweibull.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dlogis.c -o dlogis.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c plogis.c -o plogis.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qlogis.c -o qlogis.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rlogis.c -o rlogis.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnchisq.c -o dnchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnchisq.c -o pnchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnchisq.c -o qnchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnbeta.c -o dnbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnbeta.c -o pnbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnbeta.c -o qnbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnf.c -o pnf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnt.c -o pnt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnf.c -o qnf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnt.c -o qnt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ptukey.c -o ptukey.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qtukey.c -o qtukey.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c toms708.c -o toms708.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp 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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 '/<>/src/nmath/standalone' make[2]: Entering directory '/<>/src/nmath/standalone' gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c mlutils.c -o mlutils.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c d1mach.c -o d1mach.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c i1mach.c -o i1mach.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fmax2.c -o fmax2.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fmin2.c -o fmin2.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fprec.c -o fprec.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat 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-I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c imax2.c -o imax2.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c imin2.c -o imin2.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c chebyshev.c -o chebyshev.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c log1p.c -o log1p.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lgammacor.c -o lgammacor.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gammalims.c -o gammalims.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c stirlerr.c -o stirlerr.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bd0.c -o bd0.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gamma.c -o gamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lgamma.c -o lgamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gamma_cody.c -o gamma_cody.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c beta.c -o beta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lbeta.c -o lbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c polygamma.c -o polygamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c cospi.c -o cospi.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_i.c -o bessel_i.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_j.c -o bessel_j.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_k.c -o bessel_k.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_y.c -o bessel_y.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c choose.c -o choose.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c snorm.c -o snorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c sexp.c -o sexp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dgamma.c -o dgamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pgamma.c -o pgamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qgamma.c -o qgamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rgamma.c -o rgamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dbeta.c -o dbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pbeta.c -o pbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbeta.c -o qbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rbeta.c -o rbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dunif.c -o dunif.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c punif.c -o punif.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qunif.c -o qunif.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c runif.c -o runif.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnorm.c -o dnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnorm.c -o pnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnorm.c -o qnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnorm.c -o rnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dlnorm.c -o dlnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c plnorm.c -o plnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qlnorm.c -o qlnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rlnorm.c -o rlnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c df.c -o df.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pf.c -o pf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qf.c -o qf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rf.c -o rf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnf.c -o dnf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dt.c -o dt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pt.c -o pt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qt.c -o qt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rt.c -o rt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnt.c -o dnt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dchisq.c -o dchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pchisq.c -o pchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qchisq.c -o qchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rchisq.c -o rchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnchisq.c -o rnchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dbinom.c -o dbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pbinom.c -o pbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbinom.c -o qbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rbinom.c -o rbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rmultinom.c -o rmultinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dcauchy.c -o dcauchy.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pcauchy.c -o pcauchy.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qcauchy.c -o qcauchy.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rcauchy.c -o rcauchy.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dexp.c -o dexp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat 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-D_REENTRANT -c rnbinom.c -o rnbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dpois.c -o dpois.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ppois.c -o ppois.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qpois.c -o qpois.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rpois.c -o rpois.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dweibull.c -o dweibull.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pweibull.c -o pweibull.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qweibull.c -o qweibull.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rweibull.c -o rweibull.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dlogis.c -o dlogis.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c plogis.c -o plogis.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 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directory '/<>/src/modules/X11' make[5]: Entering directory '/<>/src/modules/X11' /<>/modules/R_X11.so is unchanged /<>/modules/R_de.so is unchanged make[5]: Leaving directory '/<>/src/modules/X11' make[4]: Leaving directory '/<>/src/modules/X11' make[3]: Leaving directory '/<>/src/modules' make[3]: Entering directory '/<>/src/library' make[4]: Entering directory '/<>/src/library/profile' building system startup profile make[4]: Leaving directory '/<>/src/library/profile' make[4]: Entering directory '/<>/src/library/translations' building package 'translations' make[5]: Entering directory '/<>/src/library/translations' make[5]: Leaving directory '/<>/src/library/translations' make[4]: Leaving directory '/<>/src/library/translations' make[4]: Entering directory '/<>/src/library/base' building package 'base' make[5]: Entering directory '/<>/src/library/base' all.R is unchanged make[5]: Leaving directory '/<>/src/library/base' make[4]: Leaving directory '/<>/src/library/base' make[4]: Entering directory '/<>/src/library/tools' building package 'tools' make[5]: Entering directory '/<>/src/library/tools' all.R is unchanged make[5]: Leaving directory '/<>/src/library/tools' make[5]: Entering directory '/<>/src/library/tools' make[6]: Entering directory '/<>/src/library/tools/src' make[7]: Entering directory '/<>/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory '/<>/src/library/tools/src' make[6]: Leaving directory '/<>/src/library/tools/src' make[5]: Leaving directory '/<>/src/library/tools' make[5]: Entering directory '/<>/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/<>/src/library/tools' make[4]: Leaving directory '/<>/src/library/tools' make[4]: Entering directory '/<>/src/library/compiler' building package 'compiler' make[5]: Entering directory '/<>/src/library/compiler' all.R is unchanged make[5]: Leaving directory '/<>/src/library/compiler' make[5]: Entering directory '/<>/src/library/compiler' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/compiler' make[4]: Leaving directory '/<>/src/library/compiler' make[4]: Entering directory '/<>/src/library/base' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/<>/src/library/base' make[4]: Entering directory '/<>/src/library/tools' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/<>/src/library/tools' make[4]: Entering directory '/<>/src/library/utils' building package 'utils' make[5]: Entering directory '/<>/src/library/utils' all.R is unchanged make[5]: Nothing to be done for 'iconvlist'. make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' make[6]: Entering directory '/<>/src/library/utils/src' make[7]: Entering directory '/<>/src/library/utils/src' ../../../../library/utils/libs/utils.so is unchanged make[7]: Leaving directory '/<>/src/library/utils/src' make[6]: Leaving directory '/<>/src/library/utils/src' make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/utils' make[4]: Leaving directory '/<>/src/library/utils' make[4]: Entering directory '/<>/src/library/grDevices' building package 'grDevices' make[5]: Entering directory '/<>/src/library/grDevices' all.R is unchanged make[5]: Leaving directory '/<>/src/library/grDevices' make[5]: Entering directory '/<>/src/library/grDevices' make[6]: Entering directory '/<>/src/library/grDevices/src' make[7]: Entering directory '/<>/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[8]: Entering directory '/<>/src/library/grDevices/src/cairo' make[9]: Entering directory '/<>/src/library/grDevices/src/cairo' make[10]: Entering directory '/<>/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[9]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[8]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[7]: Leaving directory '/<>/src/library/grDevices/src' make[6]: Leaving directory '/<>/src/library/grDevices/src' make[5]: Leaving directory '/<>/src/library/grDevices' make[5]: Entering directory '/<>/src/library/grDevices' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/grDevices' make[4]: Leaving directory '/<>/src/library/grDevices' make[4]: Entering directory '/<>/src/library/graphics' building package 'graphics' make[5]: Entering directory '/<>/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/<>/src/library/graphics' make[5]: Entering directory '/<>/src/library/graphics' make[6]: Entering directory '/<>/src/library/graphics/src' make[7]: Entering directory '/<>/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/<>/src/library/graphics/src' make[6]: Leaving directory '/<>/src/library/graphics/src' make[5]: Leaving directory '/<>/src/library/graphics' make[5]: Entering directory '/<>/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/graphics' make[4]: Leaving directory '/<>/src/library/graphics' make[4]: Entering directory '/<>/src/library/stats' building package 'stats' make[5]: Entering directory '/<>/src/library/stats' all.R is unchanged make[5]: Leaving directory '/<>/src/library/stats' make[5]: Entering directory '/<>/src/library/stats' make[6]: Entering directory '/<>/src/library/stats/src' make[7]: Entering directory '/<>/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/<>/src/library/stats/src' make[6]: Leaving directory '/<>/src/library/stats/src' make[5]: Leaving directory '/<>/src/library/stats' make[5]: Entering directory '/<>/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/stats' make[4]: Leaving directory '/<>/src/library/stats' make[4]: Entering directory '/<>/src/library/datasets' building package 'datasets' make[5]: Entering directory '/<>/src/library/datasets' make[5]: Leaving directory '/<>/src/library/datasets' make[4]: Leaving directory '/<>/src/library/datasets' make[4]: Entering directory '/<>/src/library/methods' building package 'methods' make[5]: Entering directory '/<>/src/library/methods' all.R is unchanged make[5]: Leaving directory '/<>/src/library/methods' make[5]: Entering directory '/<>/src/library/methods' make[6]: Entering directory '/<>/src/library/methods/src' make[7]: Entering directory '/<>/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/<>/src/library/methods/src' make[6]: Leaving directory '/<>/src/library/methods/src' make[5]: Leaving directory '/<>/src/library/methods' make[5]: Entering directory '/<>/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/<>/src/library/methods' make[4]: Leaving directory '/<>/src/library/methods' make[4]: Entering directory '/<>/src/library/grid' building package 'grid' make[5]: Entering directory '/<>/src/library/grid' all.R is unchanged make[5]: Leaving directory '/<>/src/library/grid' make[5]: Entering directory '/<>/src/library/grid' make[6]: Entering directory '/<>/src/library/grid/src' make[7]: Entering directory '/<>/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/<>/src/library/grid/src' make[6]: Leaving directory '/<>/src/library/grid/src' make[5]: Leaving directory '/<>/src/library/grid' make[5]: Entering directory '/<>/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/grid' make[4]: Leaving directory '/<>/src/library/grid' make[4]: Entering directory '/<>/src/library/splines' building package 'splines' make[5]: Entering directory '/<>/src/library/splines' all.R is unchanged make[5]: Leaving directory '/<>/src/library/splines' make[5]: Entering directory '/<>/src/library/splines' make[6]: Entering directory '/<>/src/library/splines/src' make[7]: Entering directory '/<>/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/<>/src/library/splines/src' make[6]: Leaving directory '/<>/src/library/splines/src' make[5]: Leaving directory '/<>/src/library/splines' make[5]: Entering directory '/<>/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/splines' make[4]: Leaving directory '/<>/src/library/splines' make[4]: Entering directory '/<>/src/library/stats4' building package 'stats4' make[5]: Entering directory '/<>/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/<>/src/library/stats4' make[5]: Entering directory '/<>/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/stats4' make[4]: Leaving directory '/<>/src/library/stats4' make[4]: Entering directory '/<>/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/<>/src/library/tcltk' make[5]: Leaving directory '/<>/src/library/tcltk' make[5]: Entering directory '/<>/src/library/tcltk/src' make[6]: Entering directory '/<>/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/<>/src/library/tcltk/src' make[5]: Leaving directory '/<>/src/library/tcltk/src' make[5]: Entering directory '/<>/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/tcltk' make[4]: Leaving directory '/<>/src/library/tcltk' make[4]: Entering directory '/<>/src/library/parallel' building package 'parallel' make[5]: Entering directory '/<>/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/<>/src/library/parallel' make[5]: Entering directory '/<>/src/library/parallel' make[6]: Entering directory '/<>/src/library/parallel/src' make[7]: Entering directory '/<>/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/<>/src/library/parallel/src' make[6]: Leaving directory '/<>/src/library/parallel/src' make[5]: Leaving directory '/<>/src/library/parallel' make[5]: Entering directory '/<>/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/parallel' make[4]: Leaving directory '/<>/src/library/parallel' make[4]: Entering directory '/<>/src/library/base' make[4]: Leaving directory '/<>/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/<>/src/library' make[2]: Leaving directory '/<>/src' make[2]: Entering directory '/<>/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/tests' you should 'make docs' now ... make[2]: Entering directory '/<>/doc' creating doc/NEWS creating doc/NEWS.pdf make[3]: Entering directory '/<>/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 '/<>/doc/html' make[4]: Leaving directory '/<>/doc/html' make[3]: Leaving directory '/<>/doc/manual' make[2]: Leaving directory '/<>/doc' make[2]: Entering directory '/<>/src/library' make[3]: Entering directory '/<>/src/library' installing parsed Rd make[4]: Entering directory '/<>/src/library' base stats utils methods graphics grDevices datasets grid tools tcltk splines stats4 compiler parallel make[4]: Leaving directory '/<>/src/library' make[3]: Leaving directory '/<>/src/library' make[3]: Entering directory '/<>/src/library' building/updating package metadata ... make[3]: Leaving directory '/<>/src/library' make[3]: Entering directory '/<>/src/library' writing package indices make[4]: Entering directory '/<>/src/library' make[4]: Leaving directory '/<>/src/library' make[3]: Leaving directory '/<>/src/library' make[2]: Leaving directory '/<>/src/library' make[1]: Leaving directory '/<>' /usr/bin/make javaconf make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/m4' make[2]: Entering directory '/<>/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/tools' make[2]: Entering directory '/<>/doc' make[3]: Entering directory '/<>/doc/html' make[3]: Leaving directory '/<>/doc/html' make[3]: Entering directory '/<>/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/<>/doc/manual' make[2]: Leaving directory '/<>/doc' make[2]: Entering directory '/<>/etc' make[2]: Leaving directory '/<>/etc' make[2]: Entering directory '/<>/share' make[2]: Leaving directory '/<>/share' make[2]: Entering directory '/<>/src' make[3]: Entering directory '/<>/src/scripts' make[4]: Entering directory '/<>/src/scripts' make[4]: Leaving directory '/<>/src/scripts' make[3]: Leaving directory '/<>/src/scripts' make[3]: Entering directory '/<>/src/include' make[4]: Entering directory '/<>/src/include/R_ext' make[4]: Nothing to be done for 'R'. make[4]: Leaving directory '/<>/src/include/R_ext' make[3]: Leaving directory '/<>/src/include' make[3]: Entering directory '/<>/src/extra' make[4]: Entering directory '/<>/src/extra/tre' make[5]: Entering directory '/<>/src/extra/tre' make[5]: 'Makedeps' is up to date. make[5]: Leaving directory '/<>/src/extra/tre' make[5]: Entering directory '/<>/src/extra/tre' make[5]: 'libtre.a' is up to date. make[5]: Leaving directory '/<>/src/extra/tre' make[4]: Leaving directory '/<>/src/extra/tre' make[3]: Leaving directory '/<>/src/extra' make[3]: Entering directory '/<>/src/appl' make[4]: Entering directory '/<>/src/appl' make[4]: 'libappl.a' is up to date. make[4]: Leaving directory '/<>/src/appl' make[3]: Leaving directory '/<>/src/appl' make[3]: Entering directory '/<>/src/nmath' make[4]: Entering directory '/<>/src/nmath' make[4]: 'libnmath.a' is up to date. make[4]: Leaving directory '/<>/src/nmath' make[3]: Leaving directory '/<>/src/nmath' make[3]: Entering directory '/<>/src/unix' make[4]: Entering directory '/<>/src/unix' make[4]: 'libunix.a' is up to date. make[4]: Leaving directory '/<>/src/unix' make[4]: Entering directory '/<>/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/<>"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/<>/src/unix' make[3]: Leaving directory '/<>/src/unix' make[3]: Entering directory '/<>/src/main' make[4]: Entering directory '/<>/src/main' make[5]: Entering directory '/<>/src/main' /<>/lib/libR.so is unchanged make[5]: Leaving directory '/<>/src/main' make[4]: Leaving directory '/<>/src/main' make[4]: Entering directory '/<>/src/main' make[5]: Entering directory '/<>/src/main' /<>/bin/exec/R is unchanged make[5]: Leaving directory '/<>/src/main' make[4]: Leaving directory '/<>/src/main' make[3]: Leaving directory '/<>/src/main' make[3]: Entering directory '/<>/src/modules' make[4]: Entering directory '/<>/src/modules/internet' make[5]: Entering directory '/<>/src/modules/internet' make[5]: 'internet.so' is up to date. make[5]: Leaving directory '/<>/src/modules/internet' make[4]: Leaving directory '/<>/src/modules/internet' make[4]: Entering directory '/<>/src/modules/lapack' make[5]: Entering directory '/<>/src/modules/lapack' make[5]: 'lapack.so' is up to date. make[5]: Leaving directory '/<>/src/modules/lapack' make[4]: Leaving directory '/<>/src/modules/lapack' make[4]: Entering directory '/<>/src/modules/X11' make[5]: Entering directory '/<>/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 '/<>/src/modules/X11' make[5]: Entering directory '/<>/src/modules/X11' /<>/modules/R_X11.so is unchanged /<>/modules/R_de.so is unchanged make[5]: Leaving directory '/<>/src/modules/X11' make[4]: Leaving directory '/<>/src/modules/X11' make[3]: Leaving directory '/<>/src/modules' make[3]: Entering directory '/<>/src/library' make[4]: Entering directory '/<>/src/library/profile' building system startup profile make[4]: Leaving directory '/<>/src/library/profile' make[4]: Entering directory '/<>/src/library/translations' building package 'translations' make[5]: Entering directory '/<>/src/library/translations' make[5]: Leaving directory '/<>/src/library/translations' make[4]: Leaving directory '/<>/src/library/translations' make[4]: Entering directory '/<>/src/library/base' building package 'base' make[5]: Entering directory '/<>/src/library/base' all.R is unchanged make[5]: Leaving directory '/<>/src/library/base' make[4]: Leaving directory '/<>/src/library/base' make[4]: Entering directory '/<>/src/library/tools' building package 'tools' make[5]: Entering directory '/<>/src/library/tools' all.R is unchanged make[5]: Leaving directory '/<>/src/library/tools' make[5]: Entering directory '/<>/src/library/tools' make[6]: Entering directory '/<>/src/library/tools/src' make[7]: Entering directory '/<>/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory '/<>/src/library/tools/src' make[6]: Leaving directory '/<>/src/library/tools/src' make[5]: Leaving directory '/<>/src/library/tools' make[5]: Entering directory '/<>/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/<>/src/library/tools' make[4]: Leaving directory '/<>/src/library/tools' make[4]: Entering directory '/<>/src/library/compiler' building package 'compiler' make[5]: Entering directory '/<>/src/library/compiler' all.R is unchanged make[5]: Leaving directory '/<>/src/library/compiler' make[5]: Entering directory '/<>/src/library/compiler' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/compiler' make[4]: Leaving directory '/<>/src/library/compiler' make[4]: Entering directory '/<>/src/library/base' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/<>/src/library/base' make[4]: Entering directory '/<>/src/library/tools' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/<>/src/library/tools' make[4]: Entering directory '/<>/src/library/utils' building package 'utils' make[5]: Entering directory '/<>/src/library/utils' all.R is unchanged make[5]: Nothing to be done for 'iconvlist'. make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' make[6]: Entering directory '/<>/src/library/utils/src' make[7]: Entering directory '/<>/src/library/utils/src' ../../../../library/utils/libs/utils.so is unchanged make[7]: Leaving directory '/<>/src/library/utils/src' make[6]: Leaving directory '/<>/src/library/utils/src' make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/utils' make[4]: Leaving directory '/<>/src/library/utils' make[4]: Entering directory '/<>/src/library/grDevices' building package 'grDevices' make[5]: Entering directory '/<>/src/library/grDevices' all.R is unchanged make[5]: Leaving directory '/<>/src/library/grDevices' make[5]: Entering directory '/<>/src/library/grDevices' make[6]: Entering directory '/<>/src/library/grDevices/src' make[7]: Entering directory '/<>/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[8]: Entering directory '/<>/src/library/grDevices/src/cairo' make[9]: Entering directory '/<>/src/library/grDevices/src/cairo' make[10]: Entering directory '/<>/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[9]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[8]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[7]: Leaving directory '/<>/src/library/grDevices/src' make[6]: Leaving directory '/<>/src/library/grDevices/src' make[5]: Leaving directory '/<>/src/library/grDevices' make[5]: Entering directory '/<>/src/library/grDevices' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/grDevices' make[4]: Leaving directory '/<>/src/library/grDevices' make[4]: Entering directory '/<>/src/library/graphics' building package 'graphics' make[5]: Entering directory '/<>/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/<>/src/library/graphics' make[5]: Entering directory '/<>/src/library/graphics' make[6]: Entering directory '/<>/src/library/graphics/src' make[7]: Entering directory '/<>/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/<>/src/library/graphics/src' make[6]: Leaving directory '/<>/src/library/graphics/src' make[5]: Leaving directory '/<>/src/library/graphics' make[5]: Entering directory '/<>/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/graphics' make[4]: Leaving directory '/<>/src/library/graphics' make[4]: Entering directory '/<>/src/library/stats' building package 'stats' make[5]: Entering directory '/<>/src/library/stats' all.R is unchanged make[5]: Leaving directory '/<>/src/library/stats' make[5]: Entering directory '/<>/src/library/stats' make[6]: Entering directory '/<>/src/library/stats/src' make[7]: Entering directory '/<>/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/<>/src/library/stats/src' make[6]: Leaving directory '/<>/src/library/stats/src' make[5]: Leaving directory '/<>/src/library/stats' make[5]: Entering directory '/<>/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/stats' make[4]: Leaving directory '/<>/src/library/stats' make[4]: Entering directory '/<>/src/library/datasets' building package 'datasets' make[5]: Entering directory '/<>/src/library/datasets' make[5]: Leaving directory '/<>/src/library/datasets' make[4]: Leaving directory '/<>/src/library/datasets' make[4]: Entering directory '/<>/src/library/methods' building package 'methods' make[5]: Entering directory '/<>/src/library/methods' all.R is unchanged make[5]: Leaving directory '/<>/src/library/methods' make[5]: Entering directory '/<>/src/library/methods' make[6]: Entering directory '/<>/src/library/methods/src' make[7]: Entering directory '/<>/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/<>/src/library/methods/src' make[6]: Leaving directory '/<>/src/library/methods/src' make[5]: Leaving directory '/<>/src/library/methods' make[5]: Entering directory '/<>/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/<>/src/library/methods' make[4]: Leaving directory '/<>/src/library/methods' make[4]: Entering directory '/<>/src/library/grid' building package 'grid' make[5]: Entering directory '/<>/src/library/grid' all.R is unchanged make[5]: Leaving directory '/<>/src/library/grid' make[5]: Entering directory '/<>/src/library/grid' make[6]: Entering directory '/<>/src/library/grid/src' make[7]: Entering directory '/<>/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/<>/src/library/grid/src' make[6]: Leaving directory '/<>/src/library/grid/src' make[5]: Leaving directory '/<>/src/library/grid' make[5]: Entering directory '/<>/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/grid' make[4]: Leaving directory '/<>/src/library/grid' make[4]: Entering directory '/<>/src/library/splines' building package 'splines' make[5]: Entering directory '/<>/src/library/splines' all.R is unchanged make[5]: Leaving directory '/<>/src/library/splines' make[5]: Entering directory '/<>/src/library/splines' make[6]: Entering directory '/<>/src/library/splines/src' make[7]: Entering directory '/<>/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/<>/src/library/splines/src' make[6]: Leaving directory '/<>/src/library/splines/src' make[5]: Leaving directory '/<>/src/library/splines' make[5]: Entering directory '/<>/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/splines' make[4]: Leaving directory '/<>/src/library/splines' make[4]: Entering directory '/<>/src/library/stats4' building package 'stats4' make[5]: Entering directory '/<>/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/<>/src/library/stats4' make[5]: Entering directory '/<>/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/stats4' make[4]: Leaving directory '/<>/src/library/stats4' make[4]: Entering directory '/<>/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/<>/src/library/tcltk' make[5]: Leaving directory '/<>/src/library/tcltk' make[5]: Entering directory '/<>/src/library/tcltk/src' make[6]: Entering directory '/<>/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/<>/src/library/tcltk/src' make[5]: Leaving directory '/<>/src/library/tcltk/src' make[5]: Entering directory '/<>/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/tcltk' make[4]: Leaving directory '/<>/src/library/tcltk' make[4]: Entering directory '/<>/src/library/parallel' building package 'parallel' make[5]: Entering directory '/<>/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/<>/src/library/parallel' make[5]: Entering directory '/<>/src/library/parallel' make[6]: Entering directory '/<>/src/library/parallel/src' make[7]: Entering directory '/<>/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/<>/src/library/parallel/src' make[6]: Leaving directory '/<>/src/library/parallel/src' make[5]: Leaving directory '/<>/src/library/parallel' make[5]: Entering directory '/<>/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/parallel' make[4]: Leaving directory '/<>/src/library/parallel' make[4]: Entering directory '/<>/src/library/base' make[4]: Leaving directory '/<>/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/<>/src/library' make[2]: Leaving directory '/<>/src' make[2]: Entering directory '/<>/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/tests' make[2]: Entering directory '/<>' configuring Java ... Java interpreter : /usr/lib/jvm/default-java/bin/java Java version : 11.0.6 Java home path : /usr/lib/jvm/default-java Java compiler : /usr/lib/jvm/default-java/bin/javac Java headers gen.: Java archive tool: /usr/lib/jvm/default-java/bin/jar trying to compile and link a JNI program detected JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm make[3]: Entering directory '/tmp/Rjavareconf.Px1Ums' gcc -std=gnu99 -I"/<>/include" -DNDEBUG -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.o gcc -std=gnu99 -shared -L/<>/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/default-java/lib/server -ljvm -L/<>/lib -lR make[3]: Leaving directory '/tmp/Rjavareconf.Px1Ums' JAVA_HOME : /usr/lib/jvm/default-java Java library path: $(JAVA_HOME)/lib/server JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm Updating Java configuration in /<> Done. make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' touch make-arch-stamp *** make-indep *** /usr/bin/make -k docs make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/m4' make[2]: Entering directory '/<>/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/tools' make[2]: Entering directory '/<>/doc' make[3]: Entering directory '/<>/doc/html' make[3]: Leaving directory '/<>/doc/html' make[3]: Entering directory '/<>/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/<>/doc/manual' make[2]: Leaving directory '/<>/doc' make[2]: Entering directory '/<>/etc' make[2]: Leaving directory '/<>/etc' make[2]: Entering directory '/<>/share' make[2]: Leaving directory '/<>/share' make[2]: Entering directory '/<>/src' make[3]: Entering directory '/<>/src/scripts' make[4]: Entering directory '/<>/src/scripts' make[4]: Leaving directory '/<>/src/scripts' make[3]: Leaving directory '/<>/src/scripts' make[3]: Entering directory '/<>/src/include' make[4]: Entering directory '/<>/src/include/R_ext' make[4]: Nothing to be done for 'R'. make[4]: Leaving directory '/<>/src/include/R_ext' make[3]: Leaving directory '/<>/src/include' make[3]: Entering directory '/<>/src/extra' make[4]: Entering directory '/<>/src/extra/tre' make[5]: Entering directory '/<>/src/extra/tre' make[5]: 'Makedeps' is up to date. make[5]: Leaving directory '/<>/src/extra/tre' make[5]: Entering directory '/<>/src/extra/tre' make[5]: 'libtre.a' is up to date. make[5]: Leaving directory '/<>/src/extra/tre' make[4]: Leaving directory '/<>/src/extra/tre' make[3]: Leaving directory '/<>/src/extra' make[3]: Entering directory '/<>/src/appl' make[4]: Entering directory '/<>/src/appl' make[4]: 'libappl.a' is up to date. make[4]: Leaving directory '/<>/src/appl' make[3]: Leaving directory '/<>/src/appl' make[3]: Entering directory '/<>/src/nmath' make[4]: Entering directory '/<>/src/nmath' make[4]: 'libnmath.a' is up to date. make[4]: Leaving directory '/<>/src/nmath' make[3]: Leaving directory '/<>/src/nmath' make[3]: Entering directory '/<>/src/unix' make[4]: Entering directory '/<>/src/unix' make[4]: 'libunix.a' is up to date. make[4]: Leaving directory '/<>/src/unix' make[4]: Entering directory '/<>/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/<>"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/<>/src/unix' make[3]: Leaving directory '/<>/src/unix' make[3]: Entering directory '/<>/src/main' make[4]: Entering directory '/<>/src/main' make[5]: Entering directory '/<>/src/main' /<>/lib/libR.so is unchanged make[5]: Leaving directory '/<>/src/main' make[4]: Leaving directory '/<>/src/main' make[4]: Entering directory '/<>/src/main' make[5]: Entering directory '/<>/src/main' /<>/bin/exec/R is unchanged make[5]: Leaving directory '/<>/src/main' make[4]: Leaving directory '/<>/src/main' make[3]: Leaving directory '/<>/src/main' make[3]: Entering directory '/<>/src/modules' make[4]: Entering directory '/<>/src/modules/internet' make[5]: Entering directory '/<>/src/modules/internet' make[5]: 'internet.so' is up to date. make[5]: Leaving directory '/<>/src/modules/internet' make[4]: Leaving directory '/<>/src/modules/internet' make[4]: Entering directory '/<>/src/modules/lapack' make[5]: Entering directory '/<>/src/modules/lapack' make[5]: 'lapack.so' is up to date. make[5]: Leaving directory '/<>/src/modules/lapack' make[4]: Leaving directory '/<>/src/modules/lapack' make[4]: Entering directory '/<>/src/modules/X11' make[5]: Entering directory '/<>/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 '/<>/src/modules/X11' make[5]: Entering directory '/<>/src/modules/X11' /<>/modules/R_X11.so is unchanged /<>/modules/R_de.so is unchanged make[5]: Leaving directory '/<>/src/modules/X11' make[4]: Leaving directory '/<>/src/modules/X11' make[3]: Leaving directory '/<>/src/modules' make[3]: Entering directory '/<>/src/library' make[4]: Entering directory '/<>/src/library/profile' building system startup profile make[4]: Leaving directory '/<>/src/library/profile' make[4]: Entering directory '/<>/src/library/translations' building package 'translations' make[5]: Entering directory '/<>/src/library/translations' make[5]: Leaving directory '/<>/src/library/translations' make[4]: Leaving directory '/<>/src/library/translations' make[4]: Entering directory '/<>/src/library/base' building package 'base' make[5]: Entering directory '/<>/src/library/base' all.R is unchanged make[5]: Leaving directory '/<>/src/library/base' make[4]: Leaving directory '/<>/src/library/base' make[4]: Entering directory '/<>/src/library/tools' building package 'tools' make[5]: Entering directory '/<>/src/library/tools' all.R is unchanged make[5]: Leaving directory '/<>/src/library/tools' make[5]: Entering directory '/<>/src/library/tools' make[6]: Entering directory '/<>/src/library/tools/src' make[7]: Entering directory '/<>/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory '/<>/src/library/tools/src' make[6]: Leaving directory '/<>/src/library/tools/src' make[5]: Leaving directory '/<>/src/library/tools' make[5]: Entering directory '/<>/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/<>/src/library/tools' make[4]: Leaving directory '/<>/src/library/tools' make[4]: Entering directory '/<>/src/library/compiler' building package 'compiler' make[5]: Entering directory '/<>/src/library/compiler' all.R is unchanged make[5]: Leaving directory '/<>/src/library/compiler' make[5]: Entering directory '/<>/src/library/compiler' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/compiler' make[4]: Leaving directory '/<>/src/library/compiler' make[4]: Entering directory '/<>/src/library/base' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/<>/src/library/base' make[4]: Entering directory '/<>/src/library/tools' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/<>/src/library/tools' make[4]: Entering directory '/<>/src/library/utils' building package 'utils' make[5]: Entering directory '/<>/src/library/utils' all.R is unchanged make[5]: Nothing to be done for 'iconvlist'. make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' make[6]: Entering directory '/<>/src/library/utils/src' make[7]: Entering directory '/<>/src/library/utils/src' ../../../../library/utils/libs/utils.so is unchanged make[7]: Leaving directory '/<>/src/library/utils/src' make[6]: Leaving directory '/<>/src/library/utils/src' make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/<>/src/library/utils' make[5]: Entering directory '/<>/src/library/utils' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/utils' make[4]: Leaving directory '/<>/src/library/utils' make[4]: Entering directory '/<>/src/library/grDevices' building package 'grDevices' make[5]: Entering directory '/<>/src/library/grDevices' all.R is unchanged make[5]: Leaving directory '/<>/src/library/grDevices' make[5]: Entering directory '/<>/src/library/grDevices' make[6]: Entering directory '/<>/src/library/grDevices/src' make[7]: Entering directory '/<>/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[8]: Entering directory '/<>/src/library/grDevices/src/cairo' make[9]: Entering directory '/<>/src/library/grDevices/src/cairo' make[10]: Entering directory '/<>/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[9]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[8]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[7]: Leaving directory '/<>/src/library/grDevices/src' make[6]: Leaving directory '/<>/src/library/grDevices/src' make[5]: Leaving directory '/<>/src/library/grDevices' make[5]: Entering directory '/<>/src/library/grDevices' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/grDevices' make[4]: Leaving directory '/<>/src/library/grDevices' make[4]: Entering directory '/<>/src/library/graphics' building package 'graphics' make[5]: Entering directory '/<>/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/<>/src/library/graphics' make[5]: Entering directory '/<>/src/library/graphics' make[6]: Entering directory '/<>/src/library/graphics/src' make[7]: Entering directory '/<>/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/<>/src/library/graphics/src' make[6]: Leaving directory '/<>/src/library/graphics/src' make[5]: Leaving directory '/<>/src/library/graphics' make[5]: Entering directory '/<>/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/graphics' make[4]: Leaving directory '/<>/src/library/graphics' make[4]: Entering directory '/<>/src/library/stats' building package 'stats' make[5]: Entering directory '/<>/src/library/stats' all.R is unchanged make[5]: Leaving directory '/<>/src/library/stats' make[5]: Entering directory '/<>/src/library/stats' make[6]: Entering directory '/<>/src/library/stats/src' make[7]: Entering directory '/<>/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/<>/src/library/stats/src' make[6]: Leaving directory '/<>/src/library/stats/src' make[5]: Leaving directory '/<>/src/library/stats' make[5]: Entering directory '/<>/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/stats' make[4]: Leaving directory '/<>/src/library/stats' make[4]: Entering directory '/<>/src/library/datasets' building package 'datasets' make[5]: Entering directory '/<>/src/library/datasets' make[5]: Leaving directory '/<>/src/library/datasets' make[4]: Leaving directory '/<>/src/library/datasets' make[4]: Entering directory '/<>/src/library/methods' building package 'methods' make[5]: Entering directory '/<>/src/library/methods' all.R is unchanged make[5]: Leaving directory '/<>/src/library/methods' make[5]: Entering directory '/<>/src/library/methods' make[6]: Entering directory '/<>/src/library/methods/src' make[7]: Entering directory '/<>/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/<>/src/library/methods/src' make[6]: Leaving directory '/<>/src/library/methods/src' make[5]: Leaving directory '/<>/src/library/methods' make[5]: Entering directory '/<>/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/<>/src/library/methods' make[4]: Leaving directory '/<>/src/library/methods' make[4]: Entering directory '/<>/src/library/grid' building package 'grid' make[5]: Entering directory '/<>/src/library/grid' all.R is unchanged make[5]: Leaving directory '/<>/src/library/grid' make[5]: Entering directory '/<>/src/library/grid' make[6]: Entering directory '/<>/src/library/grid/src' make[7]: Entering directory '/<>/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/<>/src/library/grid/src' make[6]: Leaving directory '/<>/src/library/grid/src' make[5]: Leaving directory '/<>/src/library/grid' make[5]: Entering directory '/<>/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/grid' make[4]: Leaving directory '/<>/src/library/grid' make[4]: Entering directory '/<>/src/library/splines' building package 'splines' make[5]: Entering directory '/<>/src/library/splines' all.R is unchanged make[5]: Leaving directory '/<>/src/library/splines' make[5]: Entering directory '/<>/src/library/splines' make[6]: Entering directory '/<>/src/library/splines/src' make[7]: Entering directory '/<>/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/<>/src/library/splines/src' make[6]: Leaving directory '/<>/src/library/splines/src' make[5]: Leaving directory '/<>/src/library/splines' make[5]: Entering directory '/<>/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/splines' make[4]: Leaving directory '/<>/src/library/splines' make[4]: Entering directory '/<>/src/library/stats4' building package 'stats4' make[5]: Entering directory '/<>/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/<>/src/library/stats4' make[5]: Entering directory '/<>/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/stats4' make[4]: Leaving directory '/<>/src/library/stats4' make[4]: Entering directory '/<>/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/<>/src/library/tcltk' make[5]: Leaving directory '/<>/src/library/tcltk' make[5]: Entering directory '/<>/src/library/tcltk/src' make[6]: Entering directory '/<>/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/<>/src/library/tcltk/src' make[5]: Leaving directory '/<>/src/library/tcltk/src' make[5]: Entering directory '/<>/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/tcltk' make[4]: Leaving directory '/<>/src/library/tcltk' make[4]: Entering directory '/<>/src/library/parallel' building package 'parallel' make[5]: Entering directory '/<>/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/<>/src/library/parallel' make[5]: Entering directory '/<>/src/library/parallel' make[6]: Entering directory '/<>/src/library/parallel/src' make[7]: Entering directory '/<>/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/<>/src/library/parallel/src' make[6]: Leaving directory '/<>/src/library/parallel/src' make[5]: Leaving directory '/<>/src/library/parallel' make[5]: Entering directory '/<>/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/parallel' make[4]: Leaving directory '/<>/src/library/parallel' make[4]: Entering directory '/<>/src/library/base' make[4]: Leaving directory '/<>/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/<>/src/library' make[2]: Leaving directory '/<>/src' make[2]: Entering directory '/<>/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/tests' make[2]: Entering directory '/<>/doc' make[3]: Entering directory '/<>/doc/manual' make[4]: Entering directory '/<>/doc/html' make[4]: Leaving directory '/<>/doc/html' make[3]: Leaving directory '/<>/doc/manual' make[2]: Leaving directory '/<>/doc' make[2]: Entering directory '/<>/src/library' make[3]: Entering directory '/<>/src/library' installing parsed Rd make[4]: Entering directory '/<>/src/library' base stats utils methods graphics grDevices datasets grid tools tcltk splines stats4 compiler parallel make[4]: Leaving directory '/<>/src/library' make[3]: Leaving directory '/<>/src/library' make[3]: Entering directory '/<>/src/library' building/updating package metadata ... make[3]: Leaving directory '/<>/src/library' make[3]: Entering directory '/<>/src/library' writing package indices make[4]: Entering directory '/<>/src/library' make[4]: Leaving directory '/<>/src/library' make[3]: Leaving directory '/<>/src/library' make[2]: Leaving directory '/<>/src/library' make[1]: Leaving directory '/<>' (cd doc/manual && /usr/bin/make html) make[1]: Entering directory '/<>/doc/manual' make[2]: Entering directory '/<>/doc/html' make[2]: Leaving directory '/<>/doc/html' make[1]: Leaving directory '/<>/doc/manual' /usr/bin/make info make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/doc' make[3]: Entering directory '/<>/doc/manual' /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. 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 '/<>/doc/manual' make[2]: Leaving directory '/<>/doc' make[1]: Leaving directory '/<>' (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 '/<>/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 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2020-02-02> patch level 2 L3 programming layer <2020-02-14> (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2019/12/20 v1.4l Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (../../share/texmf/tex/latex/Rd.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe) (/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex))))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/generic/atbegshi/atbegshi.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 377. 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/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) [1] [2] Underfull \hbox (badness 6995) 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 . It Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1/pt m/m/n/10 if \T1/zi4/m/n/10 double.base Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth- er-wise, it is \T1/zi4/m/n/10 (double.base Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/zi4/m /n/10 1.110223e-16\T1/ptm/m/n/10 . As Underfull \hbox (badness 4995) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.neg.ulp.digits \T1/ptm/m/n/10 is bounded be-low by \T1/zi 4/m/n/10 -(double.digits + 3)\T1/ptm/m/n/10 , [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 297--301 []\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] [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 534--540 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/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 1178--1181 []\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] (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1966--1966 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] [34] [35] [36] [37] Underfull \hbox (badness 10000) in paragraph at lines 2402--2404 []\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci ently) by Underfull \hbox (badness 10000) in paragraph at lines 2405--2410 [][][]\T1/zi4/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le ngth re-sults, so at-tempt-ing to split via Underfull \hbox (badness 1102) in paragraph at lines 2405--2410 \T1/zi4/m/n/10 apply(x,MARGIN,identity) \T1/ptm/m/n/10 does not work (as it sim -ply gives \T1/zi4/m/n/10 x\T1/ptm/m/n/10 ). By chain-ing \T1/zi4/m/n/10 asplit [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] Underfull \hbox (badness 10000) in paragraph at lines 3784--3786 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [60] [61] [62] Overfull \hbox (6.42029pt too wide) in paragraph at lines 4025--4025 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 2521) in paragraph at lines 5046--5048 []\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 [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6202--6202 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [97] [98] [99] [100] [101] [102] Overfull \hbox (46.35893pt too wide) in paragraph at lines 6611--6613 []\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 : [103] [104] Underfull \hbox (badness 10000) in paragraph at lines 6759--6762 []\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 [105] [106] Underfull \hbox (badness 6063) in paragraph at lines 6941--6947 []\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- Underfull \hbox (badness 2343) in paragraph at lines 6941--6947 \T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files and web-pages gen-er- Underfull \hbox (badness 1708) in paragraph at lines 6941--6947 \T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it i s not rec-om-mended) when Underfull \hbox (badness 1831) in paragraph at lines 6941--6947 \T1/ptm/m/n/10 writ-ing it should be writ-ten ex-plic-itly, e.g. by \T1/zi4/m/n /10 writeChar("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or [107] Underfull \hbox (badness 3568) in paragraph at lines 7003--7010 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [108] [109] Underfull \vbox (badness 3803) has occurred while \output is active [110] Underfull \vbox (badness 10000) has occurred while \output is active [111] [112] Underfull \hbox (badness 1077) in paragraph at lines 7330--7336 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7330--7336 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [113] [114] [115] [116] [117] [118] Underfull \hbox (badness 2096) in paragraph at lines 7671--7675 \T1/zi4/m/n/10 status _ codes$[][] \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 . [119] [120] Underfull \hbox (badness 2351) in paragraph at lines 7789--7792 [][][]\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 , [121] [122] [123] [124] [125] Underfull \hbox (badness 4479) in paragraph at lines 8115--8125 [][][]\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), [126] [127] [128] [129] [130] [131] Underfull \hbox (badness 1629) in paragraph at lines 8562--8574 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 1609) in paragraph at lines 8562--8574 \T1/ptm/m/n/10 there is a prob-lem in the POSIX/C99 stan-dard with \T1/zi4/m/n/ 10 "1969-12-31 23:59:59 UTC"\T1/ptm/m/n/10 , which Underfull \hbox (badness 2426) in paragraph at lines 8562--8574 \T1/ptm/m/n/10 is \T1/zi4/m/n/10 -1 \T1/ptm/m/n/10 in cal-en-dar time and that value is on those OSes also used as an er-ror code. [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] Underfull \hbox (badness 1178) in paragraph at lines 9298--9302 []\T1/ptm/m/n/10 If true, [][]\T1/zi4/m/n/10 list[][][]\T1/ptm/m/n/10 s and ato mic vec-tors with non-[][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 names (see [][ ]\T1/zi4/m/n/10 names[][][]\T1/ptm/m/n/10 ) are de- [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] Underfull \hbox (badness 1735) in paragraph at lines 10446--10450 \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 . [161] [162] [163] [164] [165] [166] [167] Underfull \hbox (badness 6396) in paragraph at lines 10885--10893 []\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 1946) in paragraph at lines 10885--10893 \T1/zi4/m/n/10 duplicated \T1/ptm/m/n/10 and \T1/zi4/m/n/10 anyDuplicated\T1/pt m/m/n/10 , \T1/zi4/m/n/10 anyDuplicated(x,...) \T1/ptm/m/n/10 is a ``gen-er-al- ized'' short-cut for [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] Underfull \hbox (badness 4569) in paragraph at lines 12002--12006 []\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 12002--12006 \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 [184] Underfull \vbox (badness 10000) has occurred while \output is active [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] Underfull \hbox (badness 2253) in paragraph at lines 13665--13667 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [209] [210] Underfull \hbox (badness 1565) in paragraph at lines 13738--13742 [][][]\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 Underfull \hbox (badness 4927) in paragraph at lines 13782--13784 []\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 \T1/zi4 /m/n/10 fsep = [211] [212] Underfull \hbox (badness 3148) in paragraph at lines 13875--13880 [][][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[ ][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 help[][][]\T1/ptm/m/n/10 ; [][]\T1/zi4 /m/n/10 RShowDoc[][][] \T1/ptm/m/n/10 call \T1/zi4/m/n/10 file.show() \T1/ptm/m /n/10 for \T1/zi4/m/n/10 type = "text"\T1/ptm/m/n/10 . Con-sider [213] Underfull \hbox (badness 1466) in paragraph at lines 13922--13925 []\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 [214] Underfull \hbox (badness 10000) in paragraph at lines 14049--14053 [][][]\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 14060--14063 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [215] [216] [217] [218] [219] Underfull \hbox (badness 3965) in paragraph at lines 14352--14356 []\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, [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] Underfull \hbox (badness 4429) in paragraph at lines 15128--15131 []\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 [232] [233] Underfull \hbox (badness 10000) in paragraph at lines 15234--15236 []\T1/ptm/m/n/10 This works via \T1/zi4/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic h calls Underfull \hbox (badness 1215) in paragraph at lines 15234--15236 \T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times in this case, see Underfull \hbox (badness 10000) in paragraph at lines 15256--15261 []\T1/ptm/m/n/10 For num-bers, \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 calls \T 1/zi4/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls Underfull \hbox (badness 1558) in paragraph at lines 15256--15261 \T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero)\T1/ptm/m/n/10 . (\T1/ptm/m /it/10 ``when needed''\T1/ptm/m/n/10 : when \T1/zi4/m/n/10 zero.print \T1/ptm/m /n/10 is not Underfull \hbox (badness 10000) in paragraph at lines 15268--15272 []\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 Underfull \hbox (badness 2426) in paragraph at lines 15268--15272 \T1/zi4/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi ves \T1/zi4/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . If you want [234] Underfull \hbox (badness 2035) in paragraph at lines 15307--15311 []\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 within [235] Underfull \vbox (badness 10000) has occurred while \output is active [236] [237] [238] [239] [240] [241] [242] [243] Underfull \hbox (badness 2452) in paragraph at lines 15906--15910 []\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 15906--15910 \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 [244] [245] [246] Underfull \hbox (badness 1092) in paragraph at lines 16079--16084 [][]\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 [247] [248] [249] Underfull \hbox (badness 6741) in paragraph at lines 16329--16333 \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 , [250] [251] [252] [253] [254] [255] [256] [257] [258] Underfull \vbox (badness 3803) has occurred while \output is active [259] Underfull \vbox (badness 10000) has occurred while \output is active [260] [261] [262] [263] [264] [265] [266] [267] [268] [269] Underfull \hbox (badness 1478) in paragraph at lines 17622--17625 []\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 [270] [271] [272] [273] Underfull \hbox (badness 10000) in paragraph at lines 17877--17879 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [274] [275] [276] [277] [278] [279] [280] [281] [282] Underfull \hbox (badness 1442) in paragraph at lines 18477--18479 []\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 [283] Underfull \hbox (badness 2452) in paragraph at lines 18569--18585 [][][]\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 , [284] [285] [286] [287] [288] [289] [290] Underfull \hbox (badness 1248) in paragraph at lines 18988--18991 []\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 , [291] [292] [293] [294] Underfull \hbox (badness 4739) in paragraph at lines 19246--19248 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [295] [296] [297] [298] [299] [300] Underfull \hbox (badness 1596) in paragraph at lines 19665--19670 \T1/ptm/m/n/10 trix or, if \T1/zi4/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/zi4/m/n/10 simplify2array()\T1/ptm /m/n/10 . [301] [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] Underfull \hbox (badness 2469) in paragraph at lines 20269--20274 []\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 20283--20290 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [312] Underfull \hbox (badness 10000) in paragraph at lines 20357--20361 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 20357--20361 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$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 ' [313] [314] Underfull \hbox (badness 1014) in paragraph at lines 20527--20532 []\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 [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] Underfull \hbox (badness 1264) in paragraph at lines 21317--21322 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [327] Underfull \hbox (badness 4441) in paragraph at lines 21346--21349 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 , [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] Underfull \hbox (badness 6047) in paragraph at lines 22093--22095 []\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 \T1/zi4/m/n/10 make.unique(c(A,B)) == [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] Underfull \hbox (badness 1077) in paragraph at lines 23134--23140 \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 . [356] [357] [358] [359] [360] [361] [362] [363] Underfull \hbox (badness 2790) in paragraph at lines 23630--23633 []\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 23630--23633 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [364] [365] [366] [367] [368] Underfull \hbox (badness 1194) in paragraph at lines 23912--23915 []\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 [369] [370] [371] Underfull \hbox (badness 2368) in paragraph at lines 24118--24124 []\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 list, i.e., Underfull \hbox (badness 4981) in paragraph at lines 24118--24124 \T1/zi4/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are al so given by [][]\T1/zi4/m/n/10 ls[][][](env,all.names = [372] [373] [374] [375] [376] [377] Underfull \hbox (badness 10000) in paragraph at lines 24500--24503 []\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by [378] [379] [380] [381] [382] [383] [384] [385] [386] Underfull \hbox (badness 10000) in paragraph at lines 25105--25107 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than \T1/zi4/m/n/10 pkg %in% [387] [388] [389] [390] [391] [392] [393] [394] [395] [396] [397] [398] [399] Underfull \hbox (badness 1038) in paragraph at lines 25945--25953 []\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 1735) in paragraph at lines 25945--25953 \T1/ptm/m/n/10 set from value of the en-vi-ron-ment vari-able \T1/zi4/m/n/10 R_ DEFAULT_PACKAGES\T1/ptm/m/n/10 , or if that is un- Underfull \hbox (badness 1292) in paragraph at lines 25945--25953 \T1/ptm/m/n/10 set to \T1/zi4/m/n/10 c("datasets","utils","grDevices","graphics ","stats","methods")\T1/ptm/m/n/10 . (Set Underfull \hbox (badness 1881) in paragraph at lines 25954--25957 []\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 25973--25975 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [400] [401] Underfull \hbox (badness 2142) in paragraph at lines 26114--26118 []\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 26164--26169 []\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 [402] [403] [404] [405] Underfull \hbox (badness 10000) in paragraph at lines 26452--26458 []\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 26452--26458 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 26452--26458 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 26465--26468 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 26491--26493 []\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 26526--26531 []\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 2529) in paragraph at lines 26532--26543 \T1/ptm/m/n/10 in-di-rectly [][]\T1/zi4/m/n/10 update.packages[][][]\T1/ptm/m/n /10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si- Underfull \hbox (badness 2512) in paragraph at lines 26532--26543 \T1/ptm/m/n/10 ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi4/m /n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use and [406] Underfull \hbox (badness 7203) in paragraph at lines 26544--26547 []\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 10000) in paragraph at lines 26568--26573 []\T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma -cOS build), Underfull \hbox (badness 2057) in paragraph at lines 26568--26573 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). [407] [408] [409] [410] [411] [412] [413] [414] Underfull \hbox (badness 10000) in paragraph at lines 27086--27089 []\T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 str2lang(s ) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of [415] Underfull \hbox (badness 7925) in paragraph at lines 27165--27169 []\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 vec-to r \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n /10 cor-re-sponds to Underfull \hbox (badness 1622) in paragraph at lines 27165--27169 [][]\T1/zi4/m/n/10 parse[][][](text = s,keep.source=FALSE)\T1/ptm/m/n/10 , whic h is al-ways of type ([][]\T1/zi4/m/n/10 typeof[][][]\T1/ptm/m/n/10 ) and [][]\ T1/zi4/m/n/10 class[][][] Underfull \hbox (badness 6125) in paragraph at lines 27170--27179 []\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 string \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2lang(s) \T1/ptm/m/n/10 cor -re-sponds to [][]\T1/zi4/m/n/10 parse[][][](text = [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] Underfull \hbox (badness 2726) in paragraph at lines 27891--27894 []\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 [427] [428] [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] Underfull \vbox (badness 3803) has occurred while \output is active [445] [446] [447] [448] [449] [450] [451] [452] Underfull \hbox (badness 1533) in paragraph at lines 29582--29585 []\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 [453] [454] [455] Underfull \hbox (badness 1163) in paragraph at lines 29745--29756 []\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 [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] [473] [474] [475] [476] [477] [478] [479] Underfull \hbox (badness 10000) in paragraph at lines 31291--31295 []\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 31291--31295 \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 31313--31315 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [480] [481] [482] [483] [484] [485] [486] [487] [488] Underfull \hbox (badness 1655) in paragraph at lines 31869--31871 []\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 [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] Underfull \hbox (badness 2261) in paragraph at lines 32988--32993 []\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 [506] Underfull \hbox (badness 10000) in paragraph at lines 33015--33021 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1484) in paragraph at lines 33015--33021 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal and hex-adec-i-mal rep-re-sen-ta-tions like [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] Underfull \hbox (badness 1072) in paragraph at lines 36157--36161 []\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 36162--36166 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 36190--36196 []\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 36190--36196 \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 36190--36196 \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 3009) in paragraph at lines 36202--36209 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 36202--36209 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 36202--36209 \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 36202--36209 \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 [555] [556] [557] [558] [559] [560] Underfull \hbox (badness 1142) in paragraph at lines 36556--36562 []\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 \T1/zi4/m/n/10 "%Y-%m-%d [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] Underfull \hbox (badness 1565) in paragraph at lines 37829--37831 []\T1/ptm/m/n/10 integer code used in \T1/zi4/m/n/10 quantile(*,type=quantile.t ype) \T1/ptm/m/n/10 for the de-fault [581] [582] [583] [584] [585] [586] [587] [588] [589] [590] Underfull \hbox (badness 4967) in paragraph at lines 38428--38433 []\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 [591] [592] Underfull \hbox (badness 1616) in paragraph at lines 38541--38546 \T1/zi4/m/n/10 system("id") \T1/ptm/m/n/10 is much more portable on Unix-alikes , pro-vided only the POSIX op-tions [593] [594] [595] [596] [597] [598] [599] [600] Underfull \hbox (badness 1472) in paragraph at lines 39067--39070 []\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 [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614] Underfull \hbox (badness 10000) in paragraph at lines 39981--39985 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/zi4/m/n/10 length(bin) > [615] [616] [617] [618] Underfull \hbox (badness 10000) in paragraph at lines 40232--40235 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [619] [620] [621] Underfull \hbox (badness 10000) in paragraph at lines 40416--40420 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [622] [623] [624] [625] [626] [627] [628] [629] [630] Underfull \hbox (badness 10000) in paragraph at lines 41029--41032 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[ ]zones / [631] [632] [633] [634] [635] [636] Underfull \vbox (badness 10000) has occurred while \output is active [637] [638] [639] [640] [641] [642] [643] [644] Underfull \hbox (badness 1990) in paragraph at lines 41933--41941 []\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 41933--41941 \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 [645] [646] [647] [648] [649] [650] [651] [652] Underfull \hbox (badness 1917) in paragraph at lines 42439--42446 []\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 [653] [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] Underfull \hbox (badness 3668) in paragraph at lines 43168--43170 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [664] [665] Underfull \hbox (badness 2401) in paragraph at lines 43296--43300 []\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 [666] [667] [668] Underfull \hbox (badness 2111) in paragraph at lines 43485--43490 \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 10000) in paragraph at lines 43506--43511 []\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 [669] [670] [671] [672] [673] [674] [675] [676] [677] Underfull \hbox (badness 5417) in paragraph at lines 44088--44092 []\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 [678] Underfull \hbox (badness 10000) in paragraph at lines 44149--44153 []\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 [679] [680]) (./compiler-pkg.tex Chapter 2. [681] [682] [683] [684]) (./datasets-pkg.tex Chapter 3. [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] Underfull \hbox (badness 1097) in paragraph at lines 1031--1035 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] Underfull \vbox (badness 1448) has occurred while \output is active [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] Overfull \vbox (19.74611pt too high) has occurred while \output is active [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] Underfull \vbox (badness 10000) has occurred while \output is active [753] [754] [755] [756] Underfull \vbox (badness 10000) has occurred while \output is active [757] [758] [759] [760] [761] [762] [763] [764] [765] [766]) (./grDevices-pkg.tex Chapter 4. [767] [768] [769] [770] [771] Underfull \hbox (badness 3158) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/zi4/m/n/10 c(mi,ma,n.)\T1/ptm /m/n/10 , with iden-ti-cal mean-ing to Underfull \hbox (badness 10000) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][]\T1/zi4/m/n/10 axisTicks[][][]() \T1/ptm/ m/n/10 just calls the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/ptm/m/n/1 0 in Underfull \hbox (badness 1852) in paragraph at lines 298--303 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 /src/main/plot.c\T1/ptm/m/n/10 ' which is also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t ion [772] [773] [774] [775] [776] [777] [778] [779] Underfull \hbox (badness 1424) in paragraph at lines 830--832 [][][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 (as in-te-ger or char-ac-ter) and \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 mean trans-par-ent, which can also be spec-i -fied as [780] [781] [782] [783] [784] Underfull \hbox (badness 5175) in paragraph at lines 1124--1126 []\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 [785] [786] [787] [788] Underfull \hbox (badness 1852) in paragraph at lines 1326--1329 []\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 [789] [790] [791] Underfull \hbox (badness 1490) in paragraph at lines 1532--1537 \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 [792] [793] [794] [795] [796] [797] Underfull \hbox (badness 1325) in paragraph at lines 1938--1948 \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 , [798] [799] Underfull \hbox (badness 10000) in paragraph at lines 2050--2052 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [800] [801] [802] Underfull \hbox (badness 6758) in paragraph at lines 2228--2231 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [803] [804] [805] [806] [807] [808] [809] [810] [811] [812] Underfull \hbox (badness 10000) in paragraph at lines 2832--2833 [813] [814] [815] [816] [817] [818] [819] [820] [821] Underfull \hbox (badness 10000) in paragraph at lines 3388--3393 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [822] [823] [824] [825] [826] Underfull \vbox (badness 10000) has occurred while \output is active [827] Underfull \hbox (badness 10000) in paragraph at lines 3789--3792 []\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 [828] [829] [830] [831] [832] [833] [834] [835] [836] [837] [838] Underfull \hbox (badness 10000) in paragraph at lines 4518--4523 [][][]$\T1/zi4/m/n/10 https : / / www . adobe . com / content / dam / acom / en / devnet / actionscript / articles / PLRM . pdf$[][] Underfull \hbox (badness 4181) in paragraph at lines 4518--4523 \T1/ptm/m/n/10 or PDF [][]$\T1/zi4/m/n/10 https : / / www . adobe . com / devne t / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in [839] Underfull \vbox (badness 10000) has occurred while \output is active [840] [841] Underfull \hbox (badness 1067) in paragraph at lines 4672--4679 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [842] [843] [844] [845] Underfull \hbox (badness 1377) in paragraph at lines 4975--4980 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [846] Underfull \hbox (badness 1418) in paragraph at lines 5051--5058 \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 1755) in paragraph at lines 5069--5071 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [847] [848] Underfull \hbox (badness 1377) in paragraph at lines 5180--5185 []\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 [849] Underfull \hbox (badness 7344) in paragraph at lines 5249--5251 []\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 [850] [851] Underfull \hbox (badness 2035) in paragraph at lines 5384--5393 []\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 5384--5393 \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 5384--5393 \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 , [852] Underfull \hbox (badness 10000) in paragraph at lines 5452--5459 []\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 5452--5459 \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 . [853] [854] [855] Underfull \hbox (badness 1546) in paragraph at lines 5594--5602 []\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 , [856] [857] [858] [859] [860] [861] [862] [863] Underfull \hbox (badness 10000) in paragraph at lines 6129--6132 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [864] [865] [866] [867] [868] [869] [870] [871] [872] [873] [874] [875] [876] Underfull \hbox (badness 1189) in paragraph at lines 6951--6953 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [877] Underfull \hbox (badness 10000) in paragraph at lines 7049--7051 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [878] [879] [880] [881] [882] Underfull \hbox (badness 3780) in paragraph at lines 7349--7355 []\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 , [883] [884] [885] Underfull \hbox (badness 2680) in paragraph at lines 7550--7552 []\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 [886] [887] [888]) (./graphics-pkg.tex Chapter 5. [889] [890] [891] [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] Underfull \hbox (badness 4634) in paragraph at lines 1351--1354 [][][]\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 , [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] Underfull \hbox (badness 1728) in paragraph at lines 2308--2310 []\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use \T1/zi4/m/n/10 "n " \T1/ptm/m/n/10 to sup-press and see also [927] [928] Underfull \hbox (badness 1009) in paragraph at lines 2399--2406 \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 [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] [947] [948] [949] [950] Underfull \vbox (badness 10000) has occurred while \output is active [951] [952] [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] Underfull \hbox (badness 3229) in paragraph at lines 4544--4549 []\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 [964] [965] [966] [967] [968] Underfull \hbox (badness 10000) in paragraph at lines 4901--4907 []\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 4901--4907 \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 [969] Underfull \hbox (badness 10000) in paragraph at lines 5032--5035 [970] Underfull \hbox (badness 10000) in paragraph at lines 5093--5095 [971 >/library/graphics/help/figures/ mai.pdf>] [972 >/library/graphics/hel p/figures/oma.pdf>] [973] Underfull \hbox (badness 10000) in paragraph at lines 5283--5285 []\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 [974] Underfull \vbox (badness 3803) has occurred while \output is active [975] [976] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6761--6762 [][] [997] [998 >/library/graphics/help/fi gures/pch.pdf>] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] Underfull \hbox (badness 2012) in paragraph at lines 7586--7589 []\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 poi nt [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] Underfull \hbox (badness 10000) in paragraph at lines 8846--8848 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8848--8850 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1032]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8928 \HeaderA{units}{Graphical Units}{units} [1033] [1034] [1035] [1036]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] Underfull \hbox (badness 2680) in paragraph at lines 483--486 []\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 [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] Underfull \hbox (badness 4279) in paragraph at lines 1064--1073 [][][]\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 , [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] Underfull \vbox (badness 10000) has occurred while \output is active [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] Underfull \hbox (badness 1067) in paragraph at lines 4486--4489 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1113] [1114] [1115] [1116] Underfull \hbox (badness 7256) in paragraph at lines 4731--4733 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \hbox (badness 1824) in paragraph at lines 6535--6538 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like \T1/zi4/m/n/10 depth [1148] [1149] [1150] [1151]) (./methods-pkg.tex [1152] Chapter 7. [1153] [1154] [1155] [1156] [1157] [1158] [1159] [1160] Underfull \vbox (badness 10000) has occurred while \output is active [1161] Underfull \vbox (badness 10000) has occurred while \output is active [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171] Underfull \hbox (badness 2237) in paragraph at lines 1385--1387 []\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 [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] Underfull \hbox (badness 2181) in paragraph at lines 1932--1939 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/zi4/m/n/10 is(x,"refClass") \T1/ptm/m/n/10 tests [1180] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\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 1981--1986 \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 [1181] [1182] [1183] Underfull \hbox (badness 2213) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/zi4/m/n/10 where = [1184] [1185] [1186] [1187] [1188] Underfull \hbox (badness 10000) in paragraph at lines 2574--2577 []\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 [1189] [1190] Underfull \hbox (badness 1132) in paragraph at lines 2714--2718 []\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 [1191] Underfull \hbox (badness 1033) in paragraph at lines 2746--2751 \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 [1192] [1193] [1194] [1195] [1196] [1197] [1198] Underfull \hbox (badness 1102) in paragraph at lines 3303--3305 []\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 [1199] [1200] [1201] [1202] [1203] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\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 [1204] Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1205] Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [] \T1/zi4/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude = "numeric",altitude [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] Underfull \hbox (badness 1769) in paragraph at lines 4472--4478 []\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 4472--4478 \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 [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] Underfull \vbox (badness 10000) has occurred while \output is active [1227] [1228] [1229] Underfull \hbox (badness 4036) in paragraph at lines 5437--5440 []\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 [1230] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1231] [1232] [1233] [1234] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] Underfull \hbox (badness 1675) in paragraph at lines 6451--6457 \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 [1243] [1244] [1245] [1246] Underfull \vbox (badness 10000) has occurred while \output is active [1247] [1248] [1249] [1250]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1251] [1252] [1253]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} [1254] Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1255] [1256] [1257] Underfull \hbox (badness 1286) in paragraph at lines 7484--7486 []\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 [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] Underfull \vbox (badness 10000) has occurred while \output is active [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] Underfull \hbox (badness 1137) in paragraph at lines 10011--10019 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/n/10 ne w("signature",functionDef,...)\T1/ptm/m/n/10 . The [1293] [1294] [1295] [1296] [1297] [1298] [1299] Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., [1300] [1301] [1302] [1303]) (./parallel-pkg.tex [1304] Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\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 [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] [1324] [1325] Underfull \hbox (badness 3386) in paragraph at lines 1365--1368 []\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 [1326] [1327] [1328]) (./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 [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344]) (./stats-pkg.tex Chapter 10. [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] Underfull \hbox (badness 1412) in paragraph at lines 875--877 []\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 [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] Underfull \hbox (badness 2503) in paragraph at lines 1356--1359 []\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 , [1367] [1368] [1369] Underfull \hbox (badness 10000) in paragraph at lines 1536--1540 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov","lm") \T1/ptm/m/n/1 0 or for mul-ti-ple re-sponses of class [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] Underfull \hbox (badness 2503) in paragraph at lines 3437--3440 []\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 , [1400] [1401] [1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] Underfull \hbox (badness 1127) in paragraph at lines 4351--4354 []\T1/ptm/m/n/10 standardized resid-u-als, \T1/zi4/m/n/10 (observed -expected) / sqrt(V)\T1/ptm/m/n/10 , where \T1/zi4/m/n/10 V \T1/ptm/m/n/10 is the [1415] [1416] [1417] [1418] [1419] Underfull \hbox (badness 3989) in paragraph at lines 4681--4688 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] Underfull \hbox (badness 2556) in paragraph at lines 5317--5320 []\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 5334--5336 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/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 [1430] [1431] [1432] [1433] [1434] [1435] [1436] Underfull \hbox (badness 2503) in paragraph at lines 5726--5730 []\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 , [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] Underfull \hbox (badness 7081) in paragraph at lines 6520--6523 []\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 6524--6526 []\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 [1450] [1451] [1452] [1453] [1454] Underfull \vbox (badness 3803) has occurred while \output is active [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] Underfull \hbox (badness 10000) in paragraph at lines 7369--7372 []\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 [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] Underfull \vbox (badness 10000) has occurred while \output is active [1485] [1486] [1487] [1488] [1489] Underfull \hbox (badness 2626) in paragraph at lines 9048--9051 []\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 [1490] [1491] Underfull \hbox (badness 2503) in paragraph at lines 9155--9159 []\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 , [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] [1509] [1510] [1511] Underfull \hbox (badness 4518) in paragraph at lines 10469--10474 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1512] [1513] [1514] [1515] [1516] Underfull \hbox (badness 2142) in paragraph at lines 10830--10833 []\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 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10849--10852 []\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, [1517] Underfull \hbox (badness 1708) in paragraph at lines 10911--10915 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1518] [1519] [1520] [1521] [1522] [1523] Underfull \hbox (badness 1694) in paragraph at lines 11307--11310 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531]pdfTeX warning (ext4): d estination with the same identifier (name{Rfn.hat}) has been already used, dupl icate ignored \relax l.11791 \aliasA{hat}{influence.measures}{hat} [1532] [1533] Underfull \hbox (badness 1484) in paragraph at lines 11926--11928 []\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 [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] Underfull \hbox (badness 10000) in paragraph at lines 12519--12521 []\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 \T1/zi4/m/n/10 SSinit = [1544] [1545] [1546] [1547] [1548] [1549] Underfull \hbox (badness 2894) in paragraph at lines 12855--12859 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] Underfull \hbox (badness 4518) in paragraph at lines 13605--13610 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] Underfull \hbox (badness 4518) in paragraph at lines 14257--14262 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1572] [1573] Underfull \hbox (badness 8151) in paragraph at lines 14395--14399 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = "interp olate",statistics = Underfull \hbox (badness 1199) in paragraph at lines 14402--14404 []\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 [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] Underfull \hbox (badness 2503) in paragraph at lines 15473--15477 []\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 , [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] Underfull \hbox (badness 4621) in paragraph at lines 15985--15991 []\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 [1600] [1601] [1602] [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] [1623] [1624] [1625] [1626] [1627] Underfull \vbox (badness 10000) has occurred while \output is active [1628] Underfull \vbox (badness 10000) has occurred while \output is active [1629] [1630] [1631] [1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] Underfull \hbox (badness 1377) in paragraph at lines 18588--18593 []\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 18593--18596 []\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 [1642] Underfull \hbox (badness 2343) in paragraph at lines 18606--18610 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 3471) in paragraph at lines 18606--18610 \T1/ptm/m/n/10 the value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + re ltol) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18614--18618 []\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 [1643] [1644] [1645] Overfull \hbox (15.73795pt too wide) in paragraph at lines 18839--18839 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 18842--18842 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] Underfull \vbox (badness 10000) has occurred while \output is active [1646] [1647] [1648] [1649] [1650] [1651] [1652] Underfull \hbox (badness 1337) in paragraph at lines 19264--19267 []\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 [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] Underfull \hbox (badness 3049) in paragraph at lines 19760--19764 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1662] [1663] [1664] [1665] Underfull \hbox (badness 1194) in paragraph at lines 20018--20021 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1666] [1667] [1668] [1669] [1670] [1671] [1672] Underfull \hbox (badness 2503) in paragraph at lines 20397--20400 []\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 , Underfull \hbox (badness 3919) in paragraph at lines 20424--20426 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or \T1/zi4/m/n/10 "Comparison of Poisson [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] [1688] [1689] [1690] Underfull \hbox (badness 10000) in paragraph at lines 21501--21507 []\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 , [1691] [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] Underfull \hbox (badness 1337) in paragraph at lines 22855--22861 []\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 [1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] Overfull \hbox (27.74408pt too wide) in paragraph at lines 23420--23420 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1722] [1723] [1724] [1725] [1726] Underfull \hbox (badness 10000) in paragraph at lines 23671--23674 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 4205) in paragraph at lines 23671--23674 \T1/zi4/m/n/10 cutree(hclust.obj,k = k)\T1/ptm/m/n/10 , can be spec-i-fied for ef-fi-ciency if al-ready [1727] [1728] [1729] [1730] [1731] [1732] [1733] [1734] [1735] Underfull \hbox (badness 1824) in paragraph at lines 24257--24263 []\T1/ptm/m/n/10 Here, all the NAs in \T1/zi4/m/n/10 x \T1/ptm/m/n/10 are first re-placed by al-ter- Underfull \hbox (badness 1033) in paragraph at lines 24257--24263 \T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/ m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where [1736] Underfull \hbox (badness 10000) in paragraph at lines 24278--24281 []\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 \T1/zi4/m/n/10 y[j] = Underfull \hbox (badness 3690) in paragraph at lines 24347--24351 [][][]\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 [1737] Underfull \vbox (badness 3803) has occurred while \output is active [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] Underfull \hbox (badness 2165) in paragraph at lines 24856--24861 []\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm /m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1 0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [1746] [1747] [1748] [1749] Underfull \hbox (badness 1867) in paragraph at lines 25061--25063 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 25074--25078 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u se.fallback) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 PP [1750] [1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] Underfull \vbox (badness 3803) has occurred while \output is active [1761] [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] [1771] [1772] [1773] Underfull \vbox (badness 10000) has occurred while \output is active [1774] Underfull \hbox (badness 3514) in paragraph at lines 26634--26639 []\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 [1775] [1776] [1777] [1778] Overfull \hbox (2.23795pt too wide) in paragraph at lines 26868--26868 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1779] Underfull \hbox (badness 3514) in paragraph at lines 26904--26910 []\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 [1780] [1781] [1782] [1783] Underfull \hbox (badness 3514) in paragraph at lines 27118--27123 []\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 [1784] Underfull \hbox (badness 3514) in paragraph at lines 27205--27210 []\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 [1785] Underfull \hbox (badness 3514) in paragraph at lines 27270--27275 []\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 [1786] [1787] Underfull \hbox (badness 3514) in paragraph at lines 27364--27369 []\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 [1788] [1789] Underfull \hbox (badness 6691) in paragraph at lines 27456--27461 []\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 [1790] [1791] [1792] [1793] [1794] [1795] [1796] [1797] Underfull \hbox (badness 4024) in paragraph at lines 27984--27987 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion , which [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] Underfull \hbox (badness 5431) in paragraph at lines 28590--28592 []\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 [1808] [1809] [1810] [1811] Underfull \hbox (badness 5431) in paragraph at lines 28800--28803 []\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 [1812] [1813] [1814] [1815] [1816] Underfull \hbox (badness 1337) in paragraph at lines 29114--29118 []\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 [1817] [1818] [1819] [1820] [1821] Underfull \hbox (badness 1616) in paragraph at lines 29416--29419 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1822] [1823] [1824] [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] [1835] [1836] [1837] [1838] [1839] [1840] Underfull \hbox (badness 3557) in paragraph at lines 30546--30550 []\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 \T1/zi4 /m/n/10 interval = [1841] [1842] [1843] Underfull \vbox (badness 10000) has occurred while \output is active [1844] [1845] [1846] Underfull \hbox (badness 1337) in paragraph at lines 30910--30914 []\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 [1847] [1848] [1849] [1850] [1851] [1852] [1853] [1854] [1855] Underfull \hbox (badness 1337) in paragraph at lines 31437--31441 []\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 [1856] [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865]) (./stats4-pkg.tex [1866] Chapter 11. [1867] [1868] [1869] [1870] [1871] [1872]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} [1873] [1874] [1875]) (./tcltk-pkg.tex [1876] Chapter 12. [1877] [1878] [1879] [1880] [1881] [1882] [1883] Underfull \vbox (badness 10000) has occurred while \output is active [1884] Underfull \vbox (badness 10000) has occurred while \output is active [1885] 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 [1886] [1887] [1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897]) (./tools-pkg.tex [1898] Chapter 13. [1899] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1900] 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 [1901] [1902] 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 [1903] [1904] 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 [1905] [1906] [1907] [1908] [1909] [1910] [1911] [1912] [1913] [1914] [1915] [1916] [1917] Underfull \hbox (badness 4441) in paragraph at lines 1139--1149 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- Underfull \hbox (badness 1014) in paragraph at lines 1163--1165 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1169--1171 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous [1918] Underfull \hbox (badness 10000) in paragraph at lines 1206--1209 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1206--1209 \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 , [1919] [1920] [1921] [1922] [1923] Underfull \hbox (badness 2293) in paragraph at lines 1558--1560 []\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with its func-tion-al-ity in-te-grated into that of [1924] [1925] [1926] Underfull \hbox (badness 7981) in paragraph at lines 1696--1701 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 1082) in paragraph at lines 1703--1705 []\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 [1927] [1928] [1929]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1930] [1931] [1932] [1933] [1934] [1935] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2202--2202 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1936] [1937] [1938] Underfull \hbox (badness 7981) in paragraph at lines 2371--2377 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1939] [1940] [1941] [1942] [1943] [1944] [1945] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2846. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2847. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2847. [1946] [1947] [1948] [1949] [1950] Underfull \hbox (badness 1424) in paragraph at lines 3128--3130 []\T1/zi4/m/it/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 [1951] [1952] [1953] [1954] [1955] [1956] [1957] [1958] [1959] [1960] [1961] Underfull \hbox (badness 10000) in paragraph at lines 3832--3834 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1962] [1963] Underfull \hbox (badness 10000) in paragraph at lines 3971--3974 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/it/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/it/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1964] [1965] Underfull \hbox (badness 1137) in paragraph at lines 4073--4075 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1966] [1967] [1968] [1969] [1970] Underfull \hbox (badness 1796) in paragraph at lines 4381--4386 []\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over \T 1/zi4/m/it/10 write_PACKAGES \T1/ptm/m/n/10 in the \T1/zi4/m/it/10 type == [1971] Underfull \hbox (badness 1838) in paragraph at lines 4455--4461 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/it/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/it/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4455--4461 \T1/ptm/m/n/10 `\T1/zi4/m/it/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 [1972] [1973] [1974] Underfull \hbox (badness 2197) in paragraph at lines 4671--4681 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/it/10 available.packages[][][]\T1/ptm/m/n/10 : [1975] Underfull \hbox (badness 1571) in paragraph at lines 4734--4738 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [1976] [1977] [1978]) (./utils-pkg.tex Chapter 14. [1979] 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/it/10 insertions\T1/ptm/m/n/10 ', [1980] [1981] [1982] [1983] [1984] Underfull \hbox (badness 10000) in paragraph at lines 376--381 \T1/zi4/m/it/10 c("vertical","horizontal","cascade","minimize","restore") \T1/p tm/m/n/10 with [1985] [1986] [1987] [1988] [1989] Underfull \hbox (badness 10000) in paragraph at lines 717--723 []\T1/ptm/m/n/10 Functions \T1/zi4/m/it/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/it/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 717--723 \T1/zi4/m/it/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/it/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1990] [1991] Underfull \hbox (badness 5847) in paragraph at lines 850--856 []\T1/ptm/m/n/10 Argument \T1/zi4/m/it/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 850--856 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/it/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1992] Underfull \hbox (badness 3861) in paragraph at lines 918--923 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/it/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/it/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/it/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1993] [1994] Underfull \hbox (badness 3323) in paragraph at lines 1089--1097 []\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/zi4/m/it/1 0 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1 /ptm/m/n/10 , in-di-cat- Underfull \hbox (badness 2961) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f or-mat- Underfull \hbox (badness 3919) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 3735) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/it/10 getOption[][][]("citation.bibtex.ma x",1) \T1/ptm/m/n/10 which is \T1/zi4/m/it/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by [1995] Underfull \hbox (badness 10000) in paragraph at lines 1101--1103 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1996] [1997] Underfull \vbox (badness 3803) has occurred while \output is active [1998] [1999] [2000] [2001] [2002] Underfull \hbox (badness 1371) in paragraph at lines 1606--1608 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/it/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/it/10 ccaddress \T1/ptm/m/n/10 to pass to [2003] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 1676. [2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] Underfull \hbox (badness 2057) in paragraph at lines 2215--2217 []\T1/ptm/m/n/10 None for \T1/zi4/m/it/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [2013] [2014] [2015] [2016] [2017] [2018]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.clipboard}) has been already used, duplicate ig nored \relax l.2566 ... the Clipboard in MS Windows}{clipboard} [2019] [2020] Underfull \hbox (badness 1748) in paragraph at lines 2733--2736 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/it/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/it/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/it/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [2021] [2022] [2023] [2024] [2025] [2026] [2027] Underfull \hbox (badness 5388) in paragraph at lines 3142--3146 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/it/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/it/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/it/10 .TXT\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/it/10 read.table[][][](...,header = Underfull \hbox (badness 2285) in paragraph at lines 3147--3150 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/it/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/it/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/it/10 read.table[] [][](...,header = TRUE,sep = [2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] Underfull \hbox (badness 1430) in paragraph at lines 3906--3914 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/it/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [2039] Underfull \hbox (badness 1231) in paragraph at lines 3983--3995 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [2040] [2041] Underfull \hbox (badness 10000) in paragraph at lines 4141--4143 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/it/10 dow nload.file[][][] \T1/ptm/m/n/10 and [2042] [2043] [2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.4839 ...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.4839 ...mat Unordered and Ordered Lists}{format} [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] Underfull \hbox (badness 1622) in paragraph at lines 5358--5362 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 5990. Underfull \hbox (badness 1371) in paragraph at lines 5994--5996 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/it/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/it/10 ccaddress \T1/ptm/m/n/10 to pass to [2072] Underfull \hbox (badness 1502) in paragraph at lines 6083--6088 []\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 6083--6088 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2073] [2074] [2075] Underfull \hbox (badness 10000) in paragraph at lines 6256--6265 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2076] Underfull \hbox (badness 2150) in paragraph at lines 6320--6323 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2077] [2078] Underfull \hbox (badness 3118) in paragraph at lines 6458--6460 []\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 [2079] [2080] [2081] Underfull \hbox (badness 1325) in paragraph at lines 6630--6634 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/it/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able Underfull \hbox (badness 4726) in paragraph at lines 6642--6648 \T1/ptm/m/n/10 used if \T1/zi4/m/it/10 repos = NULL\T1/ptm/m/n/10 . Can also be a char-ac-ter vec-tor, a sub-set of [2082] Underfull \hbox (badness 10000) in paragraph at lines 6714--6717 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be Underfull \hbox (badness 10000) in paragraph at lines 6714--6717 \T1/ptm/m/n/10 passed to \T1/zi4/m/it/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou rce pack-age in-stall. E.g., [2083] Underfull \hbox (badness 3219) in paragraph at lines 6790--6797 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/it/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6790--6797 \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 6790--6797 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1596) in paragraph at lines 6790--6797 [][]\T1/zi4/m/it/10 getOption[][][]("install.packages.compile.from.source")\T1/ ptm/m/n/10 . \T1/zi4/m/it/10 type = "both" \T1/ptm/m/n/10 will be silently Underfull \hbox (badness 2932) in paragraph at lines 6798--6801 []\T1/ptm/m/n/10 Using pack-ages with \T1/zi4/m/it/10 type = "source" \T1/ptm/m /n/10 al-ways works pro-vided the pack-age con-tains no [2084] Underfull \hbox (badness 10000) in paragraph at lines 6934--6939 [][][]\T1/zi4/m/it/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [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] Underfull \hbox (badness 10000) in paragraph at lines 8434--8436 []\T1/ptm/m/n/10 for \T1/zi4/m/it/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi 4/m/it/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 2310) in paragraph at lines 8456--8461 []\T1/ptm/m/n/10 If a `\T1/zi4/m/it/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2110] [2111] [2112] [2113] [2114] [2115] [2116] [2117] Underfull \hbox (badness 1248) in paragraph at lines 8980--8984 []\T1/zi4/m/it/10 R CMD build \T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/m/ n/10 source tar-balls. The name(s) of the pack-ages are taken from the [2118] Underfull \hbox (badness 1789) in paragraph at lines 9058--9060 []\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 [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131] Underfull \hbox (badness 1097) in paragraph at lines 9895--9898 []\T1/ptm/m/n/10 The name \T1/zi4/m/it/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2132] [2133] Underfull \hbox (badness 3000) in paragraph at lines 10031--10036 [][][]\T1/zi4/m/it/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/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/it/10 read.t able[][][]\T1/ptm/m/n/10 ; [2134] [2135] [2136] [2137] [2138] [2139] [2140] [2141] [2142] Underfull \hbox (badness 2134) in paragraph at lines 10614--10619 [][][]\T1/zi4/m/it/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/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/it/10 write. table[][][]\T1/ptm/m/n/10 ; Underfull \hbox (badness 10000) in paragraph at lines 10670--10675 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for Underfull \hbox (badness 10000) in paragraph at lines 10670--10675 \T1/zi4/m/it/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/zi4/m/it/10 HKEY_CLASSES _ROOT\T1/ptm/m/n/10 . \T1/zi4/m/it/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] Underfull \hbox (badness 2469) in paragraph at lines 11163--11167 []\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 11163--11167 [][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2152] [2153] [2154] [2155] [2156] Underfull \hbox (badness 4060) in paragraph at lines 11494--11497 []\T1/ptm/m/n/10 If `\T1/zi4/m/it/10 --default-packages\T1/ptm/m/n/10 ' is not used, then \T1/zi4/m/it/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var i-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 11517--11517 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [2157] [2158] [2159] [2160] Underfull \hbox (badness 2150) in paragraph at lines 11756--11758 [][][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/it/10 https : / / www . gnu . org / software / emac s / manual / [2161] [2162] [2163] [2164] Underfull \hbox (badness 10000) in paragraph at lines 11975--11979 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/it/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12006--12012 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2165] [2166] Underfull \hbox (badness 1009) in paragraph at lines 12200--12212 []\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 [2167] Underfull \hbox (badness 4779) in paragraph at lines 12237--12239 []\T1/ptm/m/n/10 The file `\T1/zi4/m/it/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ure s the R GUI (\T1/zi4/m/it/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows a nd Underfull \hbox (badness 1077) in paragraph at lines 12267--12274 \T1/ptm/m/n/10 (strip-ping any trail-ing slash), oth-er-wise to the Win-dows `p er-sonal' di-rec-tory, oth-er-wise to [2168] [2169] [2170] [2171] [2172] [2173] [2174] Underfull \hbox (badness 3780) in paragraph at lines 12668--12672 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/it/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 12684--12687 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/it/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2175] [2176] [2177] [2178] Underfull \hbox (badness 2302) in paragraph at lines 12889--12891 []\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t o the Win-dows API call [2179] [2180] [2181] [2182] Underfull \hbox (badness 10000) in paragraph at lines 13185--13190 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/it/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/it/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 13194--13197 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2183] [2184] Underfull \vbox (badness 10000) has occurred while \output is active [2185] [2186] [2187] [2188] [2189] Underfull \hbox (badness 2932) in paragraph at lines 13614--13621 []\T1/ptm/m/n/10 If \T1/zi4/m/it/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in turn, Underfull \hbox (badness 1688) in paragraph at lines 13614--13621 \T1/ptm/m/n/10 and se-lected if their \T1/zi4/m/it/10 extension \T1/ptm/m/n/10 com-po-nent matches (as a reg-exp) the file name. Ob- [2190] [2191] [2192] [2193] [2194] Underfull \hbox (badness 6510) in paragraph at lines 13923--13927 []\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/it/10 tar \T1/ptm/m/n/10 is set to t he com-mand \T1/zi4/m/it/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a ble Underfull \hbox (badness 10000) in paragraph at lines 13930--13933 [][][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/it/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 13930--13933 \T1/zi4/m/it/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2195] [2196] [2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] Underfull \hbox (badness 10000) in paragraph at lines 14594--14599 []\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/it/10 destdir \T1/ptm/m/n/10 and \ T1/zi4/m/it/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 3861) in paragraph at lines 14594--14599 [][]\T1/zi4/m/it/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/it/10 i gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/it/10 max_repo_cache_age \T1/ptm/m/n /10 and Underfull \hbox (badness 1052) in paragraph at lines 14600--14602 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. 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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.lmList} 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 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Output written on tctt0900.600gf (128 characters, 17564 bytes). Transcript written on tctt0900.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tctt0900.600pk: successfully generated. {/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/ usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc} Output written on refman.pdf (2225 pages, 5571283 bytes). Transcript written on refman.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file refman.idx.................done (13939 entries accepted, 34 rejected). Sorting entries................................................................................................................................................done (210880 comparisons). Generating output file refman.ind................done (13726 lines written, 55 warnings). Output written in refman.ind. Transcript written in refman.ilg. 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[1] [2] Underfull \hbox (badness 6995) 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 . It Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1/pt m/m/n/10 if \T1/zi4/m/n/10 double.base Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth- er-wise, it is \T1/zi4/m/n/10 (double.base Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/zi4/m /n/10 1.110223e-16\T1/ptm/m/n/10 . As Underfull \hbox (badness 4995) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.neg.ulp.digits \T1/ptm/m/n/10 is bounded be-low by \T1/zi 4/m/n/10 -(double.digits + 3)\T1/ptm/m/n/10 , [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 297--301 []\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] [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 534--540 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/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 1178--1181 []\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] (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1966--1966 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] [34] [35] [36] [37] Underfull \hbox (badness 10000) in paragraph at lines 2402--2404 []\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci ently) by Underfull \hbox (badness 10000) in paragraph at lines 2405--2410 [][][]\T1/zi4/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le ngth re-sults, so at-tempt-ing to split via Underfull \hbox (badness 1102) in paragraph at lines 2405--2410 \T1/zi4/m/n/10 apply(x,MARGIN,identity) \T1/ptm/m/n/10 does not work (as it sim -ply gives \T1/zi4/m/n/10 x\T1/ptm/m/n/10 ). By chain-ing \T1/zi4/m/n/10 asplit [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] Underfull \hbox (badness 10000) in paragraph at lines 3784--3786 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [60] [61] [62] Overfull \hbox (6.42029pt too wide) in paragraph at lines 4025--4025 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 2521) in paragraph at lines 5046--5048 []\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 [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6202--6202 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [97] [98] [99] [100] [101] [102] Overfull \hbox (46.35893pt too wide) in paragraph at lines 6611--6613 []\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 : [103] [104] Underfull \hbox (badness 10000) in paragraph at lines 6759--6762 []\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 [105] [106] Underfull \hbox (badness 6063) in paragraph at lines 6941--6947 []\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- Underfull \hbox (badness 2343) in paragraph at lines 6941--6947 \T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files and web-pages gen-er- Underfull \hbox (badness 1708) in paragraph at lines 6941--6947 \T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it i s not rec-om-mended) when Underfull \hbox (badness 1831) in paragraph at lines 6941--6947 \T1/ptm/m/n/10 writ-ing it should be writ-ten ex-plic-itly, e.g. by \T1/zi4/m/n /10 writeChar("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or [107] Underfull \hbox (badness 3568) in paragraph at lines 7003--7010 \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 [108] [109] Underfull \vbox (badness 3803) has occurred while \output is active [110] Underfull \vbox (badness 10000) has occurred while \output is active [111] [112] Underfull \hbox (badness 1077) in paragraph at lines 7330--7336 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7330--7336 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [113] [114] [115] [116] [117] [118] Underfull \hbox (badness 2096) in paragraph at lines 7671--7675 \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 . [119] [120] Underfull \hbox (badness 2351) in paragraph at lines 7789--7792 [][][]\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 , [121] [122] [123] [124] [125] Underfull \hbox (badness 4479) in paragraph at lines 8115--8125 [][][]\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), [126] [127] [128] [129] [130] [131] Underfull \hbox (badness 1629) in paragraph at lines 8562--8574 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 1609) in paragraph at lines 8562--8574 \T1/ptm/m/n/10 there is a prob-lem in the POSIX/C99 stan-dard with \T1/zi4/m/n/ 10 "1969-12-31 23:59:59 UTC"\T1/ptm/m/n/10 , which Underfull \hbox (badness 2426) in paragraph at lines 8562--8574 \T1/ptm/m/n/10 is \T1/zi4/m/n/10 -1 \T1/ptm/m/n/10 in cal-en-dar time and that value is on those OSes also used as an er-ror code. [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] Underfull \hbox (badness 1178) in paragraph at lines 9298--9302 []\T1/ptm/m/n/10 If true, [][]\T1/zi4/m/n/10 list[][][]\T1/ptm/m/n/10 s and ato mic vec-tors with non-[][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 names (see [][ ]\T1/zi4/m/n/10 names[][][]\T1/ptm/m/n/10 ) are de- [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] Underfull \hbox (badness 1735) in paragraph at lines 10446--10450 \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 . [161] [162] [163] [164] [165] [166] [167] Underfull \hbox (badness 6396) in paragraph at lines 10885--10893 []\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 1946) in paragraph at lines 10885--10893 \T1/zi4/m/n/10 duplicated \T1/ptm/m/n/10 and \T1/zi4/m/n/10 anyDuplicated\T1/pt m/m/n/10 , \T1/zi4/m/n/10 anyDuplicated(x,...) \T1/ptm/m/n/10 is a ``gen-er-al- ized'' short-cut for [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] Underfull \hbox (badness 4569) in paragraph at lines 12002--12006 []\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 12002--12006 \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 [184] Underfull \vbox (badness 10000) has occurred while \output is active [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] Underfull \hbox (badness 2253) in paragraph at lines 13665--13667 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [209] [210] Underfull \hbox (badness 1565) in paragraph at lines 13738--13742 [][][]\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 Underfull \hbox (badness 4927) in paragraph at lines 13782--13784 []\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 \T1/zi4 /m/n/10 fsep = [211] [212] Underfull \hbox (badness 3148) in paragraph at lines 13875--13880 [][][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[ ][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 help[][][]\T1/ptm/m/n/10 ; [][]\T1/zi4 /m/n/10 RShowDoc[][][] \T1/ptm/m/n/10 call \T1/zi4/m/n/10 file.show() \T1/ptm/m /n/10 for \T1/zi4/m/n/10 type = "text"\T1/ptm/m/n/10 . Con-sider [213] Underfull \hbox (badness 1466) in paragraph at lines 13922--13925 []\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 [214] Underfull \hbox (badness 10000) in paragraph at lines 14049--14053 [][][]\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 14060--14063 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [215] [216] [217] [218] [219] Underfull \hbox (badness 3965) in paragraph at lines 14352--14356 []\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, [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] Underfull \hbox (badness 4429) in paragraph at lines 15128--15131 []\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 [232] [233] Underfull \hbox (badness 10000) in paragraph at lines 15234--15236 []\T1/ptm/m/n/10 This works via \T1/zi4/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic h calls Underfull \hbox (badness 1215) in paragraph at lines 15234--15236 \T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times in this case, see Underfull \hbox (badness 10000) in paragraph at lines 15256--15261 []\T1/ptm/m/n/10 For num-bers, \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 calls \T 1/zi4/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls Underfull \hbox (badness 1558) in paragraph at lines 15256--15261 \T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero)\T1/ptm/m/n/10 . (\T1/ptm/m /it/10 ``when needed''\T1/ptm/m/n/10 : when \T1/zi4/m/n/10 zero.print \T1/ptm/m /n/10 is not Underfull \hbox (badness 10000) in paragraph at lines 15268--15272 []\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 Underfull \hbox (badness 2426) in paragraph at lines 15268--15272 \T1/zi4/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi ves \T1/zi4/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . If you want [234] Underfull \hbox (badness 2035) in paragraph at lines 15307--15311 []\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 within [235] Underfull \vbox (badness 10000) has occurred while \output is active [236] [237] [238] [239] [240] [241] [242] [243] Underfull \hbox (badness 2452) in paragraph at lines 15906--15910 []\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 15906--15910 \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 [244] [245] [246] Underfull \hbox (badness 1092) in paragraph at lines 16079--16084 [][]\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 [247] [248] [249] Underfull \hbox (badness 6741) in paragraph at lines 16329--16333 \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 , [250] [251] [252] [253] [254] [255] [256] [257] [258] Underfull \vbox (badness 3803) has occurred while \output is active [259] Underfull \vbox (badness 10000) has occurred while \output is active [260] [261] [262] [263] [264] [265] [266] [267] [268] [269] Underfull \hbox (badness 1478) in paragraph at lines 17622--17625 []\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 [270] [271] [272] [273] Underfull \hbox (badness 10000) in paragraph at lines 17877--17879 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [274] [275] [276] [277] [278] [279] [280] [281] [282] Underfull \hbox (badness 1442) in paragraph at lines 18477--18479 []\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 [283] Underfull \hbox (badness 2452) in paragraph at lines 18569--18585 [][][]\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 , [284] [285] [286] [287] [288] [289] [290] Underfull \hbox (badness 1248) in paragraph at lines 18988--18991 []\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 , [291] [292] [293] [294] Underfull \hbox (badness 4739) in paragraph at lines 19246--19248 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [295] [296] [297] [298] [299] [300] Underfull \hbox (badness 1596) in paragraph at lines 19665--19670 \T1/ptm/m/n/10 trix or, if \T1/zi4/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/zi4/m/n/10 simplify2array()\T1/ptm /m/n/10 . [301] [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] Underfull \hbox (badness 2469) in paragraph at lines 20269--20274 []\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 20283--20290 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [312] Underfull \hbox (badness 10000) in paragraph at lines 20357--20361 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 20357--20361 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$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 ' [313] [314] Underfull \hbox (badness 1014) in paragraph at lines 20527--20532 []\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 [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] Underfull \hbox (badness 1264) in paragraph at lines 21317--21322 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [327] Underfull \hbox (badness 4441) in paragraph at lines 21346--21349 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 , [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] Underfull \hbox (badness 6047) in paragraph at lines 22093--22095 []\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 \T1/zi4/m/n/10 make.unique(c(A,B)) == [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] Underfull \hbox (badness 1077) in paragraph at lines 23134--23140 \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 . [356] [357] [358] [359] [360] [361] [362] [363] Underfull \hbox (badness 2790) in paragraph at lines 23630--23633 []\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 23630--23633 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [364] [365] [366] [367] [368] Underfull \hbox (badness 1194) in paragraph at lines 23912--23915 []\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 [369] [370] [371] Underfull \hbox (badness 2368) in paragraph at lines 24118--24124 []\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 list, i.e., Underfull \hbox (badness 4981) in paragraph at lines 24118--24124 \T1/zi4/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are al so given by [][]\T1/zi4/m/n/10 ls[][][](env,all.names = [372] [373] [374] [375] [376] [377] Underfull \hbox (badness 10000) in paragraph at lines 24500--24503 []\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by [378] [379] [380] [381] [382] [383] [384] [385] [386] Underfull \hbox (badness 10000) in paragraph at lines 25105--25107 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than \T1/zi4/m/n/10 pkg %in% [387] [388] [389] [390] [391] [392] [393] [394] [395] [396] [397] [398] [399] Underfull \hbox (badness 1038) in paragraph at lines 25945--25953 []\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 1735) in paragraph at lines 25945--25953 \T1/ptm/m/n/10 set from value of the en-vi-ron-ment vari-able \T1/zi4/m/n/10 R_ DEFAULT_PACKAGES\T1/ptm/m/n/10 , or if that is un- Underfull \hbox (badness 1292) in paragraph at lines 25945--25953 \T1/ptm/m/n/10 set to \T1/zi4/m/n/10 c("datasets","utils","grDevices","graphics ","stats","methods")\T1/ptm/m/n/10 . (Set Underfull \hbox (badness 1881) in paragraph at lines 25954--25957 []\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 25973--25975 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [400] [401] Underfull \hbox (badness 2142) in paragraph at lines 26114--26118 []\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 26164--26169 []\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 [402] [403] [404] [405] Underfull \hbox (badness 10000) in paragraph at lines 26452--26458 []\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 26452--26458 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 26452--26458 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 26465--26468 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 26491--26493 []\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 26526--26531 []\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 2529) in paragraph at lines 26532--26543 \T1/ptm/m/n/10 in-di-rectly [][]\T1/zi4/m/n/10 update.packages[][][]\T1/ptm/m/n /10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si- Underfull \hbox (badness 2512) in paragraph at lines 26532--26543 \T1/ptm/m/n/10 ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi4/m /n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use and [406] Underfull \hbox (badness 7203) in paragraph at lines 26544--26547 []\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 10000) in paragraph at lines 26568--26573 []\T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma -cOS build), Underfull \hbox (badness 2057) in paragraph at lines 26568--26573 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). [407] [408] [409] [410] [411] [412] [413] [414] Underfull \hbox (badness 10000) in paragraph at lines 27086--27089 []\T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 str2lang(s ) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of [415] Underfull \hbox (badness 7925) in paragraph at lines 27165--27169 []\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 vec-to r \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n /10 cor-re-sponds to Underfull \hbox (badness 1622) in paragraph at lines 27165--27169 [][]\T1/zi4/m/n/10 parse[][][](text = s,keep.source=FALSE)\T1/ptm/m/n/10 , whic h is al-ways of type ([][]\T1/zi4/m/n/10 typeof[][][]\T1/ptm/m/n/10 ) and [][]\ T1/zi4/m/n/10 class[][][] Underfull \hbox (badness 6125) in paragraph at lines 27170--27179 []\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 string \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2lang(s) \T1/ptm/m/n/10 cor -re-sponds to [][]\T1/zi4/m/n/10 parse[][][](text = [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] Underfull \hbox (badness 2726) in paragraph at lines 27891--27894 []\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 [427] [428] [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] Underfull \vbox (badness 3803) has occurred while \output is active [445] [446] [447] [448] [449] [450] [451] [452] Underfull \hbox (badness 1533) in paragraph at lines 29582--29585 []\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 [453] [454] [455] Underfull \hbox (badness 1163) in paragraph at lines 29745--29756 []\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 [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] [473] [474] [475] [476] [477] [478] [479] Underfull \hbox (badness 10000) in paragraph at lines 31291--31295 []\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 31291--31295 \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 31313--31315 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [480] [481] [482] [483] [484] [485] [486] [487] [488] Underfull \hbox (badness 1655) in paragraph at lines 31869--31871 []\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 [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] Underfull \hbox (badness 2261) in paragraph at lines 32988--32993 []\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 [506] Underfull \hbox (badness 10000) in paragraph at lines 33015--33021 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1484) in paragraph at lines 33015--33021 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal and hex-adec-i-mal rep-re-sen-ta-tions like [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] Underfull \hbox (badness 1072) in paragraph at lines 36157--36161 []\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 36162--36166 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 36190--36196 []\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 36190--36196 \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 36190--36196 \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 3009) in paragraph at lines 36202--36209 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 36202--36209 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 36202--36209 \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 36202--36209 \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 [555] [556] [557] [558] [559] [560] Underfull \hbox (badness 1142) in paragraph at lines 36556--36562 []\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 \T1/zi4/m/n/10 "%Y-%m-%d [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] Underfull \hbox (badness 1565) in paragraph at lines 37829--37831 []\T1/ptm/m/n/10 integer code used in \T1/zi4/m/n/10 quantile(*,type=quantile.t ype) \T1/ptm/m/n/10 for the de-fault [581] [582] [583] [584] [585] [586] [587] [588] [589] [590] Underfull \hbox (badness 4967) in paragraph at lines 38428--38433 []\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 [591] [592] Underfull \hbox (badness 1616) in paragraph at lines 38541--38546 \T1/zi4/m/n/10 system("id") \T1/ptm/m/n/10 is much more portable on Unix-alikes , pro-vided only the POSIX op-tions [593] [594] [595] [596] [597] [598] [599] [600] Underfull \hbox (badness 1472) in paragraph at lines 39067--39070 []\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 [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614] Underfull \hbox (badness 10000) in paragraph at lines 39981--39985 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/zi4/m/n/10 length(bin) > [615] [616] [617] [618] Underfull \hbox (badness 10000) in paragraph at lines 40232--40235 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [619] [620] [621] Underfull \hbox (badness 10000) in paragraph at lines 40416--40420 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [622] [623] [624] [625] [626] [627] [628] [629] [630] Underfull \hbox (badness 10000) in paragraph at lines 41029--41032 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[ ]zones / [631] [632] [633] [634] [635] [636] Underfull \vbox (badness 10000) has occurred while \output is active [637] [638] [639] [640] [641] [642] [643] [644] Underfull \hbox (badness 1990) in paragraph at lines 41933--41941 []\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 41933--41941 \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 [645] [646] [647] [648] [649] [650] [651] [652] Underfull \hbox (badness 1917) in paragraph at lines 42439--42446 []\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 [653] [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] Underfull \hbox (badness 3668) in paragraph at lines 43168--43170 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [664] [665] Underfull \hbox (badness 2401) in paragraph at lines 43296--43300 []\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 [666] [667] [668] Underfull \hbox (badness 2111) in paragraph at lines 43485--43490 \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 10000) in paragraph at lines 43506--43511 []\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 [669] [670] [671] [672] [673] [674] [675] [676] [677] Underfull \hbox (badness 5417) in paragraph at lines 44088--44092 []\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 [678] Underfull \hbox (badness 10000) in paragraph at lines 44149--44153 []\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 [679] [680]) (./compiler-pkg.tex Chapter 2. [681] [682] [683] [684]) (./datasets-pkg.tex Chapter 3. [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] Underfull \hbox (badness 1097) in paragraph at lines 1031--1035 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] Underfull \vbox (badness 1448) has occurred while \output is active [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] Overfull \vbox (19.74611pt too high) has occurred while \output is active [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] Underfull \vbox (badness 10000) has occurred while \output is active [753] [754] [755] [756] Underfull \vbox (badness 10000) has occurred while \output is active [757] [758] [759] [760] [761] [762] [763] [764] [765] [766]) (./grDevices-pkg.tex Chapter 4. [767] [768] [769] [770] [771] Underfull \hbox (badness 3158) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/zi4/m/n/10 c(mi,ma,n.)\T1/ptm /m/n/10 , with iden-ti-cal mean-ing to Underfull \hbox (badness 10000) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][]\T1/zi4/m/n/10 axisTicks[][][]() \T1/ptm/ m/n/10 just calls the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/ptm/m/n/1 0 in Underfull \hbox (badness 1852) in paragraph at lines 298--303 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 /src/main/plot.c\T1/ptm/m/n/10 ' which is also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t ion [772] [773] [774] [775] [776] [777] [778] [779] Underfull \hbox (badness 1424) in paragraph at lines 830--832 [][][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 (as in-te-ger or char-ac-ter) and \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 mean trans-par-ent, which can also be spec-i -fied as [780] [781] [782] [783] [784] Underfull \hbox (badness 5175) in paragraph at lines 1124--1126 []\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 [785] [786] [787] [788] Underfull \hbox (badness 1852) in paragraph at lines 1326--1329 []\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 [789] [790] [791] Underfull \hbox (badness 1490) in paragraph at lines 1532--1537 \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 [792] [793] [794] [795] [796] [797] Underfull \hbox (badness 1325) in paragraph at lines 1938--1948 \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 , [798] [799] Underfull \hbox (badness 10000) in paragraph at lines 2050--2052 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [800] [801] [802] Underfull \hbox (badness 6758) in paragraph at lines 2228--2231 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [803] [804] [805] [806] [807] [808] [809] [810] [811] [812] Underfull \hbox (badness 10000) in paragraph at lines 2832--2833 [813] [814] [815] [816] [817] [818] [819] [820] [821] Underfull \hbox (badness 10000) in paragraph at lines 3388--3393 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [822] [823] [824] [825] [826] Underfull \vbox (badness 10000) has occurred while \output is active [827] Underfull \hbox (badness 10000) in paragraph at lines 3789--3792 []\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 [828] [829] [830] [831] [832] [833] [834] [835] [836] [837] [838] Underfull \hbox (badness 10000) in paragraph at lines 4518--4523 [][][]$\T1/zi4/m/n/10 https : / / www . adobe . com / content / dam / acom / en / devnet / actionscript / articles / PLRM . pdf$[][] Underfull \hbox (badness 4181) in paragraph at lines 4518--4523 \T1/ptm/m/n/10 or PDF [][]$\T1/zi4/m/n/10 https : / / www . adobe . com / devne t / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in [839] Underfull \vbox (badness 10000) has occurred while \output is active [840] [841] Underfull \hbox (badness 1067) in paragraph at lines 4672--4679 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [842] [843] [844] [845] Underfull \hbox (badness 1377) in paragraph at lines 4975--4980 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [846] Underfull \hbox (badness 1418) in paragraph at lines 5051--5058 \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 1755) in paragraph at lines 5069--5071 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [847] [848] Underfull \hbox (badness 1377) in paragraph at lines 5180--5185 []\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 [849] Underfull \hbox (badness 7344) in paragraph at lines 5249--5251 []\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 [850] [851] Underfull \hbox (badness 2035) in paragraph at lines 5384--5393 []\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 5384--5393 \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 5384--5393 \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 , [852] Underfull \hbox (badness 10000) in paragraph at lines 5452--5459 []\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 5452--5459 \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 . [853] [854] [855] Underfull \hbox (badness 1546) in paragraph at lines 5594--5602 []\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 , [856] [857] [858] [859] [860] [861] [862] [863] Underfull \hbox (badness 10000) in paragraph at lines 6129--6132 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [864] [865] [866] [867] [868] [869] [870] [871] [872] [873] [874] [875] [876] Underfull \hbox (badness 1189) in paragraph at lines 6951--6953 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [877] Underfull \hbox (badness 10000) in paragraph at lines 7049--7051 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [878] [879] [880] [881] [882] Underfull \hbox (badness 3780) in paragraph at lines 7349--7355 []\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 , [883] [884] [885] Underfull \hbox (badness 2680) in paragraph at lines 7550--7552 []\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 [886] [887] [888]) (./graphics-pkg.tex Chapter 5. [889] [890] [891] [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] Underfull \hbox (badness 4634) in paragraph at lines 1351--1354 [][][]\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 , [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] Underfull \hbox (badness 1728) in paragraph at lines 2308--2310 []\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use \T1/zi4/m/n/10 "n " \T1/ptm/m/n/10 to sup-press and see also [927] [928] Underfull \hbox (badness 1009) in paragraph at lines 2399--2406 \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 [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] [947] [948] [949] [950] Underfull \vbox (badness 10000) has occurred while \output is active [951] [952] [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] Underfull \hbox (badness 3229) in paragraph at lines 4544--4549 []\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 [964] [965] [966] [967] [968] Underfull \hbox (badness 10000) in paragraph at lines 4901--4907 []\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 4901--4907 \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 [969] Underfull \hbox (badness 10000) in paragraph at lines 5032--5035 [970] Underfull \hbox (badness 10000) in paragraph at lines 5093--5095 [971 >/library/graphics/help/figures/ mai.pdf>] [972 >/library/graphics/hel p/figures/oma.pdf>] [973] Underfull \hbox (badness 10000) in paragraph at lines 5283--5285 []\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 [974] Underfull \vbox (badness 3803) has occurred while \output is active [975] [976] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6761--6762 [][] [997] [998 >/library/graphics/help/fi gures/pch.pdf>] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] Underfull \hbox (badness 2012) in paragraph at lines 7586--7589 []\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 poi nt [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] Underfull \hbox (badness 10000) in paragraph at lines 8846--8848 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8848--8850 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1032]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8928 \HeaderA{units}{Graphical Units}{units} [1033] [1034] [1035] [1036]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] Underfull \hbox (badness 2680) in paragraph at lines 483--486 []\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 [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] Underfull \hbox (badness 4279) in paragraph at lines 1064--1073 [][][]\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 , [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] Underfull \vbox (badness 10000) has occurred while \output is active [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] Underfull \hbox (badness 1067) in paragraph at lines 4486--4489 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1113] [1114] [1115] [1116] Underfull \hbox (badness 7256) in paragraph at lines 4731--4733 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \hbox (badness 1824) in paragraph at lines 6535--6538 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like \T1/zi4/m/n/10 depth [1148] [1149] [1150] [1151]) (./methods-pkg.tex [1152] Chapter 7. [1153] [1154] [1155] [1156] [1157] [1158] [1159] [1160] Underfull \vbox (badness 10000) has occurred while \output is active [1161] Underfull \vbox (badness 10000) has occurred while \output is active [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171] Underfull \hbox (badness 2237) in paragraph at lines 1385--1387 []\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 [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] Underfull \hbox (badness 2181) in paragraph at lines 1932--1939 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/zi4/m/n/10 is(x,"refClass") \T1/ptm/m/n/10 tests [1180] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\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 1981--1986 \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 [1181] [1182] [1183] Underfull \hbox (badness 2213) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/zi4/m/n/10 where = [1184] [1185] [1186] [1187] [1188] Underfull \hbox (badness 10000) in paragraph at lines 2574--2577 []\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 [1189] [1190] Underfull \hbox (badness 1132) in paragraph at lines 2714--2718 []\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 [1191] Underfull \hbox (badness 1033) in paragraph at lines 2746--2751 \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 [1192] [1193] [1194] [1195] [1196] [1197] [1198] Underfull \hbox (badness 1102) in paragraph at lines 3303--3305 []\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 [1199] [1200] [1201] [1202] [1203] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\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 [1204] Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1205] Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [] \T1/zi4/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude = "numeric",altitude [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] Underfull \hbox (badness 1769) in paragraph at lines 4472--4478 []\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 4472--4478 \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 [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] Underfull \vbox (badness 10000) has occurred while \output is active [1227] [1228] [1229] Underfull \hbox (badness 4036) in paragraph at lines 5437--5440 []\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 [1230] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1231] [1232] [1233] [1234] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] Underfull \hbox (badness 1675) in paragraph at lines 6451--6457 \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 [1243] [1244] [1245] [1246] Underfull \vbox (badness 10000) has occurred while \output is active [1247] [1248] [1249] [1250]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1251] [1252] [1253]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} [1254] Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1255] [1256] [1257] Underfull \hbox (badness 1286) in paragraph at lines 7484--7486 []\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 [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] Underfull \vbox (badness 10000) has occurred while \output is active [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] Underfull \hbox (badness 1137) in paragraph at lines 10011--10019 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/n/10 ne w("signature",functionDef,...)\T1/ptm/m/n/10 . The [1293] [1294] [1295] [1296] [1297] [1298] [1299] Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., [1300] [1301] [1302] [1303]) (./parallel-pkg.tex [1304] Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\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 [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] [1324] [1325] Underfull \hbox (badness 3386) in paragraph at lines 1365--1368 []\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 [1326] [1327] [1328]) (./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 [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344]) (./stats-pkg.tex Chapter 10. [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] Underfull \hbox (badness 1412) in paragraph at lines 875--877 []\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 [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] Underfull \hbox (badness 2503) in paragraph at lines 1356--1359 []\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 , [1367] [1368] [1369] Underfull \hbox (badness 10000) in paragraph at lines 1536--1540 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov","lm") \T1/ptm/m/n/1 0 or for mul-ti-ple re-sponses of class [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] Underfull \hbox (badness 2503) in paragraph at lines 3437--3440 []\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 , [1400] [1401] [1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] Underfull \hbox (badness 1127) in paragraph at lines 4351--4354 []\T1/ptm/m/n/10 standardized resid-u-als, \T1/zi4/m/n/10 (observed -expected) / sqrt(V)\T1/ptm/m/n/10 , where \T1/zi4/m/n/10 V \T1/ptm/m/n/10 is the [1415] [1416] [1417] [1418] [1419] Underfull \hbox (badness 3989) in paragraph at lines 4681--4688 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] Underfull \hbox (badness 2556) in paragraph at lines 5317--5320 []\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 5334--5336 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/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 [1430] [1431] [1432] [1433] [1434] [1435] [1436] Underfull \hbox (badness 2503) in paragraph at lines 5726--5730 []\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 , [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] Underfull \hbox (badness 7081) in paragraph at lines 6520--6523 []\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 6524--6526 []\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 [1450] [1451] [1452] [1453] [1454] Underfull \vbox (badness 3803) has occurred while \output is active [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] Underfull \hbox (badness 10000) in paragraph at lines 7369--7372 []\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 [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] Underfull \vbox (badness 10000) has occurred while \output is active [1485] [1486] [1487] [1488] [1489] Underfull \hbox (badness 2626) in paragraph at lines 9048--9051 []\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 [1490] [1491] Underfull \hbox (badness 2503) in paragraph at lines 9155--9159 []\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 , [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] [1509] [1510] [1511] Underfull \hbox (badness 4518) in paragraph at lines 10469--10474 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1512] [1513] [1514] [1515] [1516] Underfull \hbox (badness 2142) in paragraph at lines 10830--10833 []\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 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10849--10852 []\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, [1517] Underfull \hbox (badness 1708) in paragraph at lines 10911--10915 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1518] [1519] [1520] [1521] [1522] [1523] Underfull \hbox (badness 1694) in paragraph at lines 11307--11310 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531]pdfTeX warning (ext4): d estination with the same identifier (name{Rfn.hat}) has been already used, dupl icate ignored \relax l.11791 \aliasA{hat}{influence.measures}{hat} [1532] [1533] Underfull \hbox (badness 1484) in paragraph at lines 11926--11928 []\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 [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] Underfull \hbox (badness 10000) in paragraph at lines 12519--12521 []\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 \T1/zi4/m/n/10 SSinit = [1544] [1545] [1546] [1547] [1548] [1549] Underfull \hbox (badness 2894) in paragraph at lines 12855--12859 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] Underfull \hbox (badness 4518) in paragraph at lines 13605--13610 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] Underfull \hbox (badness 4518) in paragraph at lines 14257--14262 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1572] [1573] Underfull \hbox (badness 8151) in paragraph at lines 14395--14399 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = "interp olate",statistics = Underfull \hbox (badness 1199) in paragraph at lines 14402--14404 []\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 [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] Underfull \hbox (badness 2503) in paragraph at lines 15473--15477 []\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 , [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] Underfull \hbox (badness 4621) in paragraph at lines 15985--15991 []\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 [1600] [1601] [1602] [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] [1623] [1624] [1625] [1626] [1627] Underfull \vbox (badness 10000) has occurred while \output is active [1628] Underfull \vbox (badness 10000) has occurred while \output is active [1629] [1630] [1631] [1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] Underfull \hbox (badness 1377) in paragraph at lines 18588--18593 []\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 18593--18596 []\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 [1642] Underfull \hbox (badness 2343) in paragraph at lines 18606--18610 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 3471) in paragraph at lines 18606--18610 \T1/ptm/m/n/10 the value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + re ltol) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18614--18618 []\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 [1643] [1644] [1645] Overfull \hbox (15.73795pt too wide) in paragraph at lines 18839--18839 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 18842--18842 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] Underfull \vbox (badness 10000) has occurred while \output is active [1646] [1647] [1648] [1649] [1650] [1651] [1652] Underfull \hbox (badness 1337) in paragraph at lines 19264--19267 []\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 [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] Underfull \hbox (badness 3049) in paragraph at lines 19760--19764 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1662] [1663] [1664] [1665] Underfull \hbox (badness 1194) in paragraph at lines 20018--20021 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1666] [1667] [1668] [1669] [1670] [1671] [1672] Underfull \hbox (badness 2503) in paragraph at lines 20397--20400 []\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 , Underfull \hbox (badness 3919) in paragraph at lines 20424--20426 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or \T1/zi4/m/n/10 "Comparison of Poisson [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] [1688] [1689] [1690] Underfull \hbox (badness 10000) in paragraph at lines 21501--21507 []\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 , [1691] [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] Underfull \hbox (badness 1337) in paragraph at lines 22855--22861 []\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 [1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] Overfull \hbox (27.74408pt too wide) in paragraph at lines 23420--23420 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1722] [1723] [1724] [1725] [1726] Underfull \hbox (badness 10000) in paragraph at lines 23671--23674 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 4205) in paragraph at lines 23671--23674 \T1/zi4/m/n/10 cutree(hclust.obj,k = k)\T1/ptm/m/n/10 , can be spec-i-fied for ef-fi-ciency if al-ready [1727] [1728] [1729] [1730] [1731] [1732] [1733] [1734] [1735] Underfull \hbox (badness 1824) in paragraph at lines 24257--24263 []\T1/ptm/m/n/10 Here, all the NAs in \T1/zi4/m/n/10 x \T1/ptm/m/n/10 are first re-placed by al-ter- Underfull \hbox (badness 1033) in paragraph at lines 24257--24263 \T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/ m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where [1736] Underfull \hbox (badness 10000) in paragraph at lines 24278--24281 []\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 \T1/zi4/m/n/10 y[j] = Underfull \hbox (badness 3690) in paragraph at lines 24347--24351 [][][]\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 [1737] Underfull \vbox (badness 3803) has occurred while \output is active [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] Underfull \hbox (badness 2165) in paragraph at lines 24856--24861 []\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm /m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1 0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [1746] [1747] [1748] [1749] Underfull \hbox (badness 1867) in paragraph at lines 25061--25063 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 25074--25078 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u se.fallback) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 PP [1750] [1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] Underfull \vbox (badness 3803) has occurred while \output is active [1761] [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] [1771] [1772] [1773] Underfull \vbox (badness 10000) has occurred while \output is active [1774] Underfull \hbox (badness 3514) in paragraph at lines 26634--26639 []\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 [1775] [1776] [1777] [1778] Overfull \hbox (2.23795pt too wide) in paragraph at lines 26868--26868 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1779] Underfull \hbox (badness 3514) in paragraph at lines 26904--26910 []\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 [1780] [1781] [1782] [1783] Underfull \hbox (badness 3514) in paragraph at lines 27118--27123 []\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 [1784] Underfull \hbox (badness 3514) in paragraph at lines 27205--27210 []\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 [1785] Underfull \hbox (badness 3514) in paragraph at lines 27270--27275 []\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 [1786] [1787] Underfull \hbox (badness 3514) in paragraph at lines 27364--27369 []\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 [1788] [1789] Underfull \hbox (badness 6691) in paragraph at lines 27456--27461 []\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 [1790] [1791] [1792] [1793] [1794] [1795] [1796] [1797] Underfull \hbox (badness 4024) in paragraph at lines 27984--27987 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion , which [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] Underfull \hbox (badness 5431) in paragraph at lines 28590--28592 []\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 [1808] [1809] [1810] [1811] Underfull \hbox (badness 5431) in paragraph at lines 28800--28803 []\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 [1812] [1813] [1814] [1815] [1816] Underfull \hbox (badness 1337) in paragraph at lines 29114--29118 []\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 [1817] [1818] [1819] [1820] [1821] Underfull \hbox (badness 1616) in paragraph at lines 29416--29419 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1822] [1823] [1824] [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] [1835] [1836] [1837] [1838] [1839] [1840] Underfull \hbox (badness 3557) in paragraph at lines 30546--30550 []\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 \T1/zi4 /m/n/10 interval = [1841] [1842] [1843] Underfull \vbox (badness 10000) has occurred while \output is active [1844] [1845] [1846] Underfull \hbox (badness 1337) in paragraph at lines 30910--30914 []\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 [1847] [1848] [1849] [1850] [1851] [1852] [1853] [1854] [1855] Underfull \hbox (badness 1337) in paragraph at lines 31437--31441 []\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 [1856] [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865]) (./stats4-pkg.tex [1866] Chapter 11. [1867] [1868] [1869] [1870] [1871] [1872]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} [1873] [1874] [1875]) (./tcltk-pkg.tex [1876] Chapter 12. [1877] [1878] [1879] [1880] [1881] [1882] [1883] Underfull \vbox (badness 10000) has occurred while \output is active [1884] Underfull \vbox (badness 10000) has occurred while \output is active [1885] 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 [1886] [1887] [1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897]) (./tools-pkg.tex [1898] Chapter 13. [1899] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1900] 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 [1901] [1902] 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 [1903] [1904] 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 [1905] [1906] [1907] [1908] [1909] [1910] [1911] [1912] [1913] [1914] [1915] [1916] [1917] Underfull \hbox (badness 4441) in paragraph at lines 1139--1149 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- Underfull \hbox (badness 1014) in paragraph at lines 1163--1165 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1169--1171 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous [1918] Underfull \hbox (badness 10000) in paragraph at lines 1206--1209 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1206--1209 \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 , [1919] [1920] [1921] [1922] [1923] Underfull \hbox (badness 2293) in paragraph at lines 1558--1560 []\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with its func-tion-al-ity in-te-grated into that of [1924] [1925] [1926] Underfull \hbox (badness 7981) in paragraph at lines 1696--1701 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 1082) in paragraph at lines 1703--1705 []\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 [1927] [1928] [1929]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1930] [1931] [1932] [1933] [1934] [1935] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2202--2202 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1936] [1937] [1938] Underfull \hbox (badness 7981) in paragraph at lines 2371--2377 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1939] [1940] [1941] [1942] [1943] [1944] [1945] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2846. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2847. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2847. [1946] [1947] [1948] [1949] [1950] Underfull \hbox (badness 1424) in paragraph at lines 3128--3130 []\T1/zi4/m/it/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 [1951] [1952] [1953] [1954] [1955] [1956] [1957] [1958] [1959] [1960] [1961] Underfull \hbox (badness 10000) in paragraph at lines 3832--3834 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1962] [1963] Underfull \hbox (badness 10000) in paragraph at lines 3971--3974 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/it/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/it/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1964] [1965] Underfull \hbox (badness 1137) in paragraph at lines 4073--4075 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1966] [1967] [1968] [1969] [1970] Underfull \hbox (badness 1796) in paragraph at lines 4381--4386 []\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over \T 1/zi4/m/it/10 write_PACKAGES \T1/ptm/m/n/10 in the \T1/zi4/m/it/10 type == [1971] Underfull \hbox (badness 1838) in paragraph at lines 4455--4461 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/it/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/it/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4455--4461 \T1/ptm/m/n/10 `\T1/zi4/m/it/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 [1972] [1973] [1974] Underfull \hbox (badness 2197) in paragraph at lines 4671--4681 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/it/10 available.packages[][][]\T1/ptm/m/n/10 : [1975] Underfull \hbox (badness 1571) in paragraph at lines 4734--4738 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [1976] [1977] [1978]) (./utils-pkg.tex Chapter 14. [1979] 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/it/10 insertions\T1/ptm/m/n/10 ', [1980] [1981] [1982] [1983] [1984] Underfull \hbox (badness 10000) in paragraph at lines 376--381 \T1/zi4/m/it/10 c("vertical","horizontal","cascade","minimize","restore") \T1/p tm/m/n/10 with [1985] [1986] [1987] [1988] [1989] Underfull \hbox (badness 10000) in paragraph at lines 717--723 []\T1/ptm/m/n/10 Functions \T1/zi4/m/it/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/it/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 717--723 \T1/zi4/m/it/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/it/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1990] [1991] Underfull \hbox (badness 5847) in paragraph at lines 850--856 []\T1/ptm/m/n/10 Argument \T1/zi4/m/it/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 850--856 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/it/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1992] Underfull \hbox (badness 3861) in paragraph at lines 918--923 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/it/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/it/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/it/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1993] [1994] Underfull \hbox (badness 3323) in paragraph at lines 1089--1097 []\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/zi4/m/it/1 0 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1 /ptm/m/n/10 , in-di-cat- Underfull \hbox (badness 2961) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f or-mat- Underfull \hbox (badness 3919) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 3735) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/it/10 getOption[][][]("citation.bibtex.ma x",1) \T1/ptm/m/n/10 which is \T1/zi4/m/it/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by [1995] Underfull \hbox (badness 10000) in paragraph at lines 1101--1103 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1996] [1997] Underfull \vbox (badness 3803) has occurred while \output is active [1998] [1999] [2000] [2001] [2002] Underfull \hbox (badness 1371) in paragraph at lines 1606--1608 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/it/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/it/10 ccaddress \T1/ptm/m/n/10 to pass to [2003] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 1676. [2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] Underfull \hbox (badness 2057) in paragraph at lines 2215--2217 []\T1/ptm/m/n/10 None for \T1/zi4/m/it/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [2013] [2014] [2015] [2016] [2017] [2018]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.clipboard}) has been already used, duplicate ig nored \relax l.2566 ... the Clipboard in MS Windows}{clipboard} [2019] [2020] Underfull \hbox (badness 1748) in paragraph at lines 2733--2736 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/it/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/it/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/it/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [2021] [2022] [2023] [2024] [2025] [2026] [2027] Underfull \hbox (badness 5388) in paragraph at lines 3142--3146 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/it/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/it/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/it/10 .TXT\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/it/10 read.table[][][](...,header = Underfull \hbox (badness 2285) in paragraph at lines 3147--3150 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/it/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/it/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/it/10 read.table[] [][](...,header = TRUE,sep = [2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] Underfull \hbox (badness 1430) in paragraph at lines 3906--3914 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/it/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [2039] Underfull \hbox (badness 1231) in paragraph at lines 3983--3995 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [2040] [2041] Underfull \hbox (badness 10000) in paragraph at lines 4141--4143 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/it/10 dow nload.file[][][] \T1/ptm/m/n/10 and [2042] [2043] [2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.4839 ...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.4839 ...mat Unordered and Ordered Lists}{format} [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] Underfull \hbox (badness 1622) in paragraph at lines 5358--5362 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 5990. Underfull \hbox (badness 1371) in paragraph at lines 5994--5996 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/it/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/it/10 ccaddress \T1/ptm/m/n/10 to pass to [2072] Underfull \hbox (badness 1502) in paragraph at lines 6083--6088 []\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 6083--6088 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2073] [2074] [2075] Underfull \hbox (badness 10000) in paragraph at lines 6256--6265 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2076] Underfull \hbox (badness 2150) in paragraph at lines 6320--6323 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2077] [2078] Underfull \hbox (badness 3118) in paragraph at lines 6458--6460 []\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 [2079] [2080] [2081] Underfull \hbox (badness 1325) in paragraph at lines 6630--6634 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/it/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able Underfull \hbox (badness 4726) in paragraph at lines 6642--6648 \T1/ptm/m/n/10 used if \T1/zi4/m/it/10 repos = NULL\T1/ptm/m/n/10 . Can also be a char-ac-ter vec-tor, a sub-set of [2082] Underfull \hbox (badness 10000) in paragraph at lines 6714--6717 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be Underfull \hbox (badness 10000) in paragraph at lines 6714--6717 \T1/ptm/m/n/10 passed to \T1/zi4/m/it/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou rce pack-age in-stall. E.g., [2083] Underfull \hbox (badness 3219) in paragraph at lines 6790--6797 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/it/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6790--6797 \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 6790--6797 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1596) in paragraph at lines 6790--6797 [][]\T1/zi4/m/it/10 getOption[][][]("install.packages.compile.from.source")\T1/ ptm/m/n/10 . \T1/zi4/m/it/10 type = "both" \T1/ptm/m/n/10 will be silently Underfull \hbox (badness 2932) in paragraph at lines 6798--6801 []\T1/ptm/m/n/10 Using pack-ages with \T1/zi4/m/it/10 type = "source" \T1/ptm/m /n/10 al-ways works pro-vided the pack-age con-tains no [2084] Underfull \hbox (badness 10000) in paragraph at lines 6934--6939 [][][]\T1/zi4/m/it/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [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] Underfull \hbox (badness 10000) in paragraph at lines 8434--8436 []\T1/ptm/m/n/10 for \T1/zi4/m/it/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi 4/m/it/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 2310) in paragraph at lines 8456--8461 []\T1/ptm/m/n/10 If a `\T1/zi4/m/it/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2110] [2111] [2112] [2113] [2114] [2115] [2116] [2117] Underfull \hbox (badness 1248) in paragraph at lines 8980--8984 []\T1/zi4/m/it/10 R CMD build \T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/m/ n/10 source tar-balls. The name(s) of the pack-ages are taken from the [2118] Underfull \hbox (badness 1789) in paragraph at lines 9058--9060 []\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 [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131] Underfull \hbox (badness 1097) in paragraph at lines 9895--9898 []\T1/ptm/m/n/10 The name \T1/zi4/m/it/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2132] [2133] Underfull \hbox (badness 3000) in paragraph at lines 10031--10036 [][][]\T1/zi4/m/it/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/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/it/10 read.t able[][][]\T1/ptm/m/n/10 ; [2134] [2135] [2136] [2137] [2138] [2139] [2140] [2141] [2142] Underfull \hbox (badness 2134) in paragraph at lines 10614--10619 [][][]\T1/zi4/m/it/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/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/it/10 write. table[][][]\T1/ptm/m/n/10 ; Underfull \hbox (badness 10000) in paragraph at lines 10670--10675 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for Underfull \hbox (badness 10000) in paragraph at lines 10670--10675 \T1/zi4/m/it/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/zi4/m/it/10 HKEY_CLASSES _ROOT\T1/ptm/m/n/10 . \T1/zi4/m/it/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] Underfull \hbox (badness 2469) in paragraph at lines 11163--11167 []\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 11163--11167 [][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2152] [2153] [2154] [2155] [2156] Underfull \hbox (badness 4060) in paragraph at lines 11494--11497 []\T1/ptm/m/n/10 If `\T1/zi4/m/it/10 --default-packages\T1/ptm/m/n/10 ' is not used, then \T1/zi4/m/it/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var i-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 11517--11517 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [2157] [2158] [2159] [2160] Underfull \hbox (badness 2150) in paragraph at lines 11756--11758 [][][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/it/10 https : / / www . gnu . org / software / emac s / manual / [2161] [2162] [2163] [2164] Underfull \hbox (badness 10000) in paragraph at lines 11975--11979 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/it/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12006--12012 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2165] [2166] Underfull \hbox (badness 1009) in paragraph at lines 12200--12212 []\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 [2167] Underfull \hbox (badness 4779) in paragraph at lines 12237--12239 []\T1/ptm/m/n/10 The file `\T1/zi4/m/it/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ure s the R GUI (\T1/zi4/m/it/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows a nd Underfull \hbox (badness 1077) in paragraph at lines 12267--12274 \T1/ptm/m/n/10 (strip-ping any trail-ing slash), oth-er-wise to the Win-dows `p er-sonal' di-rec-tory, oth-er-wise to [2168] [2169] [2170] [2171] [2172] [2173] [2174] Underfull \hbox (badness 3780) in paragraph at lines 12668--12672 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/it/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 12684--12687 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/it/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2175] [2176] [2177] [2178] Underfull \hbox (badness 2302) in paragraph at lines 12889--12891 []\T1/ptm/m/n/10 Convert file paths to the short form. 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Ob- [2190] [2191] [2192] [2193] [2194] Underfull \hbox (badness 6510) in paragraph at lines 13923--13927 []\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/it/10 tar \T1/ptm/m/n/10 is set to t he com-mand \T1/zi4/m/it/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a ble Underfull \hbox (badness 10000) in paragraph at lines 13930--13933 [][][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/it/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 13930--13933 \T1/zi4/m/it/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2195] [2196] [2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] Underfull \hbox (badness 10000) in paragraph at lines 14594--14599 []\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/it/10 destdir \T1/ptm/m/n/10 and \ T1/zi4/m/it/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 3861) in paragraph at lines 14594--14599 [][]\T1/zi4/m/it/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/it/10 i gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/it/10 max_repo_cache_age \T1/ptm/m/n /10 and Underfull \hbox (badness 1052) in paragraph at lines 14600--14602 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. 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[1] [2] Underfull \hbox (badness 6995) 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 . It Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1/pt m/m/n/10 if \T1/zi4/m/n/10 double.base Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth- er-wise, it is \T1/zi4/m/n/10 (double.base Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/zi4/m /n/10 1.110223e-16\T1/ptm/m/n/10 . As Underfull \hbox (badness 4995) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.neg.ulp.digits \T1/ptm/m/n/10 is bounded be-low by \T1/zi 4/m/n/10 -(double.digits + 3)\T1/ptm/m/n/10 , [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 297--301 []\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 . 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By chain-ing \T1/zi4/m/n/10 asplit [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] Underfull \hbox (badness 10000) in paragraph at lines 3784--3786 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [60] [61] [62] Overfull \hbox (6.42029pt too wide) in paragraph at lines 4025--4025 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 2521) in paragraph at lines 5046--5048 []\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 [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6202--6202 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [97] [98] [99] [100] [101] [102] Overfull \hbox (46.35893pt too wide) in paragraph at lines 6611--6613 []\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 : [103] [104] Underfull \hbox (badness 10000) in paragraph at lines 6759--6762 []\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 [105] [106] Underfull \hbox (badness 6063) in paragraph at lines 6941--6947 []\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- Underfull \hbox (badness 2343) in paragraph at lines 6941--6947 \T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files and web-pages gen-er- Underfull \hbox (badness 1708) in paragraph at lines 6941--6947 \T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it i s not rec-om-mended) when Underfull \hbox (badness 1831) in paragraph at lines 6941--6947 \T1/ptm/m/n/10 writ-ing it should be writ-ten ex-plic-itly, e.g. by \T1/zi4/m/n /10 writeChar("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or [107] Underfull \hbox (badness 3568) in paragraph at lines 7003--7010 \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 [108] [109] Underfull \vbox (badness 3803) has occurred while \output is active [110] Underfull \vbox (badness 10000) has occurred while \output is active [111] [112] Underfull \hbox (badness 1077) in paragraph at lines 7330--7336 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7330--7336 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [113] [114] [115] [116] [117] [118] Underfull \hbox (badness 2096) in paragraph at lines 7671--7675 \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 . [119] [120] Underfull \hbox (badness 2351) in paragraph at lines 7789--7792 [][][]\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 , [121] [122] [123] [124] [125] Underfull \hbox (badness 4479) in paragraph at lines 8115--8125 [][][]\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), [126] [127] [128] [129] [130] [131] Underfull \hbox (badness 1629) in paragraph at lines 8562--8574 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 1609) in paragraph at lines 8562--8574 \T1/ptm/m/n/10 there is a prob-lem in the POSIX/C99 stan-dard with \T1/zi4/m/n/ 10 "1969-12-31 23:59:59 UTC"\T1/ptm/m/n/10 , which Underfull \hbox (badness 2426) in paragraph at lines 8562--8574 \T1/ptm/m/n/10 is \T1/zi4/m/n/10 -1 \T1/ptm/m/n/10 in cal-en-dar time and that value is on those OSes also used as an er-ror code. [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] Underfull \hbox (badness 1178) in paragraph at lines 9298--9302 []\T1/ptm/m/n/10 If true, [][]\T1/zi4/m/n/10 list[][][]\T1/ptm/m/n/10 s and ato mic vec-tors with non-[][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 names (see [][ ]\T1/zi4/m/n/10 names[][][]\T1/ptm/m/n/10 ) are de- [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] Underfull \hbox (badness 1735) in paragraph at lines 10446--10450 \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 . [161] [162] [163] [164] [165] [166] [167] Underfull \hbox (badness 6396) in paragraph at lines 10885--10893 []\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 1946) in paragraph at lines 10885--10893 \T1/zi4/m/n/10 duplicated \T1/ptm/m/n/10 and \T1/zi4/m/n/10 anyDuplicated\T1/pt m/m/n/10 , \T1/zi4/m/n/10 anyDuplicated(x,...) \T1/ptm/m/n/10 is a ``gen-er-al- ized'' short-cut for [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] Underfull \hbox (badness 4569) in paragraph at lines 12002--12006 []\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 12002--12006 \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 [184] Underfull \vbox (badness 10000) has occurred while \output is active [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] Underfull \hbox (badness 2253) in paragraph at lines 13665--13667 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [209] [210] Underfull \hbox (badness 1565) in paragraph at lines 13738--13742 [][][]\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 Underfull \hbox (badness 4927) in paragraph at lines 13782--13784 []\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 \T1/zi4 /m/n/10 fsep = [211] [212] Underfull \hbox (badness 3148) in paragraph at lines 13875--13880 [][][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[ ][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 help[][][]\T1/ptm/m/n/10 ; [][]\T1/zi4 /m/n/10 RShowDoc[][][] \T1/ptm/m/n/10 call \T1/zi4/m/n/10 file.show() \T1/ptm/m /n/10 for \T1/zi4/m/n/10 type = "text"\T1/ptm/m/n/10 . Con-sider [213] Underfull \hbox (badness 1466) in paragraph at lines 13922--13925 []\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 [214] Underfull \hbox (badness 10000) in paragraph at lines 14049--14053 [][][]\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 14060--14063 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [215] [216] [217] [218] [219] Underfull \hbox (badness 3965) in paragraph at lines 14352--14356 []\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, [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] Underfull \hbox (badness 4429) in paragraph at lines 15128--15131 []\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 [232] [233] Underfull \hbox (badness 10000) in paragraph at lines 15234--15236 []\T1/ptm/m/n/10 This works via \T1/zi4/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic h calls Underfull \hbox (badness 1215) in paragraph at lines 15234--15236 \T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times in this case, see Underfull \hbox (badness 10000) in paragraph at lines 15256--15261 []\T1/ptm/m/n/10 For num-bers, \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 calls \T 1/zi4/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls Underfull \hbox (badness 1558) in paragraph at lines 15256--15261 \T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero)\T1/ptm/m/n/10 . (\T1/ptm/m /it/10 ``when needed''\T1/ptm/m/n/10 : when \T1/zi4/m/n/10 zero.print \T1/ptm/m /n/10 is not Underfull \hbox (badness 10000) in paragraph at lines 15268--15272 []\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 Underfull \hbox (badness 2426) in paragraph at lines 15268--15272 \T1/zi4/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi ves \T1/zi4/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . If you want [234] Underfull \hbox (badness 2035) in paragraph at lines 15307--15311 []\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 within [235] Underfull \vbox (badness 10000) has occurred while \output is active [236] [237] [238] [239] [240] [241] [242] [243] Underfull \hbox (badness 2452) in paragraph at lines 15906--15910 []\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 15906--15910 \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 [244] [245] [246] Underfull \hbox (badness 1092) in paragraph at lines 16079--16084 [][]\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 [247] [248] [249] Underfull \hbox (badness 6741) in paragraph at lines 16329--16333 \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 , [250] [251] [252] [253] [254] [255] [256] [257] [258] Underfull \vbox (badness 3803) has occurred while \output is active [259] Underfull \vbox (badness 10000) has occurred while \output is active [260] [261] [262] [263] [264] [265] [266] [267] [268] [269] Underfull \hbox (badness 1478) in paragraph at lines 17622--17625 []\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 [270] [271] [272] [273] Underfull \hbox (badness 10000) in paragraph at lines 17877--17879 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [274] [275] [276] [277] [278] [279] [280] [281] [282] Underfull \hbox (badness 1442) in paragraph at lines 18477--18479 []\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 [283] Underfull \hbox (badness 2452) in paragraph at lines 18569--18585 [][][]\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 , [284] [285] [286] [287] [288] [289] [290] Underfull \hbox (badness 1248) in paragraph at lines 18988--18991 []\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 , [291] [292] [293] [294] Underfull \hbox (badness 4739) in paragraph at lines 19246--19248 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [295] [296] [297] [298] [299] [300] Underfull \hbox (badness 1596) in paragraph at lines 19665--19670 \T1/ptm/m/n/10 trix or, if \T1/zi4/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/zi4/m/n/10 simplify2array()\T1/ptm /m/n/10 . [301] [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] Underfull \hbox (badness 2469) in paragraph at lines 20269--20274 []\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 20283--20290 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [312] Underfull \hbox (badness 10000) in paragraph at lines 20357--20361 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 20357--20361 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$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 ' [313] [314] Underfull \hbox (badness 1014) in paragraph at lines 20527--20532 []\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 [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] Underfull \hbox (badness 1264) in paragraph at lines 21317--21322 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [327] Underfull \hbox (badness 4441) in paragraph at lines 21346--21349 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 , [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] Underfull \hbox (badness 6047) in paragraph at lines 22093--22095 []\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 \T1/zi4/m/n/10 make.unique(c(A,B)) == [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] Underfull \hbox (badness 1077) in paragraph at lines 23134--23140 \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 . [356] [357] [358] [359] [360] [361] [362] [363] Underfull \hbox (badness 2790) in paragraph at lines 23630--23633 []\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 23630--23633 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [364] [365] [366] [367] [368] Underfull \hbox (badness 1194) in paragraph at lines 23912--23915 []\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 [369] [370] [371] Underfull \hbox (badness 2368) in paragraph at lines 24118--24124 []\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 list, i.e., Underfull \hbox (badness 4981) in paragraph at lines 24118--24124 \T1/zi4/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are al so given by [][]\T1/zi4/m/n/10 ls[][][](env,all.names = [372] [373] [374] [375] [376] [377] Underfull \hbox (badness 10000) in paragraph at lines 24500--24503 []\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by [378] [379] [380] [381] [382] [383] [384] [385] [386] Underfull \hbox (badness 10000) in paragraph at lines 25105--25107 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than \T1/zi4/m/n/10 pkg %in% [387] [388] [389] [390] [391] [392] [393] [394] [395] [396] [397] [398] [399] Underfull \hbox (badness 1038) in paragraph at lines 25945--25953 []\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 1735) in paragraph at lines 25945--25953 \T1/ptm/m/n/10 set from value of the en-vi-ron-ment vari-able \T1/zi4/m/n/10 R_ DEFAULT_PACKAGES\T1/ptm/m/n/10 , or if that is un- Underfull \hbox (badness 1292) in paragraph at lines 25945--25953 \T1/ptm/m/n/10 set to \T1/zi4/m/n/10 c("datasets","utils","grDevices","graphics ","stats","methods")\T1/ptm/m/n/10 . (Set Underfull \hbox (badness 1881) in paragraph at lines 25954--25957 []\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 25973--25975 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [400] [401] Underfull \hbox (badness 2142) in paragraph at lines 26114--26118 []\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 26164--26169 []\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 [402] [403] [404] [405] Underfull \hbox (badness 10000) in paragraph at lines 26452--26458 []\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 26452--26458 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 26452--26458 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 26465--26468 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 26491--26493 []\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 26526--26531 []\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 2529) in paragraph at lines 26532--26543 \T1/ptm/m/n/10 in-di-rectly [][]\T1/zi4/m/n/10 update.packages[][][]\T1/ptm/m/n /10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si- Underfull \hbox (badness 2512) in paragraph at lines 26532--26543 \T1/ptm/m/n/10 ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi4/m /n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use and [406] Underfull \hbox (badness 7203) in paragraph at lines 26544--26547 []\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 10000) in paragraph at lines 26568--26573 []\T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma -cOS build), Underfull \hbox (badness 2057) in paragraph at lines 26568--26573 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). [407] [408] [409] [410] [411] [412] [413] [414] Underfull \hbox (badness 10000) in paragraph at lines 27086--27089 []\T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 str2lang(s ) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of [415] Underfull \hbox (badness 7925) in paragraph at lines 27165--27169 []\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 vec-to r \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n /10 cor-re-sponds to Underfull \hbox (badness 1622) in paragraph at lines 27165--27169 [][]\T1/zi4/m/n/10 parse[][][](text = s,keep.source=FALSE)\T1/ptm/m/n/10 , whic h is al-ways of type ([][]\T1/zi4/m/n/10 typeof[][][]\T1/ptm/m/n/10 ) and [][]\ T1/zi4/m/n/10 class[][][] Underfull \hbox (badness 6125) in paragraph at lines 27170--27179 []\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 string \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2lang(s) \T1/ptm/m/n/10 cor -re-sponds to [][]\T1/zi4/m/n/10 parse[][][](text = [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] Underfull \hbox (badness 2726) in paragraph at lines 27891--27894 []\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 [427] [428] [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] Underfull \vbox (badness 3803) has occurred while \output is active [445] [446] [447] [448] [449] [450] [451] [452] Underfull \hbox (badness 1533) in paragraph at lines 29582--29585 []\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 [453] [454] [455] Underfull \hbox (badness 1163) in paragraph at lines 29745--29756 []\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 [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] [473] [474] [475] [476] [477] [478] [479] Underfull \hbox (badness 10000) in paragraph at lines 31291--31295 []\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 31291--31295 \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 31313--31315 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [480] [481] [482] [483] [484] [485] [486] [487] [488] Underfull \hbox (badness 1655) in paragraph at lines 31869--31871 []\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 [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] Underfull \hbox (badness 2261) in paragraph at lines 32988--32993 []\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 [506] Underfull \hbox (badness 10000) in paragraph at lines 33015--33021 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1484) in paragraph at lines 33015--33021 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal and hex-adec-i-mal rep-re-sen-ta-tions like [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] Underfull \hbox (badness 1072) in paragraph at lines 36157--36161 []\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 36162--36166 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 36190--36196 []\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 36190--36196 \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 36190--36196 \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 3009) in paragraph at lines 36202--36209 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 36202--36209 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 36202--36209 \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 36202--36209 \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 [555] [556] [557] [558] [559] [560] Underfull \hbox (badness 1142) in paragraph at lines 36556--36562 []\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 \T1/zi4/m/n/10 "%Y-%m-%d [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] Underfull \hbox (badness 1565) in paragraph at lines 37829--37831 []\T1/ptm/m/n/10 integer code used in \T1/zi4/m/n/10 quantile(*,type=quantile.t ype) \T1/ptm/m/n/10 for the de-fault [581] [582] [583] [584] [585] [586] [587] [588] [589] [590] Underfull \hbox (badness 4967) in paragraph at lines 38428--38433 []\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 [591] [592] Underfull \hbox (badness 1616) in paragraph at lines 38541--38546 \T1/zi4/m/n/10 system("id") \T1/ptm/m/n/10 is much more portable on Unix-alikes , pro-vided only the POSIX op-tions [593] [594] [595] [596] [597] [598] [599] [600] Underfull \hbox (badness 1472) in paragraph at lines 39067--39070 []\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 [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614] Underfull \hbox (badness 10000) in paragraph at lines 39981--39985 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/zi4/m/n/10 length(bin) > [615] [616] [617] [618] Underfull \hbox (badness 10000) in paragraph at lines 40232--40235 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [619] [620] [621] Underfull \hbox (badness 10000) in paragraph at lines 40416--40420 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [622] [623] [624] [625] [626] [627] [628] [629] [630] Underfull \hbox (badness 10000) in paragraph at lines 41029--41032 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[ ]zones / [631] [632] [633] [634] [635] [636] Underfull \vbox (badness 10000) has occurred while \output is active [637] [638] [639] [640] [641] [642] [643] [644] Underfull \hbox (badness 1990) in paragraph at lines 41933--41941 []\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 41933--41941 \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 [645] [646] [647] [648] [649] [650] [651] [652] Underfull \hbox (badness 1917) in paragraph at lines 42439--42446 []\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 [653] [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] Underfull \hbox (badness 3668) in paragraph at lines 43168--43170 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [664] [665] Underfull \hbox (badness 2401) in paragraph at lines 43296--43300 []\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 [666] [667] [668] Underfull \hbox (badness 2111) in paragraph at lines 43485--43490 \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 10000) in paragraph at lines 43506--43511 []\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 [669] [670] [671] [672] [673] [674] [675] [676] [677] Underfull \hbox (badness 5417) in paragraph at lines 44088--44092 []\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 [678] Underfull \hbox (badness 10000) in paragraph at lines 44149--44153 []\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 [679] [680]) (./compiler-pkg.tex Chapter 2. [681] [682] [683] [684]) (./datasets-pkg.tex Chapter 3. [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] Underfull \hbox (badness 1097) in paragraph at lines 1031--1035 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] Underfull \vbox (badness 1448) has occurred while \output is active [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] Overfull \vbox (19.74611pt too high) has occurred while \output is active [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] Underfull \vbox (badness 10000) has occurred while \output is active [753] [754] [755] [756] Underfull \vbox (badness 10000) has occurred while \output is active [757] [758] [759] [760] [761] [762] [763] [764] [765] [766]) (./grDevices-pkg.tex Chapter 4. [767] [768] [769] [770] [771] Underfull \hbox (badness 3158) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/zi4/m/n/10 c(mi,ma,n.)\T1/ptm /m/n/10 , with iden-ti-cal mean-ing to Underfull \hbox (badness 10000) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][]\T1/zi4/m/n/10 axisTicks[][][]() \T1/ptm/ m/n/10 just calls the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/ptm/m/n/1 0 in Underfull \hbox (badness 1852) in paragraph at lines 298--303 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 /src/main/plot.c\T1/ptm/m/n/10 ' which is also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t ion [772] [773] [774] [775] [776] [777] [778] [779] Underfull \hbox (badness 1424) in paragraph at lines 830--832 [][][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 (as in-te-ger or char-ac-ter) and \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 mean trans-par-ent, which can also be spec-i -fied as [780] [781] [782] [783] [784] Underfull \hbox (badness 5175) in paragraph at lines 1124--1126 []\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 [785] [786] [787] [788] Underfull \hbox (badness 1852) in paragraph at lines 1326--1329 []\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 [789] [790] [791] Underfull \hbox (badness 1490) in paragraph at lines 1532--1537 \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 [792] [793] [794] [795] [796] [797] Underfull \hbox (badness 1325) in paragraph at lines 1938--1948 \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 , [798] [799] Underfull \hbox (badness 10000) in paragraph at lines 2050--2052 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [800] [801] [802] Underfull \hbox (badness 6758) in paragraph at lines 2228--2231 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [803] [804] [805] [806] [807] [808] [809] [810] [811] [812] Underfull \hbox (badness 10000) in paragraph at lines 2832--2833 [813] [814] [815] [816] [817] [818] [819] [820] [821] Underfull \hbox (badness 10000) in paragraph at lines 3388--3393 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [822] [823] [824] [825] [826] Underfull \vbox (badness 10000) has occurred while \output is active [827] Underfull \hbox (badness 10000) in paragraph at lines 3789--3792 []\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 [828] [829] [830] [831] [832] [833] [834] [835] [836] [837] [838] Underfull \hbox (badness 10000) in paragraph at lines 4518--4523 [][][]$\T1/zi4/m/n/10 https : / / www . adobe . com / content / dam / acom / en / devnet / actionscript / articles / PLRM . pdf$[][] Underfull \hbox (badness 4181) in paragraph at lines 4518--4523 \T1/ptm/m/n/10 or PDF [][]$\T1/zi4/m/n/10 https : / / www . adobe . com / devne t / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in [839] Underfull \vbox (badness 10000) has occurred while \output is active [840] [841] Underfull \hbox (badness 1067) in paragraph at lines 4672--4679 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [842] [843] [844] [845] Underfull \hbox (badness 1377) in paragraph at lines 4975--4980 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [846] Underfull \hbox (badness 1418) in paragraph at lines 5051--5058 \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 1755) in paragraph at lines 5069--5071 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [847] [848] Underfull \hbox (badness 1377) in paragraph at lines 5180--5185 []\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 [849] Underfull \hbox (badness 7344) in paragraph at lines 5249--5251 []\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 [850] [851] Underfull \hbox (badness 2035) in paragraph at lines 5384--5393 []\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 5384--5393 \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 5384--5393 \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 , [852] Underfull \hbox (badness 10000) in paragraph at lines 5452--5459 []\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 5452--5459 \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 . [853] [854] [855] Underfull \hbox (badness 1546) in paragraph at lines 5594--5602 []\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 , [856] [857] [858] [859] [860] [861] [862] [863] Underfull \hbox (badness 10000) in paragraph at lines 6129--6132 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [864] [865] [866] [867] [868] [869] [870] [871] [872] [873] [874] [875] [876] Underfull \hbox (badness 1189) in paragraph at lines 6951--6953 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [877] Underfull \hbox (badness 10000) in paragraph at lines 7049--7051 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [878] [879] [880] [881] [882] Underfull \hbox (badness 3780) in paragraph at lines 7349--7355 []\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 , [883] [884] [885] Underfull \hbox (badness 2680) in paragraph at lines 7550--7552 []\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 [886] [887] [888]) (./graphics-pkg.tex Chapter 5. [889] [890] [891] [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] Underfull \hbox (badness 4634) in paragraph at lines 1351--1354 [][][]\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 , [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] Underfull \hbox (badness 1728) in paragraph at lines 2308--2310 []\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use \T1/zi4/m/n/10 "n " \T1/ptm/m/n/10 to sup-press and see also [927] [928] Underfull \hbox (badness 1009) in paragraph at lines 2399--2406 \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 [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] [947] [948] [949] [950] Underfull \vbox (badness 10000) has occurred while \output is active [951] [952] [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] Underfull \hbox (badness 3229) in paragraph at lines 4544--4549 []\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 [964] [965] [966] [967] [968] Underfull \hbox (badness 10000) in paragraph at lines 4901--4907 []\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 4901--4907 \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 [969] Underfull \hbox (badness 10000) in paragraph at lines 5032--5035 [970] Underfull \hbox (badness 10000) in paragraph at lines 5093--5095 [971 >/library/graphics/help/figures/ mai.pdf>] [972 >/library/graphics/hel p/figures/oma.pdf>] [973] Underfull \hbox (badness 10000) in paragraph at lines 5283--5285 []\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 [974] Underfull \vbox (badness 3803) has occurred while \output is active [975] [976] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6761--6762 [][] [997] [998 >/library/graphics/help/fi gures/pch.pdf>] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] Underfull \hbox (badness 2012) in paragraph at lines 7586--7589 []\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 poi nt [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] Underfull \hbox (badness 10000) in paragraph at lines 8846--8848 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8848--8850 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1032]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8928 \HeaderA{units}{Graphical Units}{units} [1033] [1034] [1035] [1036]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] Underfull \hbox (badness 2680) in paragraph at lines 483--486 []\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 [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] Underfull \hbox (badness 4279) in paragraph at lines 1064--1073 [][][]\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 , [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] Underfull \vbox (badness 10000) has occurred while \output is active [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] Underfull \hbox (badness 1067) in paragraph at lines 4486--4489 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1113] [1114] [1115] [1116] Underfull \hbox (badness 7256) in paragraph at lines 4731--4733 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \hbox (badness 1824) in paragraph at lines 6535--6538 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like \T1/zi4/m/n/10 depth [1148] [1149] [1150] [1151]) (./methods-pkg.tex [1152] Chapter 7. [1153] [1154] [1155] [1156] [1157] [1158] [1159] [1160] Underfull \vbox (badness 10000) has occurred while \output is active [1161] Underfull \vbox (badness 10000) has occurred while \output is active [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171] Underfull \hbox (badness 2237) in paragraph at lines 1385--1387 []\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 [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] Underfull \hbox (badness 2181) in paragraph at lines 1932--1939 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/zi4/m/n/10 is(x,"refClass") \T1/ptm/m/n/10 tests [1180] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\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 1981--1986 \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 [1181] [1182] [1183] Underfull \hbox (badness 2213) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/zi4/m/n/10 where = [1184] [1185] [1186] [1187] [1188] Underfull \hbox (badness 10000) in paragraph at lines 2574--2577 []\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 [1189] [1190] Underfull \hbox (badness 1132) in paragraph at lines 2714--2718 []\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 [1191] Underfull \hbox (badness 1033) in paragraph at lines 2746--2751 \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 [1192] [1193] [1194] [1195] [1196] [1197] [1198] Underfull \hbox (badness 1102) in paragraph at lines 3303--3305 []\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 [1199] [1200] [1201] [1202] [1203] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\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 [1204] Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1205] Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [] \T1/zi4/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude = "numeric",altitude [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] Underfull \hbox (badness 1769) in paragraph at lines 4472--4478 []\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 4472--4478 \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 [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] Underfull \vbox (badness 10000) has occurred while \output is active [1227] [1228] [1229] Underfull \hbox (badness 4036) in paragraph at lines 5437--5440 []\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 [1230] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1231] [1232] [1233] [1234] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] Underfull \hbox (badness 1675) in paragraph at lines 6451--6457 \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 [1243] [1244] [1245] [1246] Underfull \vbox (badness 10000) has occurred while \output is active [1247] [1248] [1249] [1250]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1251] [1252] [1253]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} [1254] Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1255] [1256] [1257] Underfull \hbox (badness 1286) in paragraph at lines 7484--7486 []\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 [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] Underfull \vbox (badness 10000) has occurred while \output is active [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] Underfull \hbox (badness 1137) in paragraph at lines 10011--10019 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/n/10 ne w("signature",functionDef,...)\T1/ptm/m/n/10 . The [1293] [1294] [1295] [1296] [1297] [1298] [1299] Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., [1300] [1301] [1302] [1303]) (./parallel-pkg.tex [1304] Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\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 [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] [1324] [1325] Underfull \hbox (badness 3386) in paragraph at lines 1365--1368 []\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 [1326] [1327] [1328]) (./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 [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344]) (./stats-pkg.tex Chapter 10. [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] Underfull \hbox (badness 1412) in paragraph at lines 875--877 []\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 [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] Underfull \hbox (badness 2503) in paragraph at lines 1356--1359 []\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 , [1367] [1368] [1369] Underfull \hbox (badness 10000) in paragraph at lines 1536--1540 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov","lm") \T1/ptm/m/n/1 0 or for mul-ti-ple re-sponses of class [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] Underfull \hbox (badness 2503) in paragraph at lines 3437--3440 []\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 , [1400] [1401] [1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] Underfull \hbox (badness 1127) in paragraph at lines 4351--4354 []\T1/ptm/m/n/10 standardized resid-u-als, \T1/zi4/m/n/10 (observed -expected) / sqrt(V)\T1/ptm/m/n/10 , where \T1/zi4/m/n/10 V \T1/ptm/m/n/10 is the [1415] [1416] [1417] [1418] [1419] Underfull \hbox (badness 3989) in paragraph at lines 4681--4688 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] Underfull \hbox (badness 2556) in paragraph at lines 5317--5320 []\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 5334--5336 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/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 [1430] [1431] [1432] [1433] [1434] [1435] [1436] Underfull \hbox (badness 2503) in paragraph at lines 5726--5730 []\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 , [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] Underfull \hbox (badness 7081) in paragraph at lines 6520--6523 []\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 6524--6526 []\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 [1450] [1451] [1452] [1453] [1454] Underfull \vbox (badness 3803) has occurred while \output is active [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] Underfull \hbox (badness 10000) in paragraph at lines 7369--7372 []\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 [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] Underfull \vbox (badness 10000) has occurred while \output is active [1485] [1486] [1487] [1488] [1489] Underfull \hbox (badness 2626) in paragraph at lines 9048--9051 []\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 [1490] [1491] Underfull \hbox (badness 2503) in paragraph at lines 9155--9159 []\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 , [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] [1509] [1510] [1511] Underfull \hbox (badness 4518) in paragraph at lines 10469--10474 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1512] [1513] [1514] [1515] [1516] Underfull \hbox (badness 2142) in paragraph at lines 10830--10833 []\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 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10849--10852 []\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, [1517] Underfull \hbox (badness 1708) in paragraph at lines 10911--10915 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1518] [1519] [1520] [1521] [1522] [1523] Underfull \hbox (badness 1694) in paragraph at lines 11307--11310 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531]pdfTeX warning (ext4): d estination with the same identifier (name{Rfn.hat}) has been already used, dupl icate ignored \relax l.11791 \aliasA{hat}{influence.measures}{hat} [1532] [1533] Underfull \hbox (badness 1484) in paragraph at lines 11926--11928 []\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 [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] Underfull \hbox (badness 10000) in paragraph at lines 12519--12521 []\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 \T1/zi4/m/n/10 SSinit = [1544] [1545] [1546] [1547] [1548] [1549] Underfull \hbox (badness 2894) in paragraph at lines 12855--12859 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] Underfull \hbox (badness 4518) in paragraph at lines 13605--13610 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] Underfull \hbox (badness 4518) in paragraph at lines 14257--14262 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1572] [1573] Underfull \hbox (badness 8151) in paragraph at lines 14395--14399 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = "interp olate",statistics = Underfull \hbox (badness 1199) in paragraph at lines 14402--14404 []\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 [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] Underfull \hbox (badness 2503) in paragraph at lines 15473--15477 []\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 , [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] Underfull \hbox (badness 4621) in paragraph at lines 15985--15991 []\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 [1600] [1601] [1602] [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] [1623] [1624] [1625] [1626] [1627] Underfull \vbox (badness 10000) has occurred while \output is active [1628] Underfull \vbox (badness 10000) has occurred while \output is active [1629] [1630] [1631] [1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] Underfull \hbox (badness 1377) in paragraph at lines 18588--18593 []\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 18593--18596 []\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 [1642] Underfull \hbox (badness 2343) in paragraph at lines 18606--18610 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 3471) in paragraph at lines 18606--18610 \T1/ptm/m/n/10 the value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + re ltol) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18614--18618 []\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 [1643] [1644] [1645] Overfull \hbox (15.73795pt too wide) in paragraph at lines 18839--18839 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 18842--18842 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] Underfull \vbox (badness 10000) has occurred while \output is active [1646] [1647] [1648] [1649] [1650] [1651] [1652] Underfull \hbox (badness 1337) in paragraph at lines 19264--19267 []\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 [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] Underfull \hbox (badness 3049) in paragraph at lines 19760--19764 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1662] [1663] [1664] [1665] Underfull \hbox (badness 1194) in paragraph at lines 20018--20021 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1666] [1667] [1668] [1669] [1670] [1671] [1672] Underfull \hbox (badness 2503) in paragraph at lines 20397--20400 []\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 , Underfull \hbox (badness 3919) in paragraph at lines 20424--20426 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or \T1/zi4/m/n/10 "Comparison of Poisson [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] [1688] [1689] [1690] Underfull \hbox (badness 10000) in paragraph at lines 21501--21507 []\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 , [1691] [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] Underfull \hbox (badness 1337) in paragraph at lines 22855--22861 []\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 [1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] Overfull \hbox (27.74408pt too wide) in paragraph at lines 23420--23420 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1722] [1723] [1724] [1725] [1726] Underfull \hbox (badness 10000) in paragraph at lines 23671--23674 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 4205) in paragraph at lines 23671--23674 \T1/zi4/m/n/10 cutree(hclust.obj,k = k)\T1/ptm/m/n/10 , can be spec-i-fied for ef-fi-ciency if al-ready [1727] [1728] [1729] [1730] [1731] [1732] [1733] [1734] [1735] Underfull \hbox (badness 1824) in paragraph at lines 24257--24263 []\T1/ptm/m/n/10 Here, all the NAs in \T1/zi4/m/n/10 x \T1/ptm/m/n/10 are first re-placed by al-ter- Underfull \hbox (badness 1033) in paragraph at lines 24257--24263 \T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/ m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where [1736] Underfull \hbox (badness 10000) in paragraph at lines 24278--24281 []\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 \T1/zi4/m/n/10 y[j] = Underfull \hbox (badness 3690) in paragraph at lines 24347--24351 [][][]\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 [1737] Underfull \vbox (badness 3803) has occurred while \output is active [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] Underfull \hbox (badness 2165) in paragraph at lines 24856--24861 []\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm /m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1 0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [1746] [1747] [1748] [1749] Underfull \hbox (badness 1867) in paragraph at lines 25061--25063 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 25074--25078 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u se.fallback) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 PP [1750] [1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] Underfull \vbox (badness 3803) has occurred while \output is active [1761] [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] [1771] [1772] [1773] Underfull \vbox (badness 10000) has occurred while \output is active [1774] Underfull \hbox (badness 3514) in paragraph at lines 26634--26639 []\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 [1775] [1776] [1777] [1778] Overfull \hbox (2.23795pt too wide) in paragraph at lines 26868--26868 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1779] Underfull \hbox (badness 3514) in paragraph at lines 26904--26910 []\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 [1780] [1781] [1782] [1783] Underfull \hbox (badness 3514) in paragraph at lines 27118--27123 []\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 [1784] Underfull \hbox (badness 3514) in paragraph at lines 27205--27210 []\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 [1785] Underfull \hbox (badness 3514) in paragraph at lines 27270--27275 []\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 [1786] [1787] Underfull \hbox (badness 3514) in paragraph at lines 27364--27369 []\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 [1788] [1789] Underfull \hbox (badness 6691) in paragraph at lines 27456--27461 []\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 [1790] [1791] [1792] [1793] [1794] [1795] [1796] [1797] Underfull \hbox (badness 4024) in paragraph at lines 27984--27987 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion , which [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] Underfull \hbox (badness 5431) in paragraph at lines 28590--28592 []\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 [1808] [1809] [1810] [1811] Underfull \hbox (badness 5431) in paragraph at lines 28800--28803 []\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 [1812] [1813] [1814] [1815] [1816] Underfull \hbox (badness 1337) in paragraph at lines 29114--29118 []\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 [1817] [1818] [1819] [1820] [1821] Underfull \hbox (badness 1616) in paragraph at lines 29416--29419 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1822] [1823] [1824] [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] [1835] [1836] [1837] [1838] [1839] [1840] Underfull \hbox (badness 3557) in paragraph at lines 30546--30550 []\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 \T1/zi4 /m/n/10 interval = [1841] [1842] [1843] Underfull \vbox (badness 10000) has occurred while \output is active [1844] [1845] [1846] Underfull \hbox (badness 1337) in paragraph at lines 30910--30914 []\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 [1847] [1848] [1849] [1850] [1851] [1852] [1853] [1854] [1855] Underfull \hbox (badness 1337) in paragraph at lines 31437--31441 []\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 [1856] [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865]) (./stats4-pkg.tex [1866] Chapter 11. [1867] [1868] [1869] [1870] [1871] [1872]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} [1873] [1874] [1875]) (./tcltk-pkg.tex [1876] Chapter 12. [1877] [1878] [1879] [1880] [1881] [1882] [1883] Underfull \vbox (badness 10000) has occurred while \output is active [1884] Underfull \vbox (badness 10000) has occurred while \output is active [1885] 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 [1886] [1887] [1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897]) (./tools-pkg.tex [1898] Chapter 13. [1899] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1900] 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 [1901] [1902] 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 [1903] [1904] 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 [1905] [1906] [1907] [1908] [1909] [1910] [1911] [1912] [1913] [1914] [1915] [1916] [1917] Underfull \hbox (badness 4441) in paragraph at lines 1139--1149 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- Underfull \hbox (badness 1014) in paragraph at lines 1163--1165 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1169--1171 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous [1918] Underfull \hbox (badness 10000) in paragraph at lines 1206--1209 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1206--1209 \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 , [1919] [1920] [1921] [1922] [1923] Underfull \hbox (badness 2293) in paragraph at lines 1558--1560 []\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with its func-tion-al-ity in-te-grated into that of [1924] [1925] [1926] Underfull \hbox (badness 7981) in paragraph at lines 1696--1701 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 1082) in paragraph at lines 1703--1705 []\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 [1927] [1928] [1929]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1930] [1931] [1932] [1933] [1934] [1935] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2202--2202 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1936] [1937] [1938] Underfull \hbox (badness 7981) in paragraph at lines 2371--2377 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1939] [1940] [1941] [1942] [1943] [1944] [1945] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2846. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2847. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2847. [1946] [1947] [1948] [1949] [1950] Underfull \hbox (badness 1424) in paragraph at lines 3128--3130 []\T1/zi4/m/it/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 [1951] [1952] [1953] [1954] [1955] [1956] [1957] [1958] [1959] [1960] [1961] Underfull \hbox (badness 10000) in paragraph at lines 3832--3834 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1962] [1963] Underfull \hbox (badness 10000) in paragraph at lines 3971--3974 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/it/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/it/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1964] [1965] Underfull \hbox (badness 1137) in paragraph at lines 4073--4075 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1966] [1967] [1968] [1969] [1970] Underfull \hbox (badness 1796) in paragraph at lines 4381--4386 []\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over \T 1/zi4/m/it/10 write_PACKAGES \T1/ptm/m/n/10 in the \T1/zi4/m/it/10 type == [1971] Underfull \hbox (badness 1838) in paragraph at lines 4455--4461 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/it/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/it/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4455--4461 \T1/ptm/m/n/10 `\T1/zi4/m/it/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 [1972] [1973] [1974] Underfull \hbox (badness 2197) in paragraph at lines 4671--4681 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/it/10 available.packages[][][]\T1/ptm/m/n/10 : [1975] Underfull \hbox (badness 1571) in paragraph at lines 4734--4738 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [1976] [1977] [1978]) (./utils-pkg.tex Chapter 14. [1979] 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/it/10 insertions\T1/ptm/m/n/10 ', [1980] [1981] [1982] [1983] [1984] Underfull \hbox (badness 10000) in paragraph at lines 376--381 \T1/zi4/m/it/10 c("vertical","horizontal","cascade","minimize","restore") \T1/p tm/m/n/10 with [1985] [1986] [1987] [1988] [1989] Underfull \hbox (badness 10000) in paragraph at lines 717--723 []\T1/ptm/m/n/10 Functions \T1/zi4/m/it/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/it/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 717--723 \T1/zi4/m/it/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/it/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1990] [1991] Underfull \hbox (badness 5847) in paragraph at lines 850--856 []\T1/ptm/m/n/10 Argument \T1/zi4/m/it/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 850--856 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/it/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1992] Underfull \hbox (badness 3861) in paragraph at lines 918--923 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/it/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/it/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/it/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1993] [1994] Underfull \hbox (badness 3323) in paragraph at lines 1089--1097 []\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/zi4/m/it/1 0 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1 /ptm/m/n/10 , in-di-cat- Underfull \hbox (badness 2961) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f or-mat- Underfull \hbox (badness 3919) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 3735) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/it/10 getOption[][][]("citation.bibtex.ma x",1) \T1/ptm/m/n/10 which is \T1/zi4/m/it/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by [1995] Underfull \hbox (badness 10000) in paragraph at lines 1101--1103 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1996] [1997] Underfull \vbox (badness 3803) has occurred while \output is active [1998] [1999] [2000] [2001] [2002] Underfull \hbox (badness 1371) in paragraph at lines 1606--1608 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/it/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/it/10 ccaddress \T1/ptm/m/n/10 to pass to [2003] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 1676. [2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] Underfull \hbox (badness 2057) in paragraph at lines 2215--2217 []\T1/ptm/m/n/10 None for \T1/zi4/m/it/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [2013] [2014] [2015] [2016] [2017] [2018]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.clipboard}) has been already used, duplicate ig nored \relax l.2566 ... the Clipboard in MS Windows}{clipboard} [2019] [2020] Underfull \hbox (badness 1748) in paragraph at lines 2733--2736 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/it/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/it/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/it/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [2021] [2022] [2023] [2024] [2025] [2026] [2027] Underfull \hbox (badness 5388) in paragraph at lines 3142--3146 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/it/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/it/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/it/10 .TXT\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/it/10 read.table[][][](...,header = Underfull \hbox (badness 2285) in paragraph at lines 3147--3150 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/it/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/it/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/it/10 read.table[] [][](...,header = TRUE,sep = [2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] Underfull \hbox (badness 1430) in paragraph at lines 3906--3914 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/it/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [2039] Underfull \hbox (badness 1231) in paragraph at lines 3983--3995 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [2040] [2041] Underfull \hbox (badness 10000) in paragraph at lines 4141--4143 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/it/10 dow nload.file[][][] \T1/ptm/m/n/10 and [2042] [2043] [2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.4839 ...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.4839 ...mat Unordered and Ordered Lists}{format} [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] Underfull \hbox (badness 1622) in paragraph at lines 5358--5362 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 5990. Underfull \hbox (badness 1371) in paragraph at lines 5994--5996 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/it/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/it/10 ccaddress \T1/ptm/m/n/10 to pass to [2072] Underfull \hbox (badness 1502) in paragraph at lines 6083--6088 []\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 6083--6088 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2073] [2074] [2075] Underfull \hbox (badness 10000) in paragraph at lines 6256--6265 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2076] Underfull \hbox (badness 2150) in paragraph at lines 6320--6323 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2077] [2078] Underfull \hbox (badness 3118) in paragraph at lines 6458--6460 []\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 [2079] [2080] [2081] Underfull \hbox (badness 1325) in paragraph at lines 6630--6634 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/it/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able Underfull \hbox (badness 4726) in paragraph at lines 6642--6648 \T1/ptm/m/n/10 used if \T1/zi4/m/it/10 repos = NULL\T1/ptm/m/n/10 . Can also be a char-ac-ter vec-tor, a sub-set of [2082] Underfull \hbox (badness 10000) in paragraph at lines 6714--6717 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be Underfull \hbox (badness 10000) in paragraph at lines 6714--6717 \T1/ptm/m/n/10 passed to \T1/zi4/m/it/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou rce pack-age in-stall. E.g., [2083] Underfull \hbox (badness 3219) in paragraph at lines 6790--6797 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/it/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6790--6797 \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 6790--6797 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1596) in paragraph at lines 6790--6797 [][]\T1/zi4/m/it/10 getOption[][][]("install.packages.compile.from.source")\T1/ ptm/m/n/10 . \T1/zi4/m/it/10 type = "both" \T1/ptm/m/n/10 will be silently Underfull \hbox (badness 2932) in paragraph at lines 6798--6801 []\T1/ptm/m/n/10 Using pack-ages with \T1/zi4/m/it/10 type = "source" \T1/ptm/m /n/10 al-ways works pro-vided the pack-age con-tains no [2084] Underfull \hbox (badness 10000) in paragraph at lines 6934--6939 [][][]\T1/zi4/m/it/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [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] Underfull \hbox (badness 10000) in paragraph at lines 8434--8436 []\T1/ptm/m/n/10 for \T1/zi4/m/it/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi 4/m/it/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 2310) in paragraph at lines 8456--8461 []\T1/ptm/m/n/10 If a `\T1/zi4/m/it/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2110] [2111] [2112] [2113] [2114] [2115] [2116] [2117] Underfull \hbox (badness 1248) in paragraph at lines 8980--8984 []\T1/zi4/m/it/10 R CMD build \T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/m/ n/10 source tar-balls. The name(s) of the pack-ages are taken from the [2118] Underfull \hbox (badness 1789) in paragraph at lines 9058--9060 []\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 [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131] Underfull \hbox (badness 1097) in paragraph at lines 9895--9898 []\T1/ptm/m/n/10 The name \T1/zi4/m/it/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2132] [2133] Underfull \hbox (badness 3000) in paragraph at lines 10031--10036 [][][]\T1/zi4/m/it/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/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/it/10 read.t able[][][]\T1/ptm/m/n/10 ; [2134] [2135] [2136] [2137] [2138] [2139] [2140] [2141] [2142] Underfull \hbox (badness 2134) in paragraph at lines 10614--10619 [][][]\T1/zi4/m/it/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/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/it/10 write. table[][][]\T1/ptm/m/n/10 ; Underfull \hbox (badness 10000) in paragraph at lines 10670--10675 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for Underfull \hbox (badness 10000) in paragraph at lines 10670--10675 \T1/zi4/m/it/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/zi4/m/it/10 HKEY_CLASSES _ROOT\T1/ptm/m/n/10 . \T1/zi4/m/it/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] Underfull \hbox (badness 2469) in paragraph at lines 11163--11167 []\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 11163--11167 [][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2152] [2153] [2154] [2155] [2156] Underfull \hbox (badness 4060) in paragraph at lines 11494--11497 []\T1/ptm/m/n/10 If `\T1/zi4/m/it/10 --default-packages\T1/ptm/m/n/10 ' is not used, then \T1/zi4/m/it/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var i-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 11517--11517 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [2157] [2158] [2159] [2160] Underfull \hbox (badness 2150) in paragraph at lines 11756--11758 [][][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/it/10 https : / / www . gnu . org / software / emac s / manual / [2161] [2162] [2163] [2164] Underfull \hbox (badness 10000) in paragraph at lines 11975--11979 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/it/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12006--12012 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2165] [2166] Underfull \hbox (badness 1009) in paragraph at lines 12200--12212 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. 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Transcript written on refman.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-admin.texi @setfilename R-admin.info This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-admin.t2d/pdf/xtr/R-ad min.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2019-09-20.22]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-admin.vr (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-admin.cp Writing index file R-admin.en [1] Chapter 2 [2] Cross reference values unknown; you must run TeX again. [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15] [16] [17] [18] [19] [20] [21] Chapter 4 [22] [23] Underfull \hbox (badness 10000) in paragraph at lines 1963--1975 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [24] Chapter 5 [25] Chapter 6 [26] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2113--2113 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [27] [28] Underfull \hbox (badness 6842) in paragraph at lines 2307--2318 []@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age s. No ad-di- [29] [30] [31] [32] [33] [34] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2783--2783 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text tt --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] [35] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2803--2803 []@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 2804--2804 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [36] [37] [38] Chapter 8 [39] Chapter 9 [40] [41] [42] [43] Appendix A [44] [45] Overfull \hbox (49.43388pt too wide) in paragraph at lines 3437--3437 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [46] [47] [48] [49] Overfull \hbox (14.94176pt too wide) in paragraph at lines 3708--3708 []@texttt JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.212.b04-0.fc30.x86_6 4/jre[] [50] [51] [52] [53] [54] [55] [56] Appendix B [57] [58] [59] [60] [61] [62] Appendix C [63] [64] [65] [66] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4981--4981 []@texttt -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSER TIONS[] [67] [68] Overfull \hbox (36.62297pt too wide) in paragraph at lines 5171--5171 []@texttt curl -OL https://mac.r-project.org/libs/pcre-8.40-darwin.15-x86_64.t ar.gz[] Overfull \hbox (30.87428pt too wide) in paragraph at lines 5173--5173 []@texttt curl -OL https://mac.r-project.org/libs/xz-5.2.3-darwin.15-x86_64.ta r.gz[] Underfull \hbox (badness 6995) in paragraph at lines 5180--5183 []@textrm GNU @texttt readline[] @textrm from [][]@texttt https:// mac. R-pr oject. org/ libs[][][]@textrm , or con-fig-ure with [69] Overfull \hbox (128.60197pt too wide) in paragraph at lines 5216--5216 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 5248--5248 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig[] Overfull \hbox (43.51776pt too wide) in paragraph at lines 5265--5266 [][][]@smallrm See [][]@smalltt https:// developer. apple. com// documentat ion/ xcode/ notarizing_macos_software_before_distribution[][][]@smallrm .| [70] Overfull \hbox (78.17732pt too wide) in paragraph at lines 5317--5317 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] Overfull \hbox (135.6642pt too wide) in paragraph at lines 5326--5326 []@texttt CC="/usr/local/clang7/bin/clang -isysroot /Library/Developer/Command LineTools/SDKs/MacOSX.sdk"[] Overfull \hbox (152.91026pt too wide) in paragraph at lines 5327--5327 []@texttt CXX="/usr/local/clang7/bin/clang++ -isysroot /Library/Developer/Comm andLineTools/SDKs/MacOSX.sdk"[] [71] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5371--5371 []@texttt --enable-memory-profiling --enable-R-framework --x-libraries=/opt/X1 1/lib[] [72] Underfull \hbox (badness 10000) in paragraph at lines 5474--5479 []@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled , run [73] Overfull \hbox (20.69044pt too wide) in paragraph at lines 5498--5498 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_191.jdk/Content s/Home[] [74] [75] Overfull \hbox (32.18782pt too wide) in paragraph at lines 5666--5666 []@texttt R_LD_LIBRARY_PATH="/opt/developerstudio12.6/lib:/usr/local/lib:/opt/ csw/lib"[] [76] Underfull \hbox (badness 10000) in paragraph at lines 5755--5761 @texttt LDFLAGS=-L/usr/local/lib/amd64[] @textrm or @texttt LDFLAGS=-L/usr/loca l/lib/sparcv9[] @textrm as Overfull \hbox (141.41289pt too wide) in paragraph at lines 5763--5763 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc onfig:/usr/lib/64/pkgconfig[] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5770--5770 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s olaris"[] [77] Underfull \hbox (badness 10000) in paragraph at lines 5820--5824 []@textrm Note that paths such as @texttt /opt/csw/lib[]@textrm , @texttt /usr/ local/lib/amd64[] @textrm and [78] Appendix D [79] [80] [81] (Function and variable index) [82] No file R-admin.vrs. (Concept index) [83] No file R-admin.cps. (Environment variable index) [84] No file R-admin.ens. [85] ) (see the transcript file for additional information) Output written on R-admin.pdf (88 pages, 482957 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-admin.t2d/pdf/xtr/R-ad min.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2019-09-20.22]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-admin.vr (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-admin.toc [-1] [-2]) [-3] [-4] (/<>/doc/manual/R-admin.toc) (/<>/doc/manual/R-admin.toc) Chapter 1 (/<>/doc/manual/R-admin.aux) Writing index file R-admin.cp Writing index file R-admin.en [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15] [16] [17] [18] [19] [20] [21] Chapter 4 [22] [23] Underfull \hbox (badness 10000) in paragraph at lines 1963--1975 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [24] Chapter 5 [25] Chapter 6 [26] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2113--2113 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [27] [28] Underfull \hbox (badness 6842) in paragraph at lines 2307--2318 []@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age s. No ad-di- [29] [30] [31] [32] [33] [34] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2783--2783 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text tt --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] [35] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2803--2803 []@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 2804--2804 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [36] [37] [38] Chapter 8 [39] Chapter 9 [40] [41] [42] [43] Appendix A [44] [45] Overfull \hbox (49.43388pt too wide) in paragraph at lines 3437--3437 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [46] [47] [48] [49] Overfull \hbox (14.94176pt too wide) in paragraph at lines 3708--3708 []@texttt JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.212.b04-0.fc30.x86_6 4/jre[] [50] [51] [52] [53] [54] [55] [56] Appendix B [57] [58] [59] [60] [61] [62] Appendix C [63] [64] [65] [66] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4981--4981 []@texttt -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSER TIONS[] [67] [68] Overfull \hbox (36.62297pt too wide) in paragraph at lines 5171--5171 []@texttt curl -OL https://mac.r-project.org/libs/pcre-8.40-darwin.15-x86_64.t ar.gz[] Overfull \hbox (30.87428pt too wide) in paragraph at lines 5173--5173 []@texttt curl -OL https://mac.r-project.org/libs/xz-5.2.3-darwin.15-x86_64.ta r.gz[] Underfull \hbox (badness 6995) in paragraph at lines 5180--5183 []@textrm GNU @texttt readline[] @textrm from [][]@texttt https:// mac. R-pr oject. org/ libs[][][]@textrm , or con-fig-ure with [69] Overfull \hbox (128.60197pt too wide) in paragraph at lines 5216--5216 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 5248--5248 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig[] Overfull \hbox (43.51776pt too wide) in paragraph at lines 5265--5266 [][][]@smallrm See [][]@smalltt https:// developer. apple. com// documentat ion/ xcode/ notarizing_macos_software_before_distribution[][][]@smallrm .| [70] Overfull \hbox (78.17732pt too wide) in paragraph at lines 5317--5317 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] Overfull \hbox (135.6642pt too wide) in paragraph at lines 5326--5326 []@texttt CC="/usr/local/clang7/bin/clang -isysroot /Library/Developer/Command LineTools/SDKs/MacOSX.sdk"[] Overfull \hbox (152.91026pt too wide) in paragraph at lines 5327--5327 []@texttt CXX="/usr/local/clang7/bin/clang++ -isysroot /Library/Developer/Comm andLineTools/SDKs/MacOSX.sdk"[] [71] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5371--5371 []@texttt --enable-memory-profiling --enable-R-framework --x-libraries=/opt/X1 1/lib[] [72] Underfull \hbox (badness 10000) in paragraph at lines 5474--5479 []@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled , run [73] Overfull \hbox (20.69044pt too wide) in paragraph at lines 5498--5498 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_191.jdk/Content s/Home[] [74] [75] Overfull \hbox (32.18782pt too wide) in paragraph at lines 5666--5666 []@texttt R_LD_LIBRARY_PATH="/opt/developerstudio12.6/lib:/usr/local/lib:/opt/ csw/lib"[] [76] Underfull \hbox (badness 10000) in paragraph at lines 5755--5761 @texttt LDFLAGS=-L/usr/local/lib/amd64[] @textrm or @texttt LDFLAGS=-L/usr/loca l/lib/sparcv9[] @textrm as Overfull \hbox (141.41289pt too wide) in paragraph at lines 5763--5763 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc onfig:/usr/lib/64/pkgconfig[] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5770--5770 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s olaris"[] [77] Underfull \hbox (badness 10000) in paragraph at lines 5820--5824 []@textrm Note that paths such as @texttt /opt/csw/lib[]@textrm , @texttt /usr/ local/lib/amd64[] @textrm and [78] Appendix D [79] [80] [81] (Function and variable index) [82] (/<>/doc/manual/R-admin.vrs) (Concept index) [83] (/<>/doc/manual/R-admin.cps) (Environment variable index) [84] (/<>/doc/manual/R-admin.ens) [85] ) (see the transcript file for additional information) Output written on R-admin.pdf (91 pages, 529015 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-admin.t2d/pdf/xtr/R-ad min.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2019-09-20.22]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-admin.vr (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-admin.toc [-1] [-2]) [-3] [-4] (/<>/doc/manual/R-admin.toc) (/<>/doc/manual/R-admin.toc) Chapter 1 (/<>/doc/manual/R-admin.aux) Writing index file R-admin.cp Writing index file R-admin.en [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15] [16] [17] [18] [19] [20] [21] Chapter 4 [22] [23] Underfull \hbox (badness 10000) in paragraph at lines 1963--1975 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [24] Chapter 5 [25] Chapter 6 [26] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2113--2113 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [27] [28] Underfull \hbox (badness 6842) in paragraph at lines 2307--2318 []@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age s. No ad-di- [29] [30] [31] [32] [33] [34] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2783--2783 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text tt --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] [35] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2803--2803 []@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 2804--2804 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [36] [37] [38] Chapter 8 [39] Chapter 9 [40] [41] [42] [43] Appendix A [44] [45] Overfull \hbox (49.43388pt too wide) in paragraph at lines 3437--3437 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [46] [47] [48] [49] Overfull \hbox (14.94176pt too wide) in paragraph at lines 3708--3708 []@texttt JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.212.b04-0.fc30.x86_6 4/jre[] [50] [51] [52] [53] [54] [55] [56] Appendix B [57] [58] [59] [60] [61] [62] Appendix C [63] [64] [65] [66] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4981--4981 []@texttt -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSER TIONS[] [67] [68] Overfull \hbox (36.62297pt too wide) in paragraph at lines 5171--5171 []@texttt curl -OL https://mac.r-project.org/libs/pcre-8.40-darwin.15-x86_64.t ar.gz[] Overfull \hbox (30.87428pt too wide) in paragraph at lines 5173--5173 []@texttt curl -OL https://mac.r-project.org/libs/xz-5.2.3-darwin.15-x86_64.ta r.gz[] Underfull \hbox (badness 6995) in paragraph at lines 5180--5183 []@textrm GNU @texttt readline[] @textrm from [][]@texttt https:// mac. R-pr oject. org/ libs[][][]@textrm , or con-fig-ure with [69] Overfull \hbox (128.60197pt too wide) in paragraph at lines 5216--5216 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 5248--5248 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig[] Overfull \hbox (43.51776pt too wide) in paragraph at lines 5265--5266 [][][]@smallrm See [][]@smalltt https:// developer. apple. com// documentat ion/ xcode/ notarizing_macos_software_before_distribution[][][]@smallrm .| [70] Overfull \hbox (78.17732pt too wide) in paragraph at lines 5317--5317 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] Overfull \hbox (135.6642pt too wide) in paragraph at lines 5326--5326 []@texttt CC="/usr/local/clang7/bin/clang -isysroot /Library/Developer/Command LineTools/SDKs/MacOSX.sdk"[] Overfull \hbox (152.91026pt too wide) in paragraph at lines 5327--5327 []@texttt CXX="/usr/local/clang7/bin/clang++ -isysroot /Library/Developer/Comm andLineTools/SDKs/MacOSX.sdk"[] [71] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5371--5371 []@texttt --enable-memory-profiling --enable-R-framework --x-libraries=/opt/X1 1/lib[] [72] Underfull \hbox (badness 10000) in paragraph at lines 5474--5479 []@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled , run [73] Overfull \hbox (20.69044pt too wide) in paragraph at lines 5498--5498 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_191.jdk/Content s/Home[] [74] [75] Overfull \hbox (32.18782pt too wide) in paragraph at lines 5666--5666 []@texttt R_LD_LIBRARY_PATH="/opt/developerstudio12.6/lib:/usr/local/lib:/opt/ csw/lib"[] [76] Underfull \hbox (badness 10000) in paragraph at lines 5755--5761 @texttt LDFLAGS=-L/usr/local/lib/amd64[] @textrm or @texttt LDFLAGS=-L/usr/loca l/lib/sparcv9[] @textrm as Overfull \hbox (141.41289pt too wide) in paragraph at lines 5763--5763 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc onfig:/usr/lib/64/pkgconfig[] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5770--5770 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s olaris"[] [77] Underfull \hbox (badness 10000) in paragraph at lines 5820--5824 []@textrm Note that paths such as @texttt /opt/csw/lib[]@textrm , @texttt /usr/ local/lib/amd64[] @textrm and [78] Appendix D [79] [80] [81] (Function and variable index) [82] (/<>/doc/manual/R-admin.vrs) (Concept index) [83] (/<>/doc/manual/R-admin.cps) (Environment variable index) [84] (/<>/doc/manual/R-admin.ens) [85] ) (see the transcript file for additional information) Output written on R-admin.pdf (91 pages, 528971 bytes). Transcript written on R-admin.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-data.texi @setfilename R-data.info This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-data.t2d/pdf/xtr/R-dat a.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2019-09-20.22]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-data.vr (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Underfull \hbox (badness 10000) in paragraph at lines 87--87 [][]@textbf DBI 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 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 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 Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90 @texttt package=gdata[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 91--91 [][]@textbf ncdf4 Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91 @texttt package=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf rJava Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92 @texttt package=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf RJDBC Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RMySQL Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RNetCDF Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RODBC Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf ROracle Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL Overfull \hbox (50.49037pt too wide) in paragraph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 103--103 [][]@textbf WriteXLS Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf XLConnect Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] Writing index file R-data.cp Cross reference values unknown; you must run TeX again. [4] [5] [6] [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] Underfull \hbox (badness 10000) in paragraph at lines 1755--1761 []@textrm Packages [][]@textbf h5 @textrm (@texttt https:// CRAN. R-project. org/ package=h5[]@textrm )[][], Bio-con-duc-tor's @textbf rhdf5@textrm , Chapter 6 [25] Chapter 7 [26] [27] [28] [29] [30] Chapter 8 [31] Chapter 9 [32] Appendix A [33] (Function and variable index) [34] No file R-data.vrs. (Concept index) [35] No file R-data.cps. [36] ) (see the transcript file for additional information) Output written on R-data.pdf (39 pages, 271839 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-data.t2d/pdf/xtr/R-dat a.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2019-09-20.22]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-data.vr (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-data.toc [-1]) [-2] (/<>/doc/manual/R-data.toc) (/<>/doc/manual/R-data.toc) (Acknowledgements) (/<>/doc/manual/R-data.aux) Underfull \hbox (badness 10000) in paragraph at lines 87--87 [][]@textbf DBI 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 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 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 Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90 @texttt package=gdata[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 91--91 [][]@textbf ncdf4 Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91 @texttt package=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf rJava Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92 @texttt package=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf RJDBC Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RMySQL Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RNetCDF Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RODBC Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf ROracle Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL Overfull \hbox (50.49037pt too wide) in paragraph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 103--103 [][]@textbf WriteXLS Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf XLConnect Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] Writing index file R-data.cp [4] [5] [6] [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] Underfull \hbox (badness 10000) in paragraph at lines 1755--1761 []@textrm Packages [][]@textbf h5 @textrm (@texttt https:// CRAN. R-project. org/ package=h5[]@textrm )[][], Bio-con-duc-tor's @textbf rhdf5@textrm , Chapter 6 [25] Chapter 7 [26] [27] [28] [29] [30] Chapter 8 [31] Chapter 9 [32] Appendix A [33] (Function and variable index) [34] (/<>/doc/manual/R-data.vrs [35]) (Concept index) [36] (/<>/doc/manual/R-data.cps) [37] [38] ) (see the transcript file for additional information) Output written on R-data.pdf (42 pages, 311813 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-data.t2d/pdf/xtr/R-dat a.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2019-09-20.22]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-data.vr (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-data.toc [-1]) [-2] (/<>/doc/manual/R-data.toc) (/<>/doc/manual/R-data.toc) (Acknowledgements) (/<>/doc/manual/R-data.aux) Underfull \hbox (badness 10000) in paragraph at lines 87--87 [][]@textbf DBI 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 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 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 Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90 @texttt package=gdata[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 91--91 [][]@textbf ncdf4 Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91 @texttt package=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf rJava Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92 @texttt package=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf RJDBC Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RMySQL Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RNetCDF Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RODBC Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf ROracle Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL Overfull \hbox (50.49037pt too wide) in paragraph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 103--103 [][]@textbf WriteXLS Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf XLConnect Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] Writing index file R-data.cp [4] [5] [6] [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] Underfull \hbox (badness 10000) in paragraph at lines 1755--1761 []@textrm Packages [][]@textbf h5 @textrm (@texttt https:// CRAN. R-project. org/ package=h5[]@textrm )[][], Bio-con-duc-tor's @textbf rhdf5@textrm , Chapter 6 [25] Chapter 7 [26] [27] [28] [29] [30] Chapter 8 [31] Chapter 9 [32] Appendix A [33] (Function and variable index) [34] (/<>/doc/manual/R-data.vrs [35]) (Concept index) [36] (/<>/doc/manual/R-data.cps) [37] [38] ) (see the transcript file for additional information) Output written on R-data.pdf (42 pages, 311811 bytes). Transcript written on R-data.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-exts.texi @setfilename R-exts.info This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-exts.t2d/pdf/xtr/R-ext s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2019-09-20.22]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-exts.vr (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Chapter 1 [1] Writing index file R-exts.cp Cross reference values unknown; you must run TeX again. [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 493--496 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2002--2002 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [26] [27] [28] [29] [30] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2391--2391 []@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 2393--2393 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [31] [32] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2531--2531 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [33] [34] [35] Overfull \hbox (60.93126pt too wide) in paragraph at lines 2764--2764 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [36] Underfull \hbox (badness 7221) in paragraph at lines 2812--2818 [][][]@smallrm See [][]@smalltt https:// isocpp. org/ std/ standing-documen ts/ sd-6-sg10-feature-test-recommendations[][][] @smallrm or [37] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2906--2908 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] Overfull \hbox (53.86903pt too wide) in paragraph at lines 4795--4795 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 4797--4797 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (65.36641pt too wide) in paragraph at lines 4798--4798 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] [62] Overfull \hbox (76.86378pt too wide) in paragraph at lines 4813--4813 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [63] [64] [65] [66] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5128--5128 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [67] [68] [69] Overfull \hbox (19.3769pt too wide) in paragraph at lines 5325--5325 []@texttt abs acos atan bind calloc ceil div exp fabs floor fmod free log mall oc[] [70] Overfull \hbox (25.1256pt too wide) in paragraph at lines 5421--5421 []@texttt erf expm1 fmin fmax lgamma lround loglp round snprintf strcasecmp tr unc[] Overfull \hbox (53.86903pt too wide) in paragraph at lines 5452--5452 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [71] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5500--5500 []@texttt #if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__) )[] [72] [73] [74] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5765--5765 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [75] [76] [77] Chapter 2 [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] Underfull \hbox (badness 10000) in paragraph at lines 7023--7030 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [92] [93] [94] [95] [96] [97] Chapter 3 [98] [99] [100] [101] [102] [103] Overfull \hbox (20.69044pt too wide) in paragraph at lines 7945--7945 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [104] [105] [106] Chapter 4 [107] [108] [109] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8323--8323 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [110] Overfull \hbox (25.25755pt too wide) in paragraph at lines 8364--8364 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [111] Overfull \hbox (20.53261pt too wide) in paragraph at lines 8468--8468 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] [112] Overfull \hbox (38.96663pt too wide) in paragraph at lines 8498--8507 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [113] [114] [115] Overfull \hbox (44.18301pt too wide) in paragraph at lines 8776--8777 [][][]@smallrm see [][]@smalltt http:// llvm. org/ devmtg/ 2014-04/ PDFs/ LightningTalks/ EuroLLVM%202014%20--%20container%20overflow. [116] [117] Overfull \hbox (78.17732pt too wide) in paragraph at lines 8914--8914 []@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 8942--8944 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] [118] Overfull \hbox (32.18782pt too wide) in paragraph at lines 8956--8956 []@texttt signed-integer-overflow,unreachable,unsigned-integer-overflow,vla-bo und,vptr[] [119] Overfull \hbox (72.42863pt too wide) in paragraph at lines 9074--9074 []@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 9119--9119 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] [120] Overfull \hbox (14.94176pt too wide) in paragraph at lines 9122--9122 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [121] Overfull \hbox (26.43913pt too wide) in paragraph at lines 9201--9201 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [122] [123] Overfull \hbox (124.16682pt too wide) in paragraph at lines 9406--9406 []@texttt boot.f:61: warning: type of 'ddot' does not match original declarati on [-Wlto-type-mismatch][] [124] Overfull \hbox (147.16158pt too wide) in paragraph at lines 9423--9423 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla ration [-Wlto-type-mismatch][] Overfull \hbox (141.41289pt too wide) in paragraph at lines 9434--9434 []@texttt reg.f:78:33: warning: type of 'dqrdc' does not match original declar ation [-Wlto-type-mismatch][] Overfull \hbox (14.94176pt too wide) in paragraph at lines 9454--9454 [] @tex ttt 1[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 9463--9463 [] @tex ttt 1[] Overfull \hbox (43.6852pt too wide) in paragraph at lines 9464--9464 []@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to INTEGER(4)[] Chapter 5 [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] Overfull \hbox (30.87428pt too wide) in paragraph at lines 10241--10241 [] @texttt double *w, int *iper, double *span, double *al pha,[] Overfull \hbox (51.66371pt too wide) in paragraph at lines 10297--10297 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [136] [137] [138] [139] [140] [141] [142] [143] Overfull \hbox (37.93651pt too wide) in paragraph at lines 10876--10876 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11657--11657 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [154] Underfull \hbox (badness 10000) in paragraph at lines 11718--11720 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [155] [156] [157] [158] [159] [160] [161] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12245--12245 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [162] [163] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12368--12368 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12373--12373 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12428--12428 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [164] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12440--12440 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [165] Overfull \hbox (26.43913pt too wide) in paragraph at lines 12539--12539 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [166] [167] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12675--12675 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [168] Overfull \hbox (43.6852pt too wide) in paragraph at lines 12756--12756 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [169] Overfull \hbox (72.42863pt too wide) in paragraph at lines 12856--12856 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] Chapter 6 [170] [171] [172] [173] [174] [175] [176] [177] Overfull \hbox (20.69044pt too wide) in paragraph at lines 13549--13549 [] @texttt call cmsg(msg//c_null_char) ! need to concatenate a nul term inator[] [178] [179] [180] [181] [182] [183] [184] [185] Underfull \hbox (badness 10000) in paragraph at lines 14205--14209 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [186] Warning: unbalanced parentheses in @def... [187] [188] Overfull \hbox (26.43913pt too wide) in paragraph at lines 14418--14418 [] @texttt void (*clean)(void *data, Rboolean jump), void *cdata,[] [189] [190] [191] [192] [193] Chapter 7 [194] [195] Chapter 8 [196] [197] [198] Overfull \hbox (43.6852pt too wide) in paragraph at lines 15174--15174 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [199] Overfull \hbox (20.69044pt too wide) in paragraph at lines 15217--15217 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 15233--15233 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [200] [201] [202] [203] Underfull \hbox (badness 10000) in paragraph at lines 15476--15483 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [204] [205] [206] [207] [208] Underfull \hbox (badness 10000) in paragraph at lines 15859--15863 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [209] No file R-exts.vrs. (Concept index) [210] No file R-exts.cps. [211] ) (see the transcript file for additional information) Output written on R-exts.pdf (214 pages, 922080 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-exts.t2d/pdf/xtr/R-ext s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2019-09-20.22]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-exts.vr (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-exts.toc [-1] [-2] [-3] [-4]) [-5] (/<>/doc/manual/R-exts.toc) (/<>/doc/manual/R-exts.toc) (Acknowledgements) (/<>/doc/manual/R-exts.aux) Chapter 1 [1] Writing index file R-exts.cp [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 493--496 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2002--2002 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [26] [27] [28] [29] [30] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2391--2391 []@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 2393--2393 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [31] [32] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2531--2531 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [33] [34] [35] Overfull \hbox (60.93126pt too wide) in paragraph at lines 2764--2764 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [36] Underfull \hbox (badness 7221) in paragraph at lines 2812--2818 [][][]@smallrm See [][]@smalltt https:// isocpp. org/ std/ standing-documen ts/ sd-6-sg10-feature-test-recommendations[][][] @smallrm or [37] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2906--2908 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] Overfull \hbox (53.86903pt too wide) in paragraph at lines 4795--4795 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 4797--4797 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (65.36641pt too wide) in paragraph at lines 4798--4798 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] Overfull \hbox (76.86378pt too wide) in paragraph at lines 4813--4813 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [62] [63] [64] [65] [66] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5128--5128 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [67] [68] [69] Overfull \hbox (19.3769pt too wide) in paragraph at lines 5325--5325 []@texttt abs acos atan bind calloc ceil div exp fabs floor fmod free log mall oc[] [70] Overfull \hbox (25.1256pt too wide) in paragraph at lines 5421--5421 []@texttt erf expm1 fmin fmax lgamma lround loglp round snprintf strcasecmp tr unc[] Overfull \hbox (53.86903pt too wide) in paragraph at lines 5452--5452 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [71] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5500--5500 []@texttt #if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__) )[] [72] [73] [74] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5765--5765 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [75] [76] [77] Chapter 2 [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] Underfull \hbox (badness 10000) in paragraph at lines 7023--7030 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [92] [93] [94] [95] [96] [97] Chapter 3 [98] [99] [100] [101] [102] [103] Overfull \hbox (20.69044pt too wide) in paragraph at lines 7945--7945 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [104] [105] [106] Chapter 4 [107] [108] [109] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8323--8323 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [110] Overfull \hbox (25.25755pt too wide) in paragraph at lines 8364--8364 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [111] Overfull \hbox (20.53261pt too wide) in paragraph at lines 8468--8468 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] [112] Overfull \hbox (38.96663pt too wide) in paragraph at lines 8498--8507 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [113] [114] [115] Overfull \hbox (44.18301pt too wide) in paragraph at lines 8776--8777 [][][]@smallrm see [][]@smalltt http:// llvm. org/ devmtg/ 2014-04/ PDFs/ LightningTalks/ EuroLLVM%202014%20--%20container%20overflow. [116] [117] Overfull \hbox (78.17732pt too wide) in paragraph at lines 8914--8914 []@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 8942--8944 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] [118] Overfull \hbox (32.18782pt too wide) in paragraph at lines 8956--8956 []@texttt signed-integer-overflow,unreachable,unsigned-integer-overflow,vla-bo und,vptr[] [119] Overfull \hbox (72.42863pt too wide) in paragraph at lines 9074--9074 []@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 9119--9119 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] [120] Overfull \hbox (14.94176pt too wide) in paragraph at lines 9122--9122 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [121] Overfull \hbox (26.43913pt too wide) in paragraph at lines 9201--9201 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [122] [123] Overfull \hbox (124.16682pt too wide) in paragraph at lines 9406--9406 []@texttt boot.f:61: warning: type of 'ddot' does not match original declarati on [-Wlto-type-mismatch][] [124] Overfull \hbox (147.16158pt too wide) in paragraph at lines 9423--9423 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla ration [-Wlto-type-mismatch][] Overfull \hbox (141.41289pt too wide) in paragraph at lines 9434--9434 []@texttt reg.f:78:33: warning: type of 'dqrdc' does not match original declar ation [-Wlto-type-mismatch][] Overfull \hbox (14.94176pt too wide) in paragraph at lines 9454--9454 [] @tex ttt 1[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 9463--9463 [] @tex ttt 1[] Overfull \hbox (43.6852pt too wide) in paragraph at lines 9464--9464 []@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to INTEGER(4)[] Chapter 5 [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] Overfull \hbox (30.87428pt too wide) in paragraph at lines 10241--10241 [] @texttt double *w, int *iper, double *span, double *al pha,[] Overfull \hbox (51.66371pt too wide) in paragraph at lines 10297--10297 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [136] [137] [138] [139] [140] [141] [142] [143] Overfull \hbox (37.93651pt too wide) in paragraph at lines 10876--10876 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11657--11657 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [154] Underfull \hbox (badness 10000) in paragraph at lines 11718--11720 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [155] [156] [157] [158] [159] [160] [161] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12245--12245 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [162] [163] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12368--12368 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12373--12373 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12428--12428 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [164] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12440--12440 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [165] Overfull \hbox (26.43913pt too wide) in paragraph at lines 12539--12539 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [166] [167] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12675--12675 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [168] Overfull \hbox (43.6852pt too wide) in paragraph at lines 12756--12756 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [169] Overfull \hbox (72.42863pt too wide) in paragraph at lines 12856--12856 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] Chapter 6 [170] [171] [172] [173] [174] [175] [176] [177] Overfull \hbox (20.69044pt too wide) in paragraph at lines 13549--13549 [] @texttt call cmsg(msg//c_null_char) ! need to concatenate a nul term inator[] [178] [179] [180] [181] [182] [183] [184] [185] Underfull \hbox (badness 10000) in paragraph at lines 14205--14209 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [186] Warning: unbalanced parentheses in @def... [187] [188] Overfull \hbox (26.43913pt too wide) in paragraph at lines 14418--14418 [] @texttt void (*clean)(void *data, Rboolean jump), void *cdata,[] [189] [190] [191] [192] [193] Chapter 7 [194] [195] Chapter 8 [196] [197] [198] Overfull \hbox (43.6852pt too wide) in paragraph at lines 15174--15174 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [199] Overfull \hbox (20.69044pt too wide) in paragraph at lines 15217--15217 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 15233--15233 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [200] [201] [202] [203] Underfull \hbox (badness 10000) in paragraph at lines 15476--15483 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [204] [205] [206] [207] [208] Underfull \hbox (badness 10000) in paragraph at lines 15859--15863 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [209] (/<>/doc/manual/R-exts.vrs [210] [211] [212]) (Concept index) [213] (/<>/doc/manual/R-exts.cps [214]) [215] ) (see the transcript file for additional information) Output written on R-exts.pdf (222 pages, 986214 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-exts.t2d/pdf/xtr/R-ext s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2019-09-20.22]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-exts.vr (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-exts.toc [-1] [-2] [-3] [-4]) [-5] (/<>/doc/manual/R-exts.toc) (/<>/doc/manual/R-exts.toc) (Acknowledgements) (/<>/doc/manual/R-exts.aux) Chapter 1 [1] Writing index file R-exts.cp [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 493--496 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2002--2002 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [26] [27] [28] [29] [30] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2391--2391 []@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 2393--2393 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [31] [32] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2531--2531 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [33] [34] [35] Overfull \hbox (60.93126pt too wide) in paragraph at lines 2764--2764 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [36] Underfull \hbox (badness 7221) in paragraph at lines 2812--2818 [][][]@smallrm See [][]@smalltt https:// isocpp. org/ std/ standing-documen ts/ sd-6-sg10-feature-test-recommendations[][][] @smallrm or [37] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2906--2908 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] Overfull \hbox (53.86903pt too wide) in paragraph at lines 4795--4795 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 4797--4797 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (65.36641pt too wide) in paragraph at lines 4798--4798 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] Overfull \hbox (76.86378pt too wide) in paragraph at lines 4813--4813 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [62] [63] [64] [65] [66] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5128--5128 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [67] [68] [69] Overfull \hbox (19.3769pt too wide) in paragraph at lines 5325--5325 []@texttt abs acos atan bind calloc ceil div exp fabs floor fmod free log mall oc[] [70] Overfull \hbox (25.1256pt too wide) in paragraph at lines 5421--5421 []@texttt erf expm1 fmin fmax lgamma lround loglp round snprintf strcasecmp tr unc[] Overfull \hbox (53.86903pt too wide) in paragraph at lines 5452--5452 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [71] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5500--5500 []@texttt #if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__) )[] [72] [73] [74] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5765--5765 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [75] [76] [77] Chapter 2 [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] Underfull \hbox (badness 10000) in paragraph at lines 7023--7030 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [92] [93] [94] [95] [96] [97] Chapter 3 [98] [99] [100] [101] [102] [103] Overfull \hbox (20.69044pt too wide) in paragraph at lines 7945--7945 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [104] [105] [106] Chapter 4 [107] [108] [109] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8323--8323 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [110] Overfull \hbox (25.25755pt too wide) in paragraph at lines 8364--8364 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [111] Overfull \hbox (20.53261pt too wide) in paragraph at lines 8468--8468 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] [112] Overfull \hbox (38.96663pt too wide) in paragraph at lines 8498--8507 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [113] [114] [115] Overfull \hbox (44.18301pt too wide) in paragraph at lines 8776--8777 [][][]@smallrm see [][]@smalltt http:// llvm. org/ devmtg/ 2014-04/ PDFs/ LightningTalks/ EuroLLVM%202014%20--%20container%20overflow. [116] [117] Overfull \hbox (78.17732pt too wide) in paragraph at lines 8914--8914 []@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 8942--8944 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] [118] Overfull \hbox (32.18782pt too wide) in paragraph at lines 8956--8956 []@texttt signed-integer-overflow,unreachable,unsigned-integer-overflow,vla-bo und,vptr[] [119] Overfull \hbox (72.42863pt too wide) in paragraph at lines 9074--9074 []@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 9119--9119 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] [120] Overfull \hbox (14.94176pt too wide) in paragraph at lines 9122--9122 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [121] Overfull \hbox (26.43913pt too wide) in paragraph at lines 9201--9201 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [122] [123] Overfull \hbox (124.16682pt too wide) in paragraph at lines 9406--9406 []@texttt boot.f:61: warning: type of 'ddot' does not match original declarati on [-Wlto-type-mismatch][] [124] Overfull \hbox (147.16158pt too wide) in paragraph at lines 9423--9423 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla ration [-Wlto-type-mismatch][] Overfull \hbox (141.41289pt too wide) in paragraph at lines 9434--9434 []@texttt reg.f:78:33: warning: type of 'dqrdc' does not match original declar ation [-Wlto-type-mismatch][] Overfull \hbox (14.94176pt too wide) in paragraph at lines 9454--9454 [] @tex ttt 1[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 9463--9463 [] @tex ttt 1[] Overfull \hbox (43.6852pt too wide) in paragraph at lines 9464--9464 []@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to INTEGER(4)[] Chapter 5 [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] Overfull \hbox (30.87428pt too wide) in paragraph at lines 10241--10241 [] @texttt double *w, int *iper, double *span, double *al pha,[] Overfull \hbox (51.66371pt too wide) in paragraph at lines 10297--10297 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [136] [137] [138] [139] [140] [141] [142] [143] Overfull \hbox (37.93651pt too wide) in paragraph at lines 10876--10876 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11657--11657 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [154] Underfull \hbox (badness 10000) in paragraph at lines 11718--11720 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [155] [156] [157] [158] [159] [160] [161] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12245--12245 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [162] [163] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12368--12368 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12373--12373 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12428--12428 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [164] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12440--12440 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [165] Overfull \hbox (26.43913pt too wide) in paragraph at lines 12539--12539 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [166] [167] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12675--12675 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [168] Overfull \hbox (43.6852pt too wide) in paragraph at lines 12756--12756 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [169] Overfull \hbox (72.42863pt too wide) in paragraph at lines 12856--12856 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] Chapter 6 [170] [171] [172] [173] [174] [175] [176] [177] Overfull \hbox (20.69044pt too wide) in paragraph at lines 13549--13549 [] @texttt call cmsg(msg//c_null_char) ! need to concatenate a nul term inator[] [178] [179] [180] [181] [182] [183] [184] [185] Underfull \hbox (badness 10000) in paragraph at lines 14205--14209 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [186] Warning: unbalanced parentheses in @def... [187] [188] Overfull \hbox (26.43913pt too wide) in paragraph at lines 14418--14418 [] @texttt void (*clean)(void *data, Rboolean jump), void *cdata,[] [189] [190] [191] [192] [193] Chapter 7 [194] [195] Chapter 8 [196] [197] [198] Overfull \hbox (43.6852pt too wide) in paragraph at lines 15174--15174 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [199] Overfull \hbox (20.69044pt too wide) in paragraph at lines 15217--15217 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 15233--15233 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [200] [201] [202] [203] Underfull \hbox (badness 10000) in paragraph at lines 15476--15483 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [204] [205] [206] [207] [208] Underfull \hbox (badness 10000) in paragraph at lines 15859--15863 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [209] (/<>/doc/manual/R-exts.vrs [210] [211] [212]) (Concept index) [213] (/<>/doc/manual/R-exts.cps [214]) [215] ) (see the transcript file for additional information) Output written on R-exts.pdf (222 pages, 986185 bytes). Transcript written on R-exts.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-FAQ.texi @setfilename R-FAQ.info This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ. texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2019-09-20.22]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/var/lib/texmf/fonts/map/pdftex/up dmap/pdftex.map}] [-1] Chapter 1 Cross reference values unknown; you must run TeX again. [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] Writing index file R-FAQ.fn [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3271--3279 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [42] Chapter 8 [43] Chapter 9 [44] [45] Chapter 10 [46] [47] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (49 pages, 357795 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ. texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2019-09-20.22]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/var/lib/texmf/fonts/map/pdftex/up dmap/pdftex.map}] (/<>/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/<>/doc/manual/R-FAQ.toc) (/<>/doc/manual/R-FAQ.toc) Chapter 1 (/<>/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] Writing index file R-FAQ.fn [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3271--3279 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [42] Chapter 8 [43] Chapter 9 [44] [45] Chapter 10 [46] [47] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (51 pages, 374487 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ. texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2019-09-20.22]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/usr/share/texmf/tex/texinfo/txi-en.tex) [1{/var/lib/texmf/fonts/map/pdftex/up dmap/pdftex.map}] (/<>/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/<>/doc/manual/R-FAQ.toc) (/<>/doc/manual/R-FAQ.toc) Chapter 1 (/<>/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] Writing index file R-FAQ.fn [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3271--3279 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [42] Chapter 8 [43] Chapter 9 [44] [45] Chapter 10 [46] [47] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (51 pages, 374487 bytes). Transcript written on R-FAQ.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi @setfilename R-intro.info This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-intro.t2d/pdf/xtr/R-in tro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2019-09-20.22]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-intro.vr (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Preface) Cross reference values unknown; you must run TeX again. Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] [15] Chapter 4 [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Chapter 6 [28] [29] [30] [31] Chapter 7 [32] [33] [34] Chapter 8 [35] [36] [37] >/doc/manual /images/hist.pdf> >/doc/manual/images /ecdf.pdf> [38] >/doc/manual/images/Q Q.pdf> [39] >/doc/manual/images/ice.p df> [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Chapter 11 [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] Chapter 12 [67] [68] [69] [70] [71] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5741--5741 []@texttt > text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{ n-x})))[] [72] [73] [74] [75] [76] >/doc/manual /images/fig11.pdf> [77] >/doc/manual/ images/fig12.pdf> [78] [79] [80] [81] Chapter 13 [82] Underfull \hbox (badness 10000) in paragraph at lines 6447--6452 []@textrm Users con-nected to the In-ter-net can use the @texttt install.packag es()[] @textrm and [83] Chapter 14 [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and [86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95] [96] [97] [98] Appendix C [99] [100] Appendix D [101] No file R-intro.vrs. Appendix E [102] No file R-intro.cps. Appendix F [103] [104] ) (see the transcript file for additional information) Output written on R-intro.pdf (107 pages, 576742 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-intro.t2d/pdf/xtr/R-in tro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2019-09-20.22]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-intro.vr (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/<>/doc/manual/R-intro.toc) (/<>/doc/manual/R-intro.toc) (Preface) (/<>/doc/manual/R-intro.aux) Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] [15] Chapter 4 [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Chapter 6 [28] [29] [30] [31] Chapter 7 [32] [33] [34] Chapter 8 [35] [36] [37] >/doc/manual /images/hist.pdf> >/doc/manual/images /ecdf.pdf> [38] >/doc/manual/images/Q Q.pdf> [39] >/doc/manual/images/ice.p df> [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Chapter 11 [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] Chapter 12 [67] [68] [69] [70] [71] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5741--5741 []@texttt > text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{ n-x})))[] [72] [73] [74] [75] [76] >/doc/manual /images/fig11.pdf> [77] >/doc/manual/ images/fig12.pdf> [78] [79] [80] [81] Chapter 13 [82] Underfull \hbox (badness 10000) in paragraph at lines 6447--6452 []@textrm Users con-nected to the In-ter-net can use the @texttt install.packag es()[] @textrm and [83] Chapter 14 [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and [86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95] [96] [97] [98] Appendix C [99] [100] Appendix D [101] (/<>/doc/manual/R-intro.vrs [102] [103]) Appendix E [104] (/<>/doc/manual/R-intro.cps [105]) Appendix F [106] [107] ) (see the transcript file for additional information) Output written on R-intro.pdf (113 pages, 633226 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-intro.t2d/pdf/xtr/R-in tro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2019-09-20.22]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-intro.vr (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/<>/doc/manual/R-intro.toc) (/<>/doc/manual/R-intro.toc) (Preface) (/<>/doc/manual/R-intro.aux) Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] [15] Chapter 4 [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Chapter 6 [28] [29] [30] [31] Chapter 7 [32] [33] [34] Chapter 8 [35] [36] [37] >/doc/manual /images/hist.pdf> >/doc/manual/images /ecdf.pdf> [38] >/doc/manual/images/Q Q.pdf> [39] >/doc/manual/images/ice.p df> [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Chapter 11 [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] Chapter 12 [67] [68] [69] [70] [71] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5741--5741 []@texttt > text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{ n-x})))[] [72] [73] [74] [75] [76] >/doc/manual /images/fig11.pdf> [77] >/doc/manual/ images/fig12.pdf> [78] [79] [80] [81] Chapter 13 [82] Underfull \hbox (badness 10000) in paragraph at lines 6447--6452 []@textrm Users con-nected to the In-ter-net can use the @texttt install.packag es()[] @textrm and [83] Chapter 14 [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and [86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95] [96] [97] [98] Appendix C [99] [100] Appendix D [101] (/<>/doc/manual/R-intro.vrs [102] [103]) Appendix E [104] (/<>/doc/manual/R-intro.cps [105]) Appendix F [106] [107] ) (see the transcript file for additional information) Output written on R-intro.pdf (113 pages, 633335 bytes). Transcript written on R-intro.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-ints.texi @setfilename R-ints.info This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-ints.t2d/pdf/xtr/R-int s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2019-09-20.22]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-ints.vr (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] Overfull \hbox (49.43388pt too wide) in paragraph at lines 1455--1455 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (78.17732pt too wide) in paragraph at lines 1456--1456 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 1457--1457 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (158.65895pt too wide) in paragraph at lines 1458--1458 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [19] [20] [21] [22] [23] [24] Chapter 2 [25] Overfull \hbox (26.43913pt too wide) in paragraph at lines 1983--1983 [] @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 3631--3640 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [49] Chapter 8 [50] [51] [52] [53] [54] [55] Underfull \hbox (badness 10000) in paragraph at lines 4039--4047 []@textrm A string with comma-separated @textttsl name@texttt =@textttsl value [] @textrm pairs (with @textsl value[] @textrm a Underfull \hbox (badness 10000) in paragraph at lines 4039--4047 @textrm log-i-cal con-stant) giv-ing ad-di-tional ar-gu-ments for the [][]@tex tbf codetools Underfull \hbox (badness 10000) in paragraph at lines 4039--4047 @textrm (@texttt https:// CRAN. R-project. org/ package=codetools[]@textrm )[][] func-tions used Underfull \hbox (badness 10000) in paragraph at lines 4039--4047 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [56] [57] [58] [59] [60] Chapter 9 [61] [62] Chapter 10 [63] Chapter 11 [64] Chapter 12 [65] [66] (Function and variable index) [67] [68] No file R-ints.vrs. (Concept index) [69] No file R-ints.cps. [70] ) (see the transcript file for additional information) Output written on R-ints.pdf (73 pages, 402278 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-ints.t2d/pdf/xtr/R-int s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2019-09-20.22]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-ints.vr (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-ints.toc [-1] [-2]) [-3] (/<>/doc/manual/R-ints.toc) (/<>/doc/manual/R-ints.toc) Chapter 1 (/<>/doc/manual/R-ints.aux) Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] Overfull \hbox (49.43388pt too wide) in paragraph at lines 1455--1455 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (78.17732pt too wide) in paragraph at lines 1456--1456 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 1457--1457 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (158.65895pt too wide) in paragraph at lines 1458--1458 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [19] [20] [21] [22] [23] [24] Chapter 2 [25] Overfull \hbox (26.43913pt too wide) in paragraph at lines 1983--1983 [] @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 3631--3640 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [49] Chapter 8 [50] [51] [52] [53] [54] [55] Underfull \hbox (badness 10000) in paragraph at lines 4039--4047 []@textrm A string with comma-separated @textttsl name@texttt =@textttsl value [] @textrm pairs (with @textsl value[] @textrm a Underfull \hbox (badness 10000) in paragraph at lines 4039--4047 @textrm log-i-cal con-stant) giv-ing ad-di-tional ar-gu-ments for the [][]@tex tbf codetools Underfull \hbox (badness 10000) in paragraph at lines 4039--4047 @textrm (@texttt https:// CRAN. R-project. org/ package=codetools[]@textrm )[][] func-tions used Underfull \hbox (badness 10000) in paragraph at lines 4039--4047 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [56] [57] [58] [59] [60] Chapter 9 [61] [62] Chapter 10 [63] Chapter 11 [64] Chapter 12 [65] [66] (Function and variable index) [67] [68] (/<>/doc/manual/R-ints.vrs [69]) (Concept index) [70] (/<>/doc/manual/R-ints.cps) [71] ) (see the transcript file for additional information) Output written on R-ints.pdf (76 pages, 452849 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-ints.t2d/pdf/xtr/R-int s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2019-09-20.22]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-ints.vr (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-ints.toc [-1] [-2]) [-3] (/<>/doc/manual/R-ints.toc) (/<>/doc/manual/R-ints.toc) Chapter 1 (/<>/doc/manual/R-ints.aux) Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] Overfull \hbox (49.43388pt too wide) in paragraph at lines 1455--1455 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (78.17732pt too wide) in paragraph at lines 1456--1456 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 1457--1457 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (158.65895pt too wide) in paragraph at lines 1458--1458 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [19] [20] [21] [22] [23] [24] Chapter 2 [25] Overfull \hbox (26.43913pt too wide) in paragraph at lines 1983--1983 [] @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 3631--3640 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [49] Chapter 8 [50] [51] [52] [53] [54] [55] Underfull \hbox (badness 10000) in paragraph at lines 4039--4047 []@textrm A string with comma-separated @textttsl name@texttt =@textttsl value [] @textrm pairs (with @textsl value[] @textrm a Underfull \hbox (badness 10000) in paragraph at lines 4039--4047 @textrm log-i-cal con-stant) giv-ing ad-di-tional ar-gu-ments for the [][]@tex tbf codetools Underfull \hbox (badness 10000) in paragraph at lines 4039--4047 @textrm (@texttt https:// CRAN. R-project. org/ package=codetools[]@textrm )[][] func-tions used Underfull \hbox (badness 10000) in paragraph at lines 4039--4047 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [56] [57] [58] [59] [60] Chapter 9 [61] [62] Chapter 10 [63] Chapter 11 [64] Chapter 12 [65] [66] (Function and variable index) [67] [68] (/<>/doc/manual/R-ints.vrs [69]) (Concept index) [70] (/<>/doc/manual/R-ints.cps) [71] ) (see the transcript file for additional information) Output written on R-ints.pdf (76 pages, 452855 bytes). Transcript written on R-ints.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-lang.texi @setfilename R-lang.info This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-lang.t2d/pdf/xtr/R-lan g.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2019-09-20.22]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-lang.vr (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-lang.cp Chapter 2 [1] [2] Cross reference values unknown; you must run TeX again. Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [4] [5] [6] [7] [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] No file R-lang.vrs. (Concept Index) [60] No file R-lang.cps. Appendix A [61] [62] ) (see the transcript file for additional information) Output written on R-lang.pdf (65 pages, 330517 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-lang.t2d/pdf/xtr/R-lan g.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2019-09-20.22]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-lang.vr (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-lang.toc [-1] [-2]) [-3] (/<>/doc/manual/R-lang.toc) (/<>/doc/manual/R-lang.toc) Chapter 1 (/<>/doc/manual/R-lang.aux) Writing index file R-lang.cp Chapter 2 [1] [2] Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [4] [5] [6] [7] [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] (/<>/doc/manual/R-lang.vrs [60]) (Concept Index) [61] (/<>/doc/manual/R-lang.cps) [62] Appendix A [63] [64] ) (see the transcript file for additional information) Output written on R-lang.pdf (69 pages, 379570 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-lang.t2d/pdf/xtr/R-lan g.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2019-09-20.22]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/<>/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-lang.vr (/<>/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/<>/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-lang.toc [-1] [-2]) [-3] (/<>/doc/manual/R-lang.toc) (/<>/doc/manual/R-lang.toc) Chapter 1 (/<>/doc/manual/R-lang.aux) Writing index file R-lang.cp Chapter 2 [1] [2] Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [4] [5] [6] [7] [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] (/<>/doc/manual/R-lang.vrs [60]) (Concept Index) [61] (/<>/doc/manual/R-lang.cps) [62] Appendix A [63] [64] ) (see the transcript file for additional information) Output written on R-lang.pdf (69 pages, 379564 bytes). Transcript written on R-lang.log. make[1]: Leaving directory '/<>/doc/manual' /usr/bin/make -k pdf make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/doc' make[3]: Entering directory '/<>/doc/manual' PDF/LaTeX documentation: full reference index ... This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./fullrefman.tex LaTeX2e <2020-02-02> patch level 2 L3 programming layer <2020-02-14> (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2019/12/20 v1.4l Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (../../share/texmf/tex/latex/Rd.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe) (/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex))))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/generic/atbegshi/atbegshi.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 377. 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/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) [1] [2] Underfull \hbox (badness 6995) 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 . It Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1/pt m/m/n/10 if \T1/zi4/m/n/10 double.base Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth- er-wise, it is \T1/zi4/m/n/10 (double.base Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/zi4/m /n/10 1.110223e-16\T1/ptm/m/n/10 . As Underfull \hbox (badness 4995) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.neg.ulp.digits \T1/ptm/m/n/10 is bounded be-low by \T1/zi 4/m/n/10 -(double.digits + 3)\T1/ptm/m/n/10 , [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 297--301 []\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] [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 534--540 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/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 1178--1181 []\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] (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1966--1966 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] [34] [35] [36] [37] Underfull \hbox (badness 10000) in paragraph at lines 2402--2404 []\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci ently) by Underfull \hbox (badness 10000) in paragraph at lines 2405--2410 [][][]\T1/zi4/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le ngth re-sults, so at-tempt-ing to split via Underfull \hbox (badness 1102) in paragraph at lines 2405--2410 \T1/zi4/m/n/10 apply(x,MARGIN,identity) \T1/ptm/m/n/10 does not work (as it sim -ply gives \T1/zi4/m/n/10 x\T1/ptm/m/n/10 ). By chain-ing \T1/zi4/m/n/10 asplit [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] Underfull \hbox (badness 10000) in paragraph at lines 3784--3786 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [60] [61] [62] Overfull \hbox (6.42029pt too wide) in paragraph at lines 4025--4025 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 2521) in paragraph at lines 5046--5048 []\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 [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6202--6202 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [97] [98] [99] [100] [101] [102] Overfull \hbox (46.35893pt too wide) in paragraph at lines 6611--6613 []\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 : [103] [104] Underfull \hbox (badness 10000) in paragraph at lines 6759--6762 []\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 [105] [106] Underfull \hbox (badness 6063) in paragraph at lines 6941--6947 []\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- Underfull \hbox (badness 2343) in paragraph at lines 6941--6947 \T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files and web-pages gen-er- Underfull \hbox (badness 1708) in paragraph at lines 6941--6947 \T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it i s not rec-om-mended) when Underfull \hbox (badness 1831) in paragraph at lines 6941--6947 \T1/ptm/m/n/10 writ-ing it should be writ-ten ex-plic-itly, e.g. by \T1/zi4/m/n /10 writeChar("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or [107] Underfull \hbox (badness 3568) in paragraph at lines 7003--7010 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [108] [109] Underfull \vbox (badness 3803) has occurred while \output is active [110] Underfull \vbox (badness 10000) has occurred while \output is active [111] [112] Underfull \hbox (badness 1077) in paragraph at lines 7330--7336 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7330--7336 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [113] [114] [115] [116] [117] [118] Underfull \hbox (badness 2096) in paragraph at lines 7671--7675 \T1/zi4/m/n/10 status _ codes$[][] \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 . [119] [120] Underfull \hbox (badness 2351) in paragraph at lines 7789--7792 [][][]\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 , [121] [122] [123] [124] [125] Underfull \hbox (badness 4479) in paragraph at lines 8115--8125 [][][]\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), [126] [127] [128] [129] [130] [131] Underfull \hbox (badness 1629) in paragraph at lines 8562--8574 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 1609) in paragraph at lines 8562--8574 \T1/ptm/m/n/10 there is a prob-lem in the POSIX/C99 stan-dard with \T1/zi4/m/n/ 10 "1969-12-31 23:59:59 UTC"\T1/ptm/m/n/10 , which Underfull \hbox (badness 2426) in paragraph at lines 8562--8574 \T1/ptm/m/n/10 is \T1/zi4/m/n/10 -1 \T1/ptm/m/n/10 in cal-en-dar time and that value is on those OSes also used as an er-ror code. [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] Underfull \hbox (badness 1178) in paragraph at lines 9298--9302 []\T1/ptm/m/n/10 If true, [][]\T1/zi4/m/n/10 list[][][]\T1/ptm/m/n/10 s and ato mic vec-tors with non-[][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 names (see [][ ]\T1/zi4/m/n/10 names[][][]\T1/ptm/m/n/10 ) are de- [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] Underfull \hbox (badness 1735) in paragraph at lines 10446--10450 \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 . [161] [162] [163] [164] [165] [166] [167] Underfull \hbox (badness 6396) in paragraph at lines 10885--10893 []\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 1946) in paragraph at lines 10885--10893 \T1/zi4/m/n/10 duplicated \T1/ptm/m/n/10 and \T1/zi4/m/n/10 anyDuplicated\T1/pt m/m/n/10 , \T1/zi4/m/n/10 anyDuplicated(x,...) \T1/ptm/m/n/10 is a ``gen-er-al- ized'' short-cut for [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] Underfull \hbox (badness 4569) in paragraph at lines 12002--12006 []\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 12002--12006 \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 [184] Underfull \vbox (badness 10000) has occurred while \output is active [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] Underfull \hbox (badness 2253) in paragraph at lines 13665--13667 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [209] [210] Underfull \hbox (badness 1565) in paragraph at lines 13738--13742 [][][]\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 Underfull \hbox (badness 4927) in paragraph at lines 13782--13784 []\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 \T1/zi4 /m/n/10 fsep = [211] [212] Underfull \hbox (badness 3148) in paragraph at lines 13875--13880 [][][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[ ][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 help[][][]\T1/ptm/m/n/10 ; [][]\T1/zi4 /m/n/10 RShowDoc[][][] \T1/ptm/m/n/10 call \T1/zi4/m/n/10 file.show() \T1/ptm/m /n/10 for \T1/zi4/m/n/10 type = "text"\T1/ptm/m/n/10 . Con-sider [213] Underfull \hbox (badness 1466) in paragraph at lines 13922--13925 []\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 [214] Underfull \hbox (badness 10000) in paragraph at lines 14049--14053 [][][]\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 14060--14063 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [215] [216] [217] [218] [219] Underfull \hbox (badness 3965) in paragraph at lines 14352--14356 []\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, [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] Underfull \hbox (badness 4429) in paragraph at lines 15128--15131 []\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 [232] [233] Underfull \hbox (badness 10000) in paragraph at lines 15234--15236 []\T1/ptm/m/n/10 This works via \T1/zi4/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic h calls Underfull \hbox (badness 1215) in paragraph at lines 15234--15236 \T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times in this case, see Underfull \hbox (badness 10000) in paragraph at lines 15256--15261 []\T1/ptm/m/n/10 For num-bers, \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 calls \T 1/zi4/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls Underfull \hbox (badness 1558) in paragraph at lines 15256--15261 \T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero)\T1/ptm/m/n/10 . (\T1/ptm/m /it/10 ``when needed''\T1/ptm/m/n/10 : when \T1/zi4/m/n/10 zero.print \T1/ptm/m /n/10 is not Underfull \hbox (badness 10000) in paragraph at lines 15268--15272 []\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 Underfull \hbox (badness 2426) in paragraph at lines 15268--15272 \T1/zi4/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi ves \T1/zi4/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . If you want [234] Underfull \hbox (badness 2035) in paragraph at lines 15307--15311 []\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 within [235] Underfull \vbox (badness 10000) has occurred while \output is active [236] [237] [238] [239] [240] [241] [242] [243] Underfull \hbox (badness 2452) in paragraph at lines 15906--15910 []\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 15906--15910 \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 [244] [245] [246] Underfull \hbox (badness 1092) in paragraph at lines 16079--16084 [][]\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 [247] [248] [249] Underfull \hbox (badness 6741) in paragraph at lines 16329--16333 \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 , [250] [251] [252] [253] [254] [255] [256] [257] [258] Underfull \vbox (badness 3803) has occurred while \output is active [259] Underfull \vbox (badness 10000) has occurred while \output is active [260] [261] [262] [263] [264] [265] [266] [267] [268] [269] Underfull \hbox (badness 1478) in paragraph at lines 17622--17625 []\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 [270] [271] [272] [273] Underfull \hbox (badness 10000) in paragraph at lines 17877--17879 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [274] [275] [276] [277] [278] [279] [280] [281] [282] Underfull \hbox (badness 1442) in paragraph at lines 18477--18479 []\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 [283] Underfull \hbox (badness 2452) in paragraph at lines 18569--18585 [][][]\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 , [284] [285] [286] [287] [288] [289] [290] Underfull \hbox (badness 1248) in paragraph at lines 18988--18991 []\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 , [291] [292] [293] [294] Underfull \hbox (badness 4739) in paragraph at lines 19246--19248 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [295] [296] [297] [298] [299] [300] Underfull \hbox (badness 1596) in paragraph at lines 19665--19670 \T1/ptm/m/n/10 trix or, if \T1/zi4/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/zi4/m/n/10 simplify2array()\T1/ptm /m/n/10 . [301] [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] Underfull \hbox (badness 2469) in paragraph at lines 20269--20274 []\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 20283--20290 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [312] Underfull \hbox (badness 10000) in paragraph at lines 20357--20361 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 20357--20361 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$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 ' [313] [314] Underfull \hbox (badness 1014) in paragraph at lines 20527--20532 []\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 [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] Underfull \hbox (badness 1264) in paragraph at lines 21317--21322 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [327] Underfull \hbox (badness 4441) in paragraph at lines 21346--21349 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 , [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] Underfull \hbox (badness 6047) in paragraph at lines 22093--22095 []\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 \T1/zi4/m/n/10 make.unique(c(A,B)) == [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] Underfull \hbox (badness 1077) in paragraph at lines 23134--23140 \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 . [356] [357] [358] [359] [360] [361] [362] [363] Underfull \hbox (badness 2790) in paragraph at lines 23630--23633 []\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 23630--23633 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [364] [365] [366] [367] [368] Underfull \hbox (badness 1194) in paragraph at lines 23912--23915 []\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 [369] [370] [371] Underfull \hbox (badness 2368) in paragraph at lines 24118--24124 []\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 list, i.e., Underfull \hbox (badness 4981) in paragraph at lines 24118--24124 \T1/zi4/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are al so given by [][]\T1/zi4/m/n/10 ls[][][](env,all.names = [372] [373] [374] [375] [376] [377] Underfull \hbox (badness 10000) in paragraph at lines 24500--24503 []\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by [378] [379] [380] [381] [382] [383] [384] [385] [386] Underfull \hbox (badness 10000) in paragraph at lines 25105--25107 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than \T1/zi4/m/n/10 pkg %in% [387] [388] [389] [390] [391] [392] [393] [394] [395] [396] [397] [398] [399] Underfull \hbox (badness 1038) in paragraph at lines 25945--25953 []\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 1735) in paragraph at lines 25945--25953 \T1/ptm/m/n/10 set from value of the en-vi-ron-ment vari-able \T1/zi4/m/n/10 R_ DEFAULT_PACKAGES\T1/ptm/m/n/10 , or if that is un- Underfull \hbox (badness 1292) in paragraph at lines 25945--25953 \T1/ptm/m/n/10 set to \T1/zi4/m/n/10 c("datasets","utils","grDevices","graphics ","stats","methods")\T1/ptm/m/n/10 . (Set Underfull \hbox (badness 1881) in paragraph at lines 25954--25957 []\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 25973--25975 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [400] [401] Underfull \hbox (badness 2142) in paragraph at lines 26114--26118 []\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 26164--26169 []\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 [402] [403] [404] [405] Underfull \hbox (badness 10000) in paragraph at lines 26452--26458 []\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 26452--26458 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 26452--26458 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 26465--26468 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 26491--26493 []\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 26526--26531 []\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 2529) in paragraph at lines 26532--26543 \T1/ptm/m/n/10 in-di-rectly [][]\T1/zi4/m/n/10 update.packages[][][]\T1/ptm/m/n /10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si- Underfull \hbox (badness 2512) in paragraph at lines 26532--26543 \T1/ptm/m/n/10 ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi4/m /n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use and [406] Underfull \hbox (badness 7203) in paragraph at lines 26544--26547 []\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 10000) in paragraph at lines 26568--26573 []\T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma -cOS build), Underfull \hbox (badness 2057) in paragraph at lines 26568--26573 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). [407] [408] [409] [410] [411] [412] [413] [414] Underfull \hbox (badness 10000) in paragraph at lines 27086--27089 []\T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 str2lang(s ) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of [415] Underfull \hbox (badness 7925) in paragraph at lines 27165--27169 []\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 vec-to r \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n /10 cor-re-sponds to Underfull \hbox (badness 1622) in paragraph at lines 27165--27169 [][]\T1/zi4/m/n/10 parse[][][](text = s,keep.source=FALSE)\T1/ptm/m/n/10 , whic h is al-ways of type ([][]\T1/zi4/m/n/10 typeof[][][]\T1/ptm/m/n/10 ) and [][]\ T1/zi4/m/n/10 class[][][] Underfull \hbox (badness 6125) in paragraph at lines 27170--27179 []\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 string \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2lang(s) \T1/ptm/m/n/10 cor -re-sponds to [][]\T1/zi4/m/n/10 parse[][][](text = [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] Underfull \hbox (badness 2726) in paragraph at lines 27891--27894 []\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 [427] [428] [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] Underfull \vbox (badness 3803) has occurred while \output is active [445] [446] [447] [448] [449] [450] [451] [452] Underfull \hbox (badness 1533) in paragraph at lines 29582--29585 []\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 [453] [454] [455] Underfull \hbox (badness 1163) in paragraph at lines 29745--29756 []\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 [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] [473] [474] [475] [476] [477] [478] [479] Underfull \hbox (badness 10000) in paragraph at lines 31291--31295 []\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 31291--31295 \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 31313--31315 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [480] [481] [482] [483] [484] [485] [486] [487] [488] Underfull \hbox (badness 1655) in paragraph at lines 31869--31871 []\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 [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] Underfull \hbox (badness 2261) in paragraph at lines 32988--32993 []\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 [506] Underfull \hbox (badness 10000) in paragraph at lines 33015--33021 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1484) in paragraph at lines 33015--33021 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal and hex-adec-i-mal rep-re-sen-ta-tions like [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] Underfull \hbox (badness 1072) in paragraph at lines 36157--36161 []\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 36162--36166 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 36190--36196 []\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 36190--36196 \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 36190--36196 \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 3009) in paragraph at lines 36202--36209 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 36202--36209 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 36202--36209 \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 36202--36209 \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 [555] [556] [557] [558] [559] [560] Underfull \hbox (badness 1142) in paragraph at lines 36556--36562 []\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 \T1/zi4/m/n/10 "%Y-%m-%d [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] Underfull \hbox (badness 1565) in paragraph at lines 37829--37831 []\T1/ptm/m/n/10 integer code used in \T1/zi4/m/n/10 quantile(*,type=quantile.t ype) \T1/ptm/m/n/10 for the de-fault [581] [582] [583] [584] [585] [586] [587] [588] [589] [590] Underfull \hbox (badness 4967) in paragraph at lines 38428--38433 []\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 [591] [592] Underfull \hbox (badness 1616) in paragraph at lines 38541--38546 \T1/zi4/m/n/10 system("id") \T1/ptm/m/n/10 is much more portable on Unix-alikes , pro-vided only the POSIX op-tions [593] [594] [595] [596] [597] [598] [599] [600] Underfull \hbox (badness 1472) in paragraph at lines 39067--39070 []\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 [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614] Underfull \hbox (badness 10000) in paragraph at lines 39981--39985 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/zi4/m/n/10 length(bin) > [615] [616] [617] [618] Underfull \hbox (badness 10000) in paragraph at lines 40232--40235 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [619] [620] [621] Underfull \hbox (badness 10000) in paragraph at lines 40416--40420 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [622] [623] [624] [625] [626] [627] [628] [629] [630] Underfull \hbox (badness 10000) in paragraph at lines 41029--41032 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[ ]zones / [631] [632] [633] [634] [635] [636] Underfull \vbox (badness 10000) has occurred while \output is active [637] [638] [639] [640] [641] [642] [643] [644] Underfull \hbox (badness 1990) in paragraph at lines 41933--41941 []\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 41933--41941 \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 [645] [646] [647] [648] [649] [650] [651] [652] Underfull \hbox (badness 1917) in paragraph at lines 42439--42446 []\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 [653] [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] Underfull \hbox (badness 3668) in paragraph at lines 43168--43170 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [664] [665] Underfull \hbox (badness 2401) in paragraph at lines 43296--43300 []\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 [666] [667] [668] Underfull \hbox (badness 2111) in paragraph at lines 43485--43490 \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 10000) in paragraph at lines 43506--43511 []\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 [669] [670] [671] [672] [673] [674] [675] [676] [677] Underfull \hbox (badness 5417) in paragraph at lines 44088--44092 []\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 [678] Underfull \hbox (badness 10000) in paragraph at lines 44149--44153 []\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 [679] [680]) (./compiler-pkg.tex Chapter 2. [681] [682] [683] [684]) (./datasets-pkg.tex Chapter 3. [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] Underfull \hbox (badness 1097) in paragraph at lines 1031--1035 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] Underfull \vbox (badness 1448) has occurred while \output is active [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] Overfull \vbox (19.74611pt too high) has occurred while \output is active [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] Underfull \vbox (badness 10000) has occurred while \output is active [753] [754] [755] [756] Underfull \vbox (badness 10000) has occurred while \output is active [757] [758] [759] [760] [761] [762] [763] [764] [765] [766]) (./grDevices-pkg.tex Chapter 4. [767] [768] [769] [770] [771] Underfull \hbox (badness 3158) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/zi4/m/n/10 c(mi,ma,n.)\T1/ptm /m/n/10 , with iden-ti-cal mean-ing to Underfull \hbox (badness 10000) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][]\T1/zi4/m/n/10 axisTicks[][][]() \T1/ptm/ m/n/10 just calls the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/ptm/m/n/1 0 in Underfull \hbox (badness 1852) in paragraph at lines 298--303 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 /src/main/plot.c\T1/ptm/m/n/10 ' which is also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t ion [772] [773] [774] [775] [776] [777] [778] [779] Underfull \hbox (badness 1424) in paragraph at lines 830--832 [][][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 (as in-te-ger or char-ac-ter) and \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 mean trans-par-ent, which can also be spec-i -fied as [780] [781] [782] [783] [784] Underfull \hbox (badness 5175) in paragraph at lines 1124--1126 []\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 [785] [786] [787] [788] Underfull \hbox (badness 1852) in paragraph at lines 1326--1329 []\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 [789] [790] [791] Underfull \hbox (badness 1490) in paragraph at lines 1532--1537 \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 [792] [793] [794] [795] [796] [797] Underfull \hbox (badness 1325) in paragraph at lines 1938--1948 \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 , [798] [799] Underfull \hbox (badness 10000) in paragraph at lines 2050--2052 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [800] [801] [802] Underfull \hbox (badness 6758) in paragraph at lines 2228--2231 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [803] [804] [805] [806] [807] [808] [809] [810] [811] [812] Underfull \hbox (badness 10000) in paragraph at lines 2832--2833 [813] [814] [815] [816] [817] [818] [819] [820] [821] Underfull \hbox (badness 10000) in paragraph at lines 3388--3393 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [822] [823] [824] [825] [826] Underfull \vbox (badness 10000) has occurred while \output is active [827] Underfull \hbox (badness 10000) in paragraph at lines 3789--3792 []\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 [828] [829] [830] [831] [832] [833] [834] [835] [836] [837] [838] Underfull \hbox (badness 10000) in paragraph at lines 4518--4523 [][][]$\T1/zi4/m/n/10 https : / / www . adobe . com / content / dam / acom / en / devnet / actionscript / articles / PLRM . pdf$[][] Underfull \hbox (badness 4181) in paragraph at lines 4518--4523 \T1/ptm/m/n/10 or PDF [][]$\T1/zi4/m/n/10 https : / / www . adobe . com / devne t / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in [839] Underfull \vbox (badness 10000) has occurred while \output is active [840] [841] Underfull \hbox (badness 1067) in paragraph at lines 4672--4679 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [842] [843] [844] [845] Underfull \hbox (badness 1377) in paragraph at lines 4975--4980 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [846] Underfull \hbox (badness 1418) in paragraph at lines 5051--5058 \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 1755) in paragraph at lines 5069--5071 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [847] [848] Underfull \hbox (badness 1377) in paragraph at lines 5180--5185 []\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 [849] Underfull \hbox (badness 7344) in paragraph at lines 5249--5251 []\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 [850] [851] Underfull \hbox (badness 2035) in paragraph at lines 5384--5393 []\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 5384--5393 \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 5384--5393 \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 , [852] Underfull \hbox (badness 10000) in paragraph at lines 5452--5459 []\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 5452--5459 \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 . [853] [854] [855] Underfull \hbox (badness 1546) in paragraph at lines 5594--5602 []\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 , [856] [857] [858] [859] [860] [861] [862] [863] Underfull \hbox (badness 10000) in paragraph at lines 6129--6132 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [864] [865] [866] [867] [868] [869] [870] [871] [872] [873] [874] [875] [876] Underfull \hbox (badness 1189) in paragraph at lines 6951--6953 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [877] Underfull \hbox (badness 10000) in paragraph at lines 7049--7051 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [878] [879] [880] [881] [882] Underfull \hbox (badness 3780) in paragraph at lines 7349--7355 []\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 , [883] [884] [885] Underfull \hbox (badness 2680) in paragraph at lines 7550--7552 []\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 [886] [887] [888]) (./graphics-pkg.tex Chapter 5. [889] [890] [891] [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] Underfull \hbox (badness 4634) in paragraph at lines 1351--1354 [][][]\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 , [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] Underfull \hbox (badness 1728) in paragraph at lines 2308--2310 []\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use \T1/zi4/m/n/10 "n " \T1/ptm/m/n/10 to sup-press and see also [927] [928] Underfull \hbox (badness 1009) in paragraph at lines 2399--2406 \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 [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] [947] [948] [949] [950] Underfull \vbox (badness 10000) has occurred while \output is active [951] [952] [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] Underfull \hbox (badness 3229) in paragraph at lines 4544--4549 []\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 [964] [965] [966] [967] [968] Underfull \hbox (badness 10000) in paragraph at lines 4901--4907 []\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 4901--4907 \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 [969] Underfull \hbox (badness 10000) in paragraph at lines 5032--5035 [970] Underfull \hbox (badness 10000) in paragraph at lines 5093--5095 [971 >/library/graphics/help/figures/ mai.pdf>] [972 >/library/graphics/hel p/figures/oma.pdf>] [973] Underfull \hbox (badness 10000) in paragraph at lines 5283--5285 []\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 [974] Underfull \vbox (badness 3803) has occurred while \output is active [975] [976] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6761--6762 [][] [997] [998 >/library/graphics/help/fi gures/pch.pdf>] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] Underfull \hbox (badness 2012) in paragraph at lines 7586--7589 []\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 poi nt [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] Underfull \hbox (badness 10000) in paragraph at lines 8846--8848 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8848--8850 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1032]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8928 \HeaderA{units}{Graphical Units}{units} [1033] [1034] [1035] [1036]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] Underfull \hbox (badness 2680) in paragraph at lines 483--486 []\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 [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] Underfull \hbox (badness 4279) in paragraph at lines 1064--1073 [][][]\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 , [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] Underfull \vbox (badness 10000) has occurred while \output is active [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] Underfull \hbox (badness 1067) in paragraph at lines 4486--4489 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1113] [1114] [1115] [1116] Underfull \hbox (badness 7256) in paragraph at lines 4731--4733 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \hbox (badness 1824) in paragraph at lines 6535--6538 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like \T1/zi4/m/n/10 depth [1148] [1149] [1150] [1151]) (./methods-pkg.tex [1152] Chapter 7. [1153] [1154] [1155] [1156] [1157] [1158] [1159] [1160] Underfull \vbox (badness 10000) has occurred while \output is active [1161] Underfull \vbox (badness 10000) has occurred while \output is active [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171] Underfull \hbox (badness 2237) in paragraph at lines 1385--1387 []\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 [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] Underfull \hbox (badness 2181) in paragraph at lines 1932--1939 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/zi4/m/n/10 is(x,"refClass") \T1/ptm/m/n/10 tests [1180] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\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 1981--1986 \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 [1181] [1182] [1183] Underfull \hbox (badness 2213) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/zi4/m/n/10 where = [1184] [1185] [1186] [1187] [1188] Underfull \hbox (badness 10000) in paragraph at lines 2574--2577 []\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 [1189] [1190] Underfull \hbox (badness 1132) in paragraph at lines 2714--2718 []\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 [1191] Underfull \hbox (badness 1033) in paragraph at lines 2746--2751 \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 [1192] [1193] [1194] [1195] [1196] [1197] [1198] Underfull \hbox (badness 1102) in paragraph at lines 3303--3305 []\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 [1199] [1200] [1201] [1202] [1203] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\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 [1204] Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1205] Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [] \T1/zi4/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude = "numeric",altitude [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] Underfull \hbox (badness 1769) in paragraph at lines 4472--4478 []\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 4472--4478 \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 [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] Underfull \vbox (badness 10000) has occurred while \output is active [1227] [1228] [1229] Underfull \hbox (badness 4036) in paragraph at lines 5437--5440 []\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 [1230] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1231] [1232] [1233] [1234] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] Underfull \hbox (badness 1675) in paragraph at lines 6451--6457 \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 [1243] [1244] [1245] [1246] Underfull \vbox (badness 10000) has occurred while \output is active [1247] [1248] [1249] [1250]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1251] [1252] [1253]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} [1254] Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1255] [1256] [1257] Underfull \hbox (badness 1286) in paragraph at lines 7484--7486 []\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 [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] Underfull \vbox (badness 10000) has occurred while \output is active [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] Underfull \hbox (badness 1137) in paragraph at lines 10011--10019 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/n/10 ne w("signature",functionDef,...)\T1/ptm/m/n/10 . The [1293] [1294] [1295] [1296] [1297] [1298] [1299] Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., [1300] [1301] [1302] [1303]) (./parallel-pkg.tex [1304] Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\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 [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] [1324] [1325] Underfull \hbox (badness 3386) in paragraph at lines 1365--1368 []\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 [1326] [1327] [1328]) (./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 [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344]) (./stats-pkg.tex Chapter 10. [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] Underfull \hbox (badness 1412) in paragraph at lines 875--877 []\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 [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] Underfull \hbox (badness 2503) in paragraph at lines 1356--1359 []\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 , [1367] [1368] [1369] Underfull \hbox (badness 10000) in paragraph at lines 1536--1540 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov","lm") \T1/ptm/m/n/1 0 or for mul-ti-ple re-sponses of class [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] Underfull \hbox (badness 2503) in paragraph at lines 3437--3440 []\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 , [1400] [1401] [1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] Underfull \hbox (badness 1127) in paragraph at lines 4351--4354 []\T1/ptm/m/n/10 standardized resid-u-als, \T1/zi4/m/n/10 (observed -expected) / sqrt(V)\T1/ptm/m/n/10 , where \T1/zi4/m/n/10 V \T1/ptm/m/n/10 is the [1415] [1416] [1417] [1418] [1419] Underfull \hbox (badness 3989) in paragraph at lines 4681--4688 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] Underfull \hbox (badness 2556) in paragraph at lines 5317--5320 []\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 5334--5336 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/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 [1430] [1431] [1432] [1433] [1434] [1435] [1436] Underfull \hbox (badness 2503) in paragraph at lines 5726--5730 []\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 , [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] Underfull \hbox (badness 7081) in paragraph at lines 6520--6523 []\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 6524--6526 []\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 [1450] [1451] [1452] [1453] [1454] Underfull \vbox (badness 3803) has occurred while \output is active [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] Underfull \hbox (badness 10000) in paragraph at lines 7369--7372 []\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 [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] Underfull \vbox (badness 10000) has occurred while \output is active [1485] [1486] [1487] [1488] [1489] Underfull \hbox (badness 2626) in paragraph at lines 9048--9051 []\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 [1490] [1491] Underfull \hbox (badness 2503) in paragraph at lines 9155--9159 []\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 , [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] [1509] [1510] [1511] Underfull \hbox (badness 4518) in paragraph at lines 10469--10474 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1512] [1513] [1514] [1515] [1516] Underfull \hbox (badness 2142) in paragraph at lines 10830--10833 []\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 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10849--10852 []\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, [1517] Underfull \hbox (badness 1708) in paragraph at lines 10911--10915 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1518] [1519] [1520] [1521] [1522] [1523] Underfull \hbox (badness 1694) in paragraph at lines 11307--11310 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531]pdfTeX warning (ext4): d estination with the same identifier (name{Rfn.hat}) has been already used, dupl icate ignored \relax l.11791 \aliasA{hat}{influence.measures}{hat} [1532] [1533] Underfull \hbox (badness 1484) in paragraph at lines 11926--11928 []\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 [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] Underfull \hbox (badness 10000) in paragraph at lines 12519--12521 []\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 \T1/zi4/m/n/10 SSinit = [1544] [1545] [1546] [1547] [1548] [1549] Underfull \hbox (badness 2894) in paragraph at lines 12855--12859 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] Underfull \hbox (badness 4518) in paragraph at lines 13605--13610 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] Underfull \hbox (badness 4518) in paragraph at lines 14257--14262 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1572] [1573] Underfull \hbox (badness 8151) in paragraph at lines 14395--14399 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = "interp olate",statistics = Underfull \hbox (badness 1199) in paragraph at lines 14402--14404 []\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 [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] Underfull \hbox (badness 2503) in paragraph at lines 15473--15477 []\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 , [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] Underfull \hbox (badness 4621) in paragraph at lines 15985--15991 []\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 [1600] [1601] [1602] [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] [1623] [1624] [1625] [1626] [1627] Underfull \vbox (badness 10000) has occurred while \output is active [1628] Underfull \vbox (badness 10000) has occurred while \output is active [1629] [1630] [1631] [1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] Underfull \hbox (badness 1377) in paragraph at lines 18588--18593 []\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 18593--18596 []\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 [1642] Underfull \hbox (badness 2343) in paragraph at lines 18606--18610 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 3471) in paragraph at lines 18606--18610 \T1/ptm/m/n/10 the value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + re ltol) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18614--18618 []\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 [1643] [1644] [1645] Overfull \hbox (15.73795pt too wide) in paragraph at lines 18839--18839 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 18842--18842 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] Underfull \vbox (badness 10000) has occurred while \output is active [1646] [1647] [1648] [1649] [1650] [1651] [1652] Underfull \hbox (badness 1337) in paragraph at lines 19264--19267 []\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 [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] Underfull \hbox (badness 3049) in paragraph at lines 19760--19764 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1662] [1663] [1664] [1665] Underfull \hbox (badness 1194) in paragraph at lines 20018--20021 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1666] [1667] [1668] [1669] [1670] [1671] [1672] Underfull \hbox (badness 2503) in paragraph at lines 20397--20400 []\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 , Underfull \hbox (badness 3919) in paragraph at lines 20424--20426 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or \T1/zi4/m/n/10 "Comparison of Poisson [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] [1688] [1689] [1690] Underfull \hbox (badness 10000) in paragraph at lines 21501--21507 []\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 , [1691] [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] Underfull \hbox (badness 1337) in paragraph at lines 22855--22861 []\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 [1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] Overfull \hbox (27.74408pt too wide) in paragraph at lines 23420--23420 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1722] [1723] [1724] [1725] [1726] Underfull \hbox (badness 10000) in paragraph at lines 23671--23674 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 4205) in paragraph at lines 23671--23674 \T1/zi4/m/n/10 cutree(hclust.obj,k = k)\T1/ptm/m/n/10 , can be spec-i-fied for ef-fi-ciency if al-ready [1727] [1728] [1729] [1730] [1731] [1732] [1733] [1734] [1735] Underfull \hbox (badness 1824) in paragraph at lines 24257--24263 []\T1/ptm/m/n/10 Here, all the NAs in \T1/zi4/m/n/10 x \T1/ptm/m/n/10 are first re-placed by al-ter- Underfull \hbox (badness 1033) in paragraph at lines 24257--24263 \T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/ m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where [1736] Underfull \hbox (badness 10000) in paragraph at lines 24278--24281 []\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 \T1/zi4/m/n/10 y[j] = Underfull \hbox (badness 3690) in paragraph at lines 24347--24351 [][][]\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 [1737] Underfull \vbox (badness 3803) has occurred while \output is active [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] Underfull \hbox (badness 2165) in paragraph at lines 24856--24861 []\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm /m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1 0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [1746] [1747] [1748] [1749] Underfull \hbox (badness 1867) in paragraph at lines 25061--25063 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 25074--25078 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u se.fallback) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 PP [1750] [1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] Underfull \vbox (badness 3803) has occurred while \output is active [1761] [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] [1771] [1772] [1773] Underfull \vbox (badness 10000) has occurred while \output is active [1774] Underfull \hbox (badness 3514) in paragraph at lines 26634--26639 []\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 [1775] [1776] [1777] [1778] Overfull \hbox (2.23795pt too wide) in paragraph at lines 26868--26868 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1779] Underfull \hbox (badness 3514) in paragraph at lines 26904--26910 []\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 [1780] [1781] [1782] [1783] Underfull \hbox (badness 3514) in paragraph at lines 27118--27123 []\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 [1784] Underfull \hbox (badness 3514) in paragraph at lines 27205--27210 []\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 [1785] Underfull \hbox (badness 3514) in paragraph at lines 27270--27275 []\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 [1786] [1787] Underfull \hbox (badness 3514) in paragraph at lines 27364--27369 []\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 [1788] [1789] Underfull \hbox (badness 6691) in paragraph at lines 27456--27461 []\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 [1790] [1791] [1792] [1793] [1794] [1795] [1796] [1797] Underfull \hbox (badness 4024) in paragraph at lines 27984--27987 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion , which [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] Underfull \hbox (badness 5431) in paragraph at lines 28590--28592 []\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 [1808] [1809] [1810] [1811] Underfull \hbox (badness 5431) in paragraph at lines 28800--28803 []\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 [1812] [1813] [1814] [1815] [1816] Underfull \hbox (badness 1337) in paragraph at lines 29114--29118 []\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 [1817] [1818] [1819] [1820] [1821] Underfull \hbox (badness 1616) in paragraph at lines 29416--29419 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1822] [1823] [1824] [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] [1835] [1836] [1837] [1838] [1839] [1840] Underfull \hbox (badness 3557) in paragraph at lines 30546--30550 []\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 \T1/zi4 /m/n/10 interval = [1841] [1842] [1843] Underfull \vbox (badness 10000) has occurred while \output is active [1844] [1845] [1846] Underfull \hbox (badness 1337) in paragraph at lines 30910--30914 []\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 [1847] [1848] [1849] [1850] [1851] [1852] [1853] [1854] [1855] Underfull \hbox (badness 1337) in paragraph at lines 31437--31441 []\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 [1856] [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865]) (./stats4-pkg.tex [1866] Chapter 11. [1867] [1868] [1869] [1870] [1871] [1872]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} [1873] [1874] [1875]) (./tcltk-pkg.tex [1876] Chapter 12. [1877] [1878] [1879] [1880] [1881] [1882] [1883] Underfull \vbox (badness 10000) has occurred while \output is active [1884] Underfull \vbox (badness 10000) has occurred while \output is active [1885] 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 [1886] [1887] [1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897]) (./tools-pkg.tex [1898] Chapter 13. [1899] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1900] 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 [1901] [1902] 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 [1903] [1904] 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 [1905] [1906] [1907] [1908] [1909] [1910] [1911] [1912] [1913] [1914] [1915] [1916] [1917] Underfull \hbox (badness 4441) in paragraph at lines 1139--1149 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- Underfull \hbox (badness 1014) in paragraph at lines 1163--1165 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1169--1171 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous [1918] Underfull \hbox (badness 10000) in paragraph at lines 1206--1209 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1206--1209 \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 , [1919] [1920] [1921] [1922] [1923] Underfull \hbox (badness 2293) in paragraph at lines 1558--1560 []\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with its func-tion-al-ity in-te-grated into that of [1924] [1925] [1926] Underfull \hbox (badness 7981) in paragraph at lines 1696--1701 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 1082) in paragraph at lines 1703--1705 []\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 [1927] [1928] [1929]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1930] [1931] [1932] [1933] [1934] [1935] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2202--2202 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1936] [1937] [1938] Underfull \hbox (badness 7981) in paragraph at lines 2371--2377 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1939] [1940] [1941] [1942] [1943] [1944] [1945] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2846. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2847. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2847. [1946] [1947] [1948] [1949] [1950] Underfull \hbox (badness 1424) in paragraph at lines 3128--3130 []\T1/zi4/m/it/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 [1951] [1952] [1953] [1954] [1955] [1956] [1957] [1958] [1959] [1960] [1961] Underfull \hbox (badness 10000) in paragraph at lines 3832--3834 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1962] [1963] Underfull \hbox (badness 10000) in paragraph at lines 3971--3974 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/it/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/it/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1964] [1965] Underfull \hbox (badness 1137) in paragraph at lines 4073--4075 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1966] [1967] [1968] [1969] [1970] Underfull \hbox (badness 1796) in paragraph at lines 4381--4386 []\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over \T 1/zi4/m/it/10 write_PACKAGES \T1/ptm/m/n/10 in the \T1/zi4/m/it/10 type == [1971] Underfull \hbox (badness 1838) in paragraph at lines 4455--4461 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/it/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/it/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4455--4461 \T1/ptm/m/n/10 `\T1/zi4/m/it/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 [1972] [1973] [1974] Underfull \hbox (badness 2197) in paragraph at lines 4671--4681 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/it/10 available.packages[][][]\T1/ptm/m/n/10 : [1975] Underfull \hbox (badness 1571) in paragraph at lines 4734--4738 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [1976] [1977] [1978]) (./utils-pkg.tex Chapter 14. [1979] 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/it/10 insertions\T1/ptm/m/n/10 ', [1980] [1981] [1982] [1983] [1984] Underfull \hbox (badness 10000) in paragraph at lines 376--381 \T1/zi4/m/it/10 c("vertical","horizontal","cascade","minimize","restore") \T1/p tm/m/n/10 with [1985] [1986] [1987] [1988] [1989] Underfull \hbox (badness 10000) in paragraph at lines 717--723 []\T1/ptm/m/n/10 Functions \T1/zi4/m/it/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/it/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 717--723 \T1/zi4/m/it/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/it/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1990] [1991] Underfull \hbox (badness 5847) in paragraph at lines 850--856 []\T1/ptm/m/n/10 Argument \T1/zi4/m/it/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 850--856 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/it/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1992] Underfull \hbox (badness 3861) in paragraph at lines 918--923 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/it/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/it/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/it/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1993] [1994] Underfull \hbox (badness 3323) in paragraph at lines 1089--1097 []\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/zi4/m/it/1 0 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1 /ptm/m/n/10 , in-di-cat- Underfull \hbox (badness 2961) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f or-mat- Underfull \hbox (badness 3919) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 3735) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/it/10 getOption[][][]("citation.bibtex.ma x",1) \T1/ptm/m/n/10 which is \T1/zi4/m/it/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by [1995] Underfull \hbox (badness 10000) in paragraph at lines 1101--1103 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1996] [1997] Underfull \vbox (badness 3803) has occurred while \output is active [1998] [1999] [2000] [2001] [2002] Underfull \hbox (badness 1371) in paragraph at lines 1606--1608 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/it/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/it/10 ccaddress \T1/ptm/m/n/10 to pass to [2003] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 1676. [2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] Underfull \hbox (badness 2057) in paragraph at lines 2215--2217 []\T1/ptm/m/n/10 None for \T1/zi4/m/it/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [2013] [2014] [2015] [2016] [2017] [2018]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.clipboard}) has been already used, duplicate ig nored \relax l.2566 ... the Clipboard in MS Windows}{clipboard} [2019] [2020] Underfull \hbox (badness 1748) in paragraph at lines 2733--2736 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/it/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/it/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/it/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [2021] [2022] [2023] [2024] [2025] [2026] [2027] Underfull \hbox (badness 5388) in paragraph at lines 3142--3146 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/it/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/it/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/it/10 .TXT\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/it/10 read.table[][][](...,header = Underfull \hbox (badness 2285) in paragraph at lines 3147--3150 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/it/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/it/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/it/10 read.table[] [][](...,header = TRUE,sep = [2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] Underfull \hbox (badness 1430) in paragraph at lines 3906--3914 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/it/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [2039] Underfull \hbox (badness 1231) in paragraph at lines 3983--3995 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [2040] [2041] Underfull \hbox (badness 10000) in paragraph at lines 4141--4143 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/it/10 dow nload.file[][][] \T1/ptm/m/n/10 and [2042] [2043] [2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.4839 ...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.4839 ...mat Unordered and Ordered Lists}{format} [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] Underfull \hbox (badness 1622) in paragraph at lines 5358--5362 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 5990. Underfull \hbox (badness 1371) in paragraph at lines 5994--5996 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/it/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/it/10 ccaddress \T1/ptm/m/n/10 to pass to [2072] Underfull \hbox (badness 1502) in paragraph at lines 6083--6088 []\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 6083--6088 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2073] [2074] [2075] Underfull \hbox (badness 10000) in paragraph at lines 6256--6265 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2076] Underfull \hbox (badness 2150) in paragraph at lines 6320--6323 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2077] [2078] Underfull \hbox (badness 3118) in paragraph at lines 6458--6460 []\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 [2079] [2080] [2081] Underfull \hbox (badness 1325) in paragraph at lines 6630--6634 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/it/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able Underfull \hbox (badness 4726) in paragraph at lines 6642--6648 \T1/ptm/m/n/10 used if \T1/zi4/m/it/10 repos = NULL\T1/ptm/m/n/10 . Can also be a char-ac-ter vec-tor, a sub-set of [2082] Underfull \hbox (badness 10000) in paragraph at lines 6714--6717 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be Underfull \hbox (badness 10000) in paragraph at lines 6714--6717 \T1/ptm/m/n/10 passed to \T1/zi4/m/it/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou rce pack-age in-stall. E.g., [2083] Underfull \hbox (badness 3219) in paragraph at lines 6790--6797 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/it/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6790--6797 \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 6790--6797 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1596) in paragraph at lines 6790--6797 [][]\T1/zi4/m/it/10 getOption[][][]("install.packages.compile.from.source")\T1/ ptm/m/n/10 . \T1/zi4/m/it/10 type = "both" \T1/ptm/m/n/10 will be silently Underfull \hbox (badness 2932) in paragraph at lines 6798--6801 []\T1/ptm/m/n/10 Using pack-ages with \T1/zi4/m/it/10 type = "source" \T1/ptm/m /n/10 al-ways works pro-vided the pack-age con-tains no [2084] Underfull \hbox (badness 10000) in paragraph at lines 6934--6939 [][][]\T1/zi4/m/it/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [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] Underfull \hbox (badness 10000) in paragraph at lines 8434--8436 []\T1/ptm/m/n/10 for \T1/zi4/m/it/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi 4/m/it/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 2310) in paragraph at lines 8456--8461 []\T1/ptm/m/n/10 If a `\T1/zi4/m/it/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2110] [2111] [2112] [2113] [2114] [2115] [2116] [2117] Underfull \hbox (badness 1248) in paragraph at lines 8980--8984 []\T1/zi4/m/it/10 R CMD build \T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/m/ n/10 source tar-balls. The name(s) of the pack-ages are taken from the [2118] Underfull \hbox (badness 1789) in paragraph at lines 9058--9060 []\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 [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131] Underfull \hbox (badness 1097) in paragraph at lines 9895--9898 []\T1/ptm/m/n/10 The name \T1/zi4/m/it/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2132] [2133] Underfull \hbox (badness 3000) in paragraph at lines 10031--10036 [][][]\T1/zi4/m/it/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/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/it/10 read.t able[][][]\T1/ptm/m/n/10 ; [2134] [2135] [2136] [2137] [2138] [2139] [2140] [2141] [2142] Underfull \hbox (badness 2134) in paragraph at lines 10614--10619 [][][]\T1/zi4/m/it/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/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/it/10 write. table[][][]\T1/ptm/m/n/10 ; Underfull \hbox (badness 10000) in paragraph at lines 10670--10675 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for Underfull \hbox (badness 10000) in paragraph at lines 10670--10675 \T1/zi4/m/it/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/zi4/m/it/10 HKEY_CLASSES _ROOT\T1/ptm/m/n/10 . \T1/zi4/m/it/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] Underfull \hbox (badness 2469) in paragraph at lines 11163--11167 []\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 11163--11167 [][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2152] [2153] [2154] [2155] [2156] Underfull \hbox (badness 4060) in paragraph at lines 11494--11497 []\T1/ptm/m/n/10 If `\T1/zi4/m/it/10 --default-packages\T1/ptm/m/n/10 ' is not used, then \T1/zi4/m/it/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var i-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 11517--11517 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [2157] [2158] [2159] [2160] Underfull \hbox (badness 2150) in paragraph at lines 11756--11758 [][][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/it/10 https : / / www . gnu . org / software / emac s / manual / [2161] [2162] [2163] [2164] Underfull \hbox (badness 10000) in paragraph at lines 11975--11979 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/it/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12006--12012 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2165] [2166] Underfull \hbox (badness 1009) in paragraph at lines 12200--12212 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. 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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.lmList} 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 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Transcript written on fullrefman.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file fullrefman.idx.................done (13939 entries accepted, 34 rejected). Sorting entries................................................................................................................................................done (210880 comparisons). Generating output file fullrefman.ind................done (13726 lines written, 55 warnings). Output written in fullrefman.ind. Transcript written in fullrefman.ilg. 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[1] [2] Underfull \hbox (badness 6995) 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 . It Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1/pt m/m/n/10 if \T1/zi4/m/n/10 double.base Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth- er-wise, it is \T1/zi4/m/n/10 (double.base Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/zi4/m /n/10 1.110223e-16\T1/ptm/m/n/10 . As Underfull \hbox (badness 4995) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.neg.ulp.digits \T1/ptm/m/n/10 is bounded be-low by \T1/zi 4/m/n/10 -(double.digits + 3)\T1/ptm/m/n/10 , [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 297--301 []\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] [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 534--540 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/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 1178--1181 []\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] (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1966--1966 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] [34] [35] [36] [37] Underfull \hbox (badness 10000) in paragraph at lines 2402--2404 []\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci ently) by Underfull \hbox (badness 10000) in paragraph at lines 2405--2410 [][][]\T1/zi4/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le ngth re-sults, so at-tempt-ing to split via Underfull \hbox (badness 1102) in paragraph at lines 2405--2410 \T1/zi4/m/n/10 apply(x,MARGIN,identity) \T1/ptm/m/n/10 does not work (as it sim -ply gives \T1/zi4/m/n/10 x\T1/ptm/m/n/10 ). By chain-ing \T1/zi4/m/n/10 asplit [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] Underfull \hbox (badness 10000) in paragraph at lines 3784--3786 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [60] [61] [62] Overfull \hbox (6.42029pt too wide) in paragraph at lines 4025--4025 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 2521) in paragraph at lines 5046--5048 []\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 [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6202--6202 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [97] [98] [99] [100] [101] [102] Overfull \hbox (46.35893pt too wide) in paragraph at lines 6611--6613 []\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 : [103] [104] Underfull \hbox (badness 10000) in paragraph at lines 6759--6762 []\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 [105] [106] Underfull \hbox (badness 6063) in paragraph at lines 6941--6947 []\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- Underfull \hbox (badness 2343) in paragraph at lines 6941--6947 \T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files and web-pages gen-er- Underfull \hbox (badness 1708) in paragraph at lines 6941--6947 \T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it i s not rec-om-mended) when Underfull \hbox (badness 1831) in paragraph at lines 6941--6947 \T1/ptm/m/n/10 writ-ing it should be writ-ten ex-plic-itly, e.g. by \T1/zi4/m/n /10 writeChar("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or [107] Underfull \hbox (badness 3568) in paragraph at lines 7003--7010 \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 [108] [109] Underfull \vbox (badness 3803) has occurred while \output is active [110] Underfull \vbox (badness 10000) has occurred while \output is active [111] [112] Underfull \hbox (badness 1077) in paragraph at lines 7330--7336 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7330--7336 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [113] [114] [115] [116] [117] [118] Underfull \hbox (badness 2096) in paragraph at lines 7671--7675 \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 . [119] [120] Underfull \hbox (badness 2351) in paragraph at lines 7789--7792 [][][]\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 , [121] [122] [123] [124] [125] Underfull \hbox (badness 4479) in paragraph at lines 8115--8125 [][][]\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), [126] [127] [128] [129] [130] [131] Underfull \hbox (badness 1629) in paragraph at lines 8562--8574 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 1609) in paragraph at lines 8562--8574 \T1/ptm/m/n/10 there is a prob-lem in the POSIX/C99 stan-dard with \T1/zi4/m/n/ 10 "1969-12-31 23:59:59 UTC"\T1/ptm/m/n/10 , which Underfull \hbox (badness 2426) in paragraph at lines 8562--8574 \T1/ptm/m/n/10 is \T1/zi4/m/n/10 -1 \T1/ptm/m/n/10 in cal-en-dar time and that value is on those OSes also used as an er-ror code. [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] Underfull \hbox (badness 1178) in paragraph at lines 9298--9302 []\T1/ptm/m/n/10 If true, [][]\T1/zi4/m/n/10 list[][][]\T1/ptm/m/n/10 s and ato mic vec-tors with non-[][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 names (see [][ ]\T1/zi4/m/n/10 names[][][]\T1/ptm/m/n/10 ) are de- [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] Underfull \hbox (badness 1735) in paragraph at lines 10446--10450 \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 . [161] [162] [163] [164] [165] [166] [167] Underfull \hbox (badness 6396) in paragraph at lines 10885--10893 []\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 1946) in paragraph at lines 10885--10893 \T1/zi4/m/n/10 duplicated \T1/ptm/m/n/10 and \T1/zi4/m/n/10 anyDuplicated\T1/pt m/m/n/10 , \T1/zi4/m/n/10 anyDuplicated(x,...) \T1/ptm/m/n/10 is a ``gen-er-al- ized'' short-cut for [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] Underfull \hbox (badness 4569) in paragraph at lines 12002--12006 []\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 12002--12006 \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 [184] Underfull \vbox (badness 10000) has occurred while \output is active [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] Underfull \hbox (badness 2253) in paragraph at lines 13665--13667 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [209] [210] Underfull \hbox (badness 1565) in paragraph at lines 13738--13742 [][][]\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 Underfull \hbox (badness 4927) in paragraph at lines 13782--13784 []\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 \T1/zi4 /m/n/10 fsep = [211] [212] Underfull \hbox (badness 3148) in paragraph at lines 13875--13880 [][][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[ ][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 help[][][]\T1/ptm/m/n/10 ; [][]\T1/zi4 /m/n/10 RShowDoc[][][] \T1/ptm/m/n/10 call \T1/zi4/m/n/10 file.show() \T1/ptm/m /n/10 for \T1/zi4/m/n/10 type = "text"\T1/ptm/m/n/10 . Con-sider [213] Underfull \hbox (badness 1466) in paragraph at lines 13922--13925 []\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 [214] Underfull \hbox (badness 10000) in paragraph at lines 14049--14053 [][][]\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 14060--14063 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [215] [216] [217] [218] [219] Underfull \hbox (badness 3965) in paragraph at lines 14352--14356 []\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, [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] Underfull \hbox (badness 4429) in paragraph at lines 15128--15131 []\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 [232] [233] Underfull \hbox (badness 10000) in paragraph at lines 15234--15236 []\T1/ptm/m/n/10 This works via \T1/zi4/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic h calls Underfull \hbox (badness 1215) in paragraph at lines 15234--15236 \T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times in this case, see Underfull \hbox (badness 10000) in paragraph at lines 15256--15261 []\T1/ptm/m/n/10 For num-bers, \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 calls \T 1/zi4/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls Underfull \hbox (badness 1558) in paragraph at lines 15256--15261 \T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero)\T1/ptm/m/n/10 . (\T1/ptm/m /it/10 ``when needed''\T1/ptm/m/n/10 : when \T1/zi4/m/n/10 zero.print \T1/ptm/m /n/10 is not Underfull \hbox (badness 10000) in paragraph at lines 15268--15272 []\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 Underfull \hbox (badness 2426) in paragraph at lines 15268--15272 \T1/zi4/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi ves \T1/zi4/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . If you want [234] Underfull \hbox (badness 2035) in paragraph at lines 15307--15311 []\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 within [235] Underfull \vbox (badness 10000) has occurred while \output is active [236] [237] [238] [239] [240] [241] [242] [243] Underfull \hbox (badness 2452) in paragraph at lines 15906--15910 []\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 15906--15910 \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 [244] [245] [246] Underfull \hbox (badness 1092) in paragraph at lines 16079--16084 [][]\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 [247] [248] [249] Underfull \hbox (badness 6741) in paragraph at lines 16329--16333 \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 , [250] [251] [252] [253] [254] [255] [256] [257] [258] Underfull \vbox (badness 3803) has occurred while \output is active [259] Underfull \vbox (badness 10000) has occurred while \output is active [260] [261] [262] [263] [264] [265] [266] [267] [268] [269] Underfull \hbox (badness 1478) in paragraph at lines 17622--17625 []\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 [270] [271] [272] [273] Underfull \hbox (badness 10000) in paragraph at lines 17877--17879 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [274] [275] [276] [277] [278] [279] [280] [281] [282] Underfull \hbox (badness 1442) in paragraph at lines 18477--18479 []\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 [283] Underfull \hbox (badness 2452) in paragraph at lines 18569--18585 [][][]\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 , [284] [285] [286] [287] [288] [289] [290] Underfull \hbox (badness 1248) in paragraph at lines 18988--18991 []\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 , [291] [292] [293] [294] Underfull \hbox (badness 4739) in paragraph at lines 19246--19248 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [295] [296] [297] [298] [299] [300] Underfull \hbox (badness 1596) in paragraph at lines 19665--19670 \T1/ptm/m/n/10 trix or, if \T1/zi4/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/zi4/m/n/10 simplify2array()\T1/ptm /m/n/10 . [301] [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] Underfull \hbox (badness 2469) in paragraph at lines 20269--20274 []\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 20283--20290 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [312] Underfull \hbox (badness 10000) in paragraph at lines 20357--20361 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 20357--20361 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$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 ' [313] [314] Underfull \hbox (badness 1014) in paragraph at lines 20527--20532 []\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 [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] Underfull \hbox (badness 1264) in paragraph at lines 21317--21322 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [327] Underfull \hbox (badness 4441) in paragraph at lines 21346--21349 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 , [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] Underfull \hbox (badness 6047) in paragraph at lines 22093--22095 []\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 \T1/zi4/m/n/10 make.unique(c(A,B)) == [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] Underfull \hbox (badness 1077) in paragraph at lines 23134--23140 \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 . [356] [357] [358] [359] [360] [361] [362] [363] Underfull \hbox (badness 2790) in paragraph at lines 23630--23633 []\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 23630--23633 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [364] [365] [366] [367] [368] Underfull \hbox (badness 1194) in paragraph at lines 23912--23915 []\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 [369] [370] [371] Underfull \hbox (badness 2368) in paragraph at lines 24118--24124 []\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 list, i.e., Underfull \hbox (badness 4981) in paragraph at lines 24118--24124 \T1/zi4/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are al so given by [][]\T1/zi4/m/n/10 ls[][][](env,all.names = [372] [373] [374] [375] [376] [377] Underfull \hbox (badness 10000) in paragraph at lines 24500--24503 []\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by [378] [379] [380] [381] [382] [383] [384] [385] [386] Underfull \hbox (badness 10000) in paragraph at lines 25105--25107 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than \T1/zi4/m/n/10 pkg %in% [387] [388] [389] [390] [391] [392] [393] [394] [395] [396] [397] [398] [399] Underfull \hbox (badness 1038) in paragraph at lines 25945--25953 []\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 1735) in paragraph at lines 25945--25953 \T1/ptm/m/n/10 set from value of the en-vi-ron-ment vari-able \T1/zi4/m/n/10 R_ DEFAULT_PACKAGES\T1/ptm/m/n/10 , or if that is un- Underfull \hbox (badness 1292) in paragraph at lines 25945--25953 \T1/ptm/m/n/10 set to \T1/zi4/m/n/10 c("datasets","utils","grDevices","graphics ","stats","methods")\T1/ptm/m/n/10 . (Set Underfull \hbox (badness 1881) in paragraph at lines 25954--25957 []\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 25973--25975 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [400] [401] Underfull \hbox (badness 2142) in paragraph at lines 26114--26118 []\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 26164--26169 []\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 [402] [403] [404] [405] Underfull \hbox (badness 10000) in paragraph at lines 26452--26458 []\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 26452--26458 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 26452--26458 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 26465--26468 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 26491--26493 []\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 26526--26531 []\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 2529) in paragraph at lines 26532--26543 \T1/ptm/m/n/10 in-di-rectly [][]\T1/zi4/m/n/10 update.packages[][][]\T1/ptm/m/n /10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si- Underfull \hbox (badness 2512) in paragraph at lines 26532--26543 \T1/ptm/m/n/10 ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi4/m /n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use and [406] Underfull \hbox (badness 7203) in paragraph at lines 26544--26547 []\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 10000) in paragraph at lines 26568--26573 []\T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma -cOS build), Underfull \hbox (badness 2057) in paragraph at lines 26568--26573 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). [407] [408] [409] [410] [411] [412] [413] [414] Underfull \hbox (badness 10000) in paragraph at lines 27086--27089 []\T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 str2lang(s ) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of [415] Underfull \hbox (badness 7925) in paragraph at lines 27165--27169 []\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 vec-to r \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n /10 cor-re-sponds to Underfull \hbox (badness 1622) in paragraph at lines 27165--27169 [][]\T1/zi4/m/n/10 parse[][][](text = s,keep.source=FALSE)\T1/ptm/m/n/10 , whic h is al-ways of type ([][]\T1/zi4/m/n/10 typeof[][][]\T1/ptm/m/n/10 ) and [][]\ T1/zi4/m/n/10 class[][][] Underfull \hbox (badness 6125) in paragraph at lines 27170--27179 []\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 string \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2lang(s) \T1/ptm/m/n/10 cor -re-sponds to [][]\T1/zi4/m/n/10 parse[][][](text = [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] Underfull \hbox (badness 2726) in paragraph at lines 27891--27894 []\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 [427] [428] [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] Underfull \vbox (badness 3803) has occurred while \output is active [445] [446] [447] [448] [449] [450] [451] [452] Underfull \hbox (badness 1533) in paragraph at lines 29582--29585 []\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 [453] [454] [455] Underfull \hbox (badness 1163) in paragraph at lines 29745--29756 []\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 [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] [473] [474] [475] [476] [477] [478] [479] Underfull \hbox (badness 10000) in paragraph at lines 31291--31295 []\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 31291--31295 \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 31313--31315 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [480] [481] [482] [483] [484] [485] [486] [487] [488] Underfull \hbox (badness 1655) in paragraph at lines 31869--31871 []\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 [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] Underfull \hbox (badness 2261) in paragraph at lines 32988--32993 []\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 [506] Underfull \hbox (badness 10000) in paragraph at lines 33015--33021 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1484) in paragraph at lines 33015--33021 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal and hex-adec-i-mal rep-re-sen-ta-tions like [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] Underfull \hbox (badness 1072) in paragraph at lines 36157--36161 []\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 36162--36166 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 36190--36196 []\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 36190--36196 \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 36190--36196 \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 3009) in paragraph at lines 36202--36209 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 36202--36209 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 36202--36209 \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 36202--36209 \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 [555] [556] [557] [558] [559] [560] Underfull \hbox (badness 1142) in paragraph at lines 36556--36562 []\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 \T1/zi4/m/n/10 "%Y-%m-%d [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] Underfull \hbox (badness 1565) in paragraph at lines 37829--37831 []\T1/ptm/m/n/10 integer code used in \T1/zi4/m/n/10 quantile(*,type=quantile.t ype) \T1/ptm/m/n/10 for the de-fault [581] [582] [583] [584] [585] [586] [587] [588] [589] [590] Underfull \hbox (badness 4967) in paragraph at lines 38428--38433 []\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 [591] [592] Underfull \hbox (badness 1616) in paragraph at lines 38541--38546 \T1/zi4/m/n/10 system("id") \T1/ptm/m/n/10 is much more portable on Unix-alikes , pro-vided only the POSIX op-tions [593] [594] [595] [596] [597] [598] [599] [600] Underfull \hbox (badness 1472) in paragraph at lines 39067--39070 []\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 [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614] Underfull \hbox (badness 10000) in paragraph at lines 39981--39985 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/zi4/m/n/10 length(bin) > [615] [616] [617] [618] Underfull \hbox (badness 10000) in paragraph at lines 40232--40235 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [619] [620] [621] Underfull \hbox (badness 10000) in paragraph at lines 40416--40420 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [622] [623] [624] [625] [626] [627] [628] [629] [630] Underfull \hbox (badness 10000) in paragraph at lines 41029--41032 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[ ]zones / [631] [632] [633] [634] [635] [636] Underfull \vbox (badness 10000) has occurred while \output is active [637] [638] [639] [640] [641] [642] [643] [644] Underfull \hbox (badness 1990) in paragraph at lines 41933--41941 []\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 41933--41941 \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 [645] [646] [647] [648] [649] [650] [651] [652] Underfull \hbox (badness 1917) in paragraph at lines 42439--42446 []\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 [653] [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] Underfull \hbox (badness 3668) in paragraph at lines 43168--43170 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [664] [665] Underfull \hbox (badness 2401) in paragraph at lines 43296--43300 []\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 [666] [667] [668] Underfull \hbox (badness 2111) in paragraph at lines 43485--43490 \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 10000) in paragraph at lines 43506--43511 []\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 [669] [670] [671] [672] [673] [674] [675] [676] [677] Underfull \hbox (badness 5417) in paragraph at lines 44088--44092 []\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 [678] Underfull \hbox (badness 10000) in paragraph at lines 44149--44153 []\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 [679] [680]) (./compiler-pkg.tex Chapter 2. [681] [682] [683] [684]) (./datasets-pkg.tex Chapter 3. [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] Underfull \hbox (badness 1097) in paragraph at lines 1031--1035 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] Underfull \vbox (badness 1448) has occurred while \output is active [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] Overfull \vbox (19.74611pt too high) has occurred while \output is active [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] Underfull \vbox (badness 10000) has occurred while \output is active [753] [754] [755] [756] Underfull \vbox (badness 10000) has occurred while \output is active [757] [758] [759] [760] [761] [762] [763] [764] [765] [766]) (./grDevices-pkg.tex Chapter 4. [767] [768] [769] [770] [771] Underfull \hbox (badness 3158) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/zi4/m/n/10 c(mi,ma,n.)\T1/ptm /m/n/10 , with iden-ti-cal mean-ing to Underfull \hbox (badness 10000) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][]\T1/zi4/m/n/10 axisTicks[][][]() \T1/ptm/ m/n/10 just calls the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/ptm/m/n/1 0 in Underfull \hbox (badness 1852) in paragraph at lines 298--303 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 /src/main/plot.c\T1/ptm/m/n/10 ' which is also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t ion [772] [773] [774] [775] [776] [777] [778] [779] Underfull \hbox (badness 1424) in paragraph at lines 830--832 [][][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 (as in-te-ger or char-ac-ter) and \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 mean trans-par-ent, which can also be spec-i -fied as [780] [781] [782] [783] [784] Underfull \hbox (badness 5175) in paragraph at lines 1124--1126 []\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 [785] [786] [787] [788] Underfull \hbox (badness 1852) in paragraph at lines 1326--1329 []\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 [789] [790] [791] Underfull \hbox (badness 1490) in paragraph at lines 1532--1537 \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 [792] [793] [794] [795] [796] [797] Underfull \hbox (badness 1325) in paragraph at lines 1938--1948 \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 , [798] [799] Underfull \hbox (badness 10000) in paragraph at lines 2050--2052 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [800] [801] [802] Underfull \hbox (badness 6758) in paragraph at lines 2228--2231 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [803] [804] [805] [806] [807] [808] [809] [810] [811] [812] Underfull \hbox (badness 10000) in paragraph at lines 2832--2833 [813] [814] [815] [816] [817] [818] [819] [820] [821] Underfull \hbox (badness 10000) in paragraph at lines 3388--3393 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [822] [823] [824] [825] [826] Underfull \vbox (badness 10000) has occurred while \output is active [827] Underfull \hbox (badness 10000) in paragraph at lines 3789--3792 []\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 [828] [829] [830] [831] [832] [833] [834] [835] [836] [837] [838] Underfull \hbox (badness 10000) in paragraph at lines 4518--4523 [][][]$\T1/zi4/m/n/10 https : / / www . adobe . com / content / dam / acom / en / devnet / actionscript / articles / PLRM . pdf$[][] Underfull \hbox (badness 4181) in paragraph at lines 4518--4523 \T1/ptm/m/n/10 or PDF [][]$\T1/zi4/m/n/10 https : / / www . adobe . com / devne t / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in [839] Underfull \vbox (badness 10000) has occurred while \output is active [840] [841] Underfull \hbox (badness 1067) in paragraph at lines 4672--4679 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [842] [843] [844] [845] Underfull \hbox (badness 1377) in paragraph at lines 4975--4980 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [846] Underfull \hbox (badness 1418) in paragraph at lines 5051--5058 \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 1755) in paragraph at lines 5069--5071 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [847] [848] Underfull \hbox (badness 1377) in paragraph at lines 5180--5185 []\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 [849] Underfull \hbox (badness 7344) in paragraph at lines 5249--5251 []\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 [850] [851] Underfull \hbox (badness 2035) in paragraph at lines 5384--5393 []\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 5384--5393 \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 5384--5393 \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 , [852] Underfull \hbox (badness 10000) in paragraph at lines 5452--5459 []\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 5452--5459 \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 . [853] [854] [855] Underfull \hbox (badness 1546) in paragraph at lines 5594--5602 []\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 , [856] [857] [858] [859] [860] [861] [862] [863] Underfull \hbox (badness 10000) in paragraph at lines 6129--6132 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [864] [865] [866] [867] [868] [869] [870] [871] [872] [873] [874] [875] [876] Underfull \hbox (badness 1189) in paragraph at lines 6951--6953 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [877] Underfull \hbox (badness 10000) in paragraph at lines 7049--7051 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [878] [879] [880] [881] [882] Underfull \hbox (badness 3780) in paragraph at lines 7349--7355 []\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 , [883] [884] [885] Underfull \hbox (badness 2680) in paragraph at lines 7550--7552 []\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 [886] [887] [888]) (./graphics-pkg.tex Chapter 5. [889] [890] [891] [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] Underfull \hbox (badness 4634) in paragraph at lines 1351--1354 [][][]\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 , [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] Underfull \hbox (badness 1728) in paragraph at lines 2308--2310 []\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use \T1/zi4/m/n/10 "n " \T1/ptm/m/n/10 to sup-press and see also [927] [928] Underfull \hbox (badness 1009) in paragraph at lines 2399--2406 \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 [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] [947] [948] [949] [950] Underfull \vbox (badness 10000) has occurred while \output is active [951] [952] [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] Underfull \hbox (badness 3229) in paragraph at lines 4544--4549 []\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 [964] [965] [966] [967] [968] Underfull \hbox (badness 10000) in paragraph at lines 4901--4907 []\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 4901--4907 \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 [969] Underfull \hbox (badness 10000) in paragraph at lines 5032--5035 [970] Underfull \hbox (badness 10000) in paragraph at lines 5093--5095 [971 >/library/graphics/help/figures/ mai.pdf>] [972 >/library/graphics/hel p/figures/oma.pdf>] [973] Underfull \hbox (badness 10000) in paragraph at lines 5283--5285 []\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 [974] Underfull \vbox (badness 3803) has occurred while \output is active [975] [976] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6761--6762 [][] [997] [998 >/library/graphics/help/fi gures/pch.pdf>] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] Underfull \hbox (badness 2012) in paragraph at lines 7586--7589 []\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 poi nt [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] Underfull \hbox (badness 10000) in paragraph at lines 8846--8848 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8848--8850 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1032]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8928 \HeaderA{units}{Graphical Units}{units} [1033] [1034] [1035] [1036]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] Underfull \hbox (badness 2680) in paragraph at lines 483--486 []\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 [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] Underfull \hbox (badness 4279) in paragraph at lines 1064--1073 [][][]\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 , [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] Underfull \vbox (badness 10000) has occurred while \output is active [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] Underfull \hbox (badness 1067) in paragraph at lines 4486--4489 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1113] [1114] [1115] [1116] Underfull \hbox (badness 7256) in paragraph at lines 4731--4733 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \hbox (badness 1824) in paragraph at lines 6535--6538 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like \T1/zi4/m/n/10 depth [1148] [1149] [1150] [1151]) (./methods-pkg.tex [1152] Chapter 7. [1153] [1154] [1155] [1156] [1157] [1158] [1159] [1160] Underfull \vbox (badness 10000) has occurred while \output is active [1161] Underfull \vbox (badness 10000) has occurred while \output is active [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171] Underfull \hbox (badness 2237) in paragraph at lines 1385--1387 []\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 [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] Underfull \hbox (badness 2181) in paragraph at lines 1932--1939 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/zi4/m/n/10 is(x,"refClass") \T1/ptm/m/n/10 tests [1180] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\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 1981--1986 \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 [1181] [1182] [1183] Underfull \hbox (badness 2213) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/zi4/m/n/10 where = [1184] [1185] [1186] [1187] [1188] Underfull \hbox (badness 10000) in paragraph at lines 2574--2577 []\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 [1189] [1190] Underfull \hbox (badness 1132) in paragraph at lines 2714--2718 []\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 [1191] Underfull \hbox (badness 1033) in paragraph at lines 2746--2751 \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 [1192] [1193] [1194] [1195] [1196] [1197] [1198] Underfull \hbox (badness 1102) in paragraph at lines 3303--3305 []\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 [1199] [1200] [1201] [1202] [1203] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\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 [1204] Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1205] Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [] \T1/zi4/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude = "numeric",altitude [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] Underfull \hbox (badness 1769) in paragraph at lines 4472--4478 []\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 4472--4478 \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 [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] Underfull \vbox (badness 10000) has occurred while \output is active [1227] [1228] [1229] Underfull \hbox (badness 4036) in paragraph at lines 5437--5440 []\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 [1230] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1231] [1232] [1233] [1234] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] Underfull \hbox (badness 1675) in paragraph at lines 6451--6457 \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 [1243] [1244] [1245] [1246] Underfull \vbox (badness 10000) has occurred while \output is active [1247] [1248] [1249] [1250]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1251] [1252] [1253]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} [1254] Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1255] [1256] [1257] Underfull \hbox (badness 1286) in paragraph at lines 7484--7486 []\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 [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] Underfull \vbox (badness 10000) has occurred while \output is active [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] Underfull \hbox (badness 1137) in paragraph at lines 10011--10019 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/n/10 ne w("signature",functionDef,...)\T1/ptm/m/n/10 . The [1293] [1294] [1295] [1296] [1297] [1298] [1299] Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., [1300] [1301] [1302] [1303]) (./parallel-pkg.tex [1304] Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\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 [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] [1324] [1325] Underfull \hbox (badness 3386) in paragraph at lines 1365--1368 []\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 [1326] [1327] [1328]) (./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 [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344]) (./stats-pkg.tex Chapter 10. [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] Underfull \hbox (badness 1412) in paragraph at lines 875--877 []\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 [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] Underfull \hbox (badness 2503) in paragraph at lines 1356--1359 []\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 , [1367] [1368] [1369] Underfull \hbox (badness 10000) in paragraph at lines 1536--1540 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov","lm") \T1/ptm/m/n/1 0 or for mul-ti-ple re-sponses of class [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] Underfull \hbox (badness 2503) in paragraph at lines 3437--3440 []\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 , [1400] [1401] [1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] Underfull \hbox (badness 1127) in paragraph at lines 4351--4354 []\T1/ptm/m/n/10 standardized resid-u-als, \T1/zi4/m/n/10 (observed -expected) / sqrt(V)\T1/ptm/m/n/10 , where \T1/zi4/m/n/10 V \T1/ptm/m/n/10 is the [1415] [1416] [1417] [1418] [1419] Underfull \hbox (badness 3989) in paragraph at lines 4681--4688 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] Underfull \hbox (badness 2556) in paragraph at lines 5317--5320 []\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 5334--5336 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/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 [1430] [1431] [1432] [1433] [1434] [1435] [1436] Underfull \hbox (badness 2503) in paragraph at lines 5726--5730 []\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 , [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] Underfull \hbox (badness 7081) in paragraph at lines 6520--6523 []\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 6524--6526 []\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 [1450] [1451] [1452] [1453] [1454] Underfull \vbox (badness 3803) has occurred while \output is active [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] Underfull \hbox (badness 10000) in paragraph at lines 7369--7372 []\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 [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] Underfull \vbox (badness 10000) has occurred while \output is active [1485] [1486] [1487] [1488] [1489] Underfull \hbox (badness 2626) in paragraph at lines 9048--9051 []\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 [1490] [1491] Underfull \hbox (badness 2503) in paragraph at lines 9155--9159 []\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 , [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] [1509] [1510] [1511] Underfull \hbox (badness 4518) in paragraph at lines 10469--10474 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1512] [1513] [1514] [1515] [1516] Underfull \hbox (badness 2142) in paragraph at lines 10830--10833 []\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 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10849--10852 []\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, [1517] Underfull \hbox (badness 1708) in paragraph at lines 10911--10915 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1518] [1519] [1520] [1521] [1522] [1523] Underfull \hbox (badness 1694) in paragraph at lines 11307--11310 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531]pdfTeX warning (ext4): d estination with the same identifier (name{Rfn.hat}) has been already used, dupl icate ignored \relax l.11791 \aliasA{hat}{influence.measures}{hat} [1532] [1533] Underfull \hbox (badness 1484) in paragraph at lines 11926--11928 []\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 [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] Underfull \hbox (badness 10000) in paragraph at lines 12519--12521 []\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 \T1/zi4/m/n/10 SSinit = [1544] [1545] [1546] [1547] [1548] [1549] Underfull \hbox (badness 2894) in paragraph at lines 12855--12859 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] Underfull \hbox (badness 4518) in paragraph at lines 13605--13610 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] Underfull \hbox (badness 4518) in paragraph at lines 14257--14262 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1572] [1573] Underfull \hbox (badness 8151) in paragraph at lines 14395--14399 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = "interp olate",statistics = Underfull \hbox (badness 1199) in paragraph at lines 14402--14404 []\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 [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] Underfull \hbox (badness 2503) in paragraph at lines 15473--15477 []\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 , [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] Underfull \hbox (badness 4621) in paragraph at lines 15985--15991 []\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 [1600] [1601] [1602] [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] [1623] [1624] [1625] [1626] [1627] Underfull \vbox (badness 10000) has occurred while \output is active [1628] Underfull \vbox (badness 10000) has occurred while \output is active [1629] [1630] [1631] [1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] Underfull \hbox (badness 1377) in paragraph at lines 18588--18593 []\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 18593--18596 []\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 [1642] Underfull \hbox (badness 2343) in paragraph at lines 18606--18610 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 3471) in paragraph at lines 18606--18610 \T1/ptm/m/n/10 the value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + re ltol) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18614--18618 []\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 [1643] [1644] [1645] Overfull \hbox (15.73795pt too wide) in paragraph at lines 18839--18839 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 18842--18842 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] Underfull \vbox (badness 10000) has occurred while \output is active [1646] [1647] [1648] [1649] [1650] [1651] [1652] Underfull \hbox (badness 1337) in paragraph at lines 19264--19267 []\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 [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] Underfull \hbox (badness 3049) in paragraph at lines 19760--19764 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1662] [1663] [1664] [1665] Underfull \hbox (badness 1194) in paragraph at lines 20018--20021 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1666] [1667] [1668] [1669] [1670] [1671] [1672] Underfull \hbox (badness 2503) in paragraph at lines 20397--20400 []\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 , Underfull \hbox (badness 3919) in paragraph at lines 20424--20426 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or \T1/zi4/m/n/10 "Comparison of Poisson [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] [1688] [1689] [1690] Underfull \hbox (badness 10000) in paragraph at lines 21501--21507 []\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 , [1691] [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] Underfull \hbox (badness 1337) in paragraph at lines 22855--22861 []\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 [1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] Overfull \hbox (27.74408pt too wide) in paragraph at lines 23420--23420 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1722] [1723] [1724] [1725] [1726] Underfull \hbox (badness 10000) in paragraph at lines 23671--23674 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 4205) in paragraph at lines 23671--23674 \T1/zi4/m/n/10 cutree(hclust.obj,k = k)\T1/ptm/m/n/10 , can be spec-i-fied for ef-fi-ciency if al-ready [1727] [1728] [1729] [1730] [1731] [1732] [1733] [1734] [1735] Underfull \hbox (badness 1824) in paragraph at lines 24257--24263 []\T1/ptm/m/n/10 Here, all the NAs in \T1/zi4/m/n/10 x \T1/ptm/m/n/10 are first re-placed by al-ter- Underfull \hbox (badness 1033) in paragraph at lines 24257--24263 \T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/ m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where [1736] Underfull \hbox (badness 10000) in paragraph at lines 24278--24281 []\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 \T1/zi4/m/n/10 y[j] = Underfull \hbox (badness 3690) in paragraph at lines 24347--24351 [][][]\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 [1737] Underfull \vbox (badness 3803) has occurred while \output is active [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] Underfull \hbox (badness 2165) in paragraph at lines 24856--24861 []\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm /m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1 0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [1746] [1747] [1748] [1749] Underfull \hbox (badness 1867) in paragraph at lines 25061--25063 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 25074--25078 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u se.fallback) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 PP [1750] [1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] Underfull \vbox (badness 3803) has occurred while \output is active [1761] [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] [1771] [1772] [1773] Underfull \vbox (badness 10000) has occurred while \output is active [1774] Underfull \hbox (badness 3514) in paragraph at lines 26634--26639 []\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 [1775] [1776] [1777] [1778] Overfull \hbox (2.23795pt too wide) in paragraph at lines 26868--26868 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1779] Underfull \hbox (badness 3514) in paragraph at lines 26904--26910 []\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 [1780] [1781] [1782] [1783] Underfull \hbox (badness 3514) in paragraph at lines 27118--27123 []\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 [1784] Underfull \hbox (badness 3514) in paragraph at lines 27205--27210 []\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 [1785] Underfull \hbox (badness 3514) in paragraph at lines 27270--27275 []\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 [1786] [1787] Underfull \hbox (badness 3514) in paragraph at lines 27364--27369 []\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 [1788] [1789] Underfull \hbox (badness 6691) in paragraph at lines 27456--27461 []\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 [1790] [1791] [1792] [1793] [1794] [1795] [1796] [1797] Underfull \hbox (badness 4024) in paragraph at lines 27984--27987 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion , which [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] Underfull \hbox (badness 5431) in paragraph at lines 28590--28592 []\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 [1808] [1809] [1810] [1811] Underfull \hbox (badness 5431) in paragraph at lines 28800--28803 []\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 [1812] [1813] [1814] [1815] [1816] Underfull \hbox (badness 1337) in paragraph at lines 29114--29118 []\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 [1817] [1818] [1819] [1820] [1821] Underfull \hbox (badness 1616) in paragraph at lines 29416--29419 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1822] [1823] [1824] [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] [1835] [1836] [1837] [1838] [1839] [1840] Underfull \hbox (badness 3557) in paragraph at lines 30546--30550 []\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 \T1/zi4 /m/n/10 interval = [1841] [1842] [1843] Underfull \vbox (badness 10000) has occurred while \output is active [1844] [1845] [1846] Underfull \hbox (badness 1337) in paragraph at lines 30910--30914 []\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 [1847] [1848] [1849] [1850] [1851] [1852] [1853] [1854] [1855] Underfull \hbox (badness 1337) in paragraph at lines 31437--31441 []\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 [1856] [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865]) (./stats4-pkg.tex [1866] Chapter 11. [1867] [1868] [1869] [1870] [1871] [1872]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} [1873] [1874] [1875]) (./tcltk-pkg.tex [1876] Chapter 12. [1877] [1878] [1879] [1880] [1881] [1882] [1883] Underfull \vbox (badness 10000) has occurred while \output is active [1884] Underfull \vbox (badness 10000) has occurred while \output is active [1885] 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 [1886] [1887] [1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897]) (./tools-pkg.tex [1898] Chapter 13. [1899] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1900] 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 [1901] [1902] 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 [1903] [1904] 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 [1905] [1906] [1907] [1908] [1909] [1910] [1911] [1912] [1913] [1914] [1915] [1916] [1917] Underfull \hbox (badness 4441) in paragraph at lines 1139--1149 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- Underfull \hbox (badness 1014) in paragraph at lines 1163--1165 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1169--1171 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous [1918] Underfull \hbox (badness 10000) in paragraph at lines 1206--1209 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1206--1209 \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 , [1919] [1920] [1921] [1922] [1923] Underfull \hbox (badness 2293) in paragraph at lines 1558--1560 []\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with its func-tion-al-ity in-te-grated into that of [1924] [1925] [1926] Underfull \hbox (badness 7981) in paragraph at lines 1696--1701 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 1082) in paragraph at lines 1703--1705 []\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 [1927] [1928] [1929]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1930] [1931] [1932] [1933] [1934] [1935] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2202--2202 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1936] [1937] [1938] Underfull \hbox (badness 7981) in paragraph at lines 2371--2377 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1939] [1940] [1941] [1942] [1943] [1944] [1945] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2846. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2847. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2847. [1946] [1947] [1948] [1949] [1950] Underfull \hbox (badness 1424) in paragraph at lines 3128--3130 []\T1/zi4/m/it/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 [1951] [1952] [1953] [1954] [1955] [1956] [1957] [1958] [1959] [1960] [1961] Underfull \hbox (badness 10000) in paragraph at lines 3832--3834 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1962] [1963] Underfull \hbox (badness 10000) in paragraph at lines 3971--3974 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/it/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/it/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1964] [1965] Underfull \hbox (badness 1137) in paragraph at lines 4073--4075 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1966] [1967] [1968] [1969] [1970] Underfull \hbox (badness 1796) in paragraph at lines 4381--4386 []\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over \T 1/zi4/m/it/10 write_PACKAGES \T1/ptm/m/n/10 in the \T1/zi4/m/it/10 type == [1971] Underfull \hbox (badness 1838) in paragraph at lines 4455--4461 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/it/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/it/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4455--4461 \T1/ptm/m/n/10 `\T1/zi4/m/it/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 [1972] [1973] [1974] Underfull \hbox (badness 2197) in paragraph at lines 4671--4681 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/it/10 available.packages[][][]\T1/ptm/m/n/10 : [1975] Underfull \hbox (badness 1571) in paragraph at lines 4734--4738 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [1976] [1977] [1978]) (./utils-pkg.tex Chapter 14. [1979] 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/it/10 insertions\T1/ptm/m/n/10 ', [1980] [1981] [1982] [1983] [1984] Underfull \hbox (badness 10000) in paragraph at lines 376--381 \T1/zi4/m/it/10 c("vertical","horizontal","cascade","minimize","restore") \T1/p tm/m/n/10 with [1985] [1986] [1987] [1988] [1989] Underfull \hbox (badness 10000) in paragraph at lines 717--723 []\T1/ptm/m/n/10 Functions \T1/zi4/m/it/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/it/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 717--723 \T1/zi4/m/it/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/it/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1990] [1991] Underfull \hbox (badness 5847) in paragraph at lines 850--856 []\T1/ptm/m/n/10 Argument \T1/zi4/m/it/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 850--856 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/it/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1992] Underfull \hbox (badness 3861) in paragraph at lines 918--923 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/it/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/it/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/it/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1993] [1994] Underfull \hbox (badness 3323) in paragraph at lines 1089--1097 []\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/zi4/m/it/1 0 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1 /ptm/m/n/10 , in-di-cat- Underfull \hbox (badness 2961) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f or-mat- Underfull \hbox (badness 3919) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 3735) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/it/10 getOption[][][]("citation.bibtex.ma x",1) \T1/ptm/m/n/10 which is \T1/zi4/m/it/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by [1995] Underfull \hbox (badness 10000) in paragraph at lines 1101--1103 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1996] [1997] Underfull \vbox (badness 3803) has occurred while \output is active [1998] [1999] [2000] [2001] [2002] Underfull \hbox (badness 1371) in paragraph at lines 1606--1608 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/it/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/it/10 ccaddress \T1/ptm/m/n/10 to pass to [2003] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 1676. [2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] Underfull \hbox (badness 2057) in paragraph at lines 2215--2217 []\T1/ptm/m/n/10 None for \T1/zi4/m/it/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [2013] [2014] [2015] [2016] [2017] [2018]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.clipboard}) has been already used, duplicate ig nored \relax l.2566 ... the Clipboard in MS Windows}{clipboard} [2019] [2020] Underfull \hbox (badness 1748) in paragraph at lines 2733--2736 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/it/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/it/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/it/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [2021] [2022] [2023] [2024] [2025] [2026] [2027] Underfull \hbox (badness 5388) in paragraph at lines 3142--3146 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/it/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/it/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/it/10 .TXT\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/it/10 read.table[][][](...,header = Underfull \hbox (badness 2285) in paragraph at lines 3147--3150 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/it/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/it/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/it/10 read.table[] [][](...,header = TRUE,sep = [2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] Underfull \hbox (badness 1430) in paragraph at lines 3906--3914 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/it/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [2039] Underfull \hbox (badness 1231) in paragraph at lines 3983--3995 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [2040] [2041] Underfull \hbox (badness 10000) in paragraph at lines 4141--4143 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/it/10 dow nload.file[][][] \T1/ptm/m/n/10 and [2042] [2043] [2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.4839 ...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.4839 ...mat Unordered and Ordered Lists}{format} [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] Underfull \hbox (badness 1622) in paragraph at lines 5358--5362 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 5990. Underfull \hbox (badness 1371) in paragraph at lines 5994--5996 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/it/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/it/10 ccaddress \T1/ptm/m/n/10 to pass to [2072] Underfull \hbox (badness 1502) in paragraph at lines 6083--6088 []\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 6083--6088 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2073] [2074] [2075] Underfull \hbox (badness 10000) in paragraph at lines 6256--6265 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2076] Underfull \hbox (badness 2150) in paragraph at lines 6320--6323 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2077] [2078] Underfull \hbox (badness 3118) in paragraph at lines 6458--6460 []\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 [2079] [2080] [2081] Underfull \hbox (badness 1325) in paragraph at lines 6630--6634 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/it/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able Underfull \hbox (badness 4726) in paragraph at lines 6642--6648 \T1/ptm/m/n/10 used if \T1/zi4/m/it/10 repos = NULL\T1/ptm/m/n/10 . Can also be a char-ac-ter vec-tor, a sub-set of [2082] Underfull \hbox (badness 10000) in paragraph at lines 6714--6717 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be Underfull \hbox (badness 10000) in paragraph at lines 6714--6717 \T1/ptm/m/n/10 passed to \T1/zi4/m/it/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou rce pack-age in-stall. E.g., [2083] Underfull \hbox (badness 3219) in paragraph at lines 6790--6797 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/it/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6790--6797 \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 6790--6797 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1596) in paragraph at lines 6790--6797 [][]\T1/zi4/m/it/10 getOption[][][]("install.packages.compile.from.source")\T1/ ptm/m/n/10 . \T1/zi4/m/it/10 type = "both" \T1/ptm/m/n/10 will be silently Underfull \hbox (badness 2932) in paragraph at lines 6798--6801 []\T1/ptm/m/n/10 Using pack-ages with \T1/zi4/m/it/10 type = "source" \T1/ptm/m /n/10 al-ways works pro-vided the pack-age con-tains no [2084] Underfull \hbox (badness 10000) in paragraph at lines 6934--6939 [][][]\T1/zi4/m/it/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [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] Underfull \hbox (badness 10000) in paragraph at lines 8434--8436 []\T1/ptm/m/n/10 for \T1/zi4/m/it/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi 4/m/it/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 2310) in paragraph at lines 8456--8461 []\T1/ptm/m/n/10 If a `\T1/zi4/m/it/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2110] [2111] [2112] [2113] [2114] [2115] [2116] [2117] Underfull \hbox (badness 1248) in paragraph at lines 8980--8984 []\T1/zi4/m/it/10 R CMD build \T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/m/ n/10 source tar-balls. The name(s) of the pack-ages are taken from the [2118] Underfull \hbox (badness 1789) in paragraph at lines 9058--9060 []\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 [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131] Underfull \hbox (badness 1097) in paragraph at lines 9895--9898 []\T1/ptm/m/n/10 The name \T1/zi4/m/it/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2132] [2133] Underfull \hbox (badness 3000) in paragraph at lines 10031--10036 [][][]\T1/zi4/m/it/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/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/it/10 read.t able[][][]\T1/ptm/m/n/10 ; [2134] [2135] [2136] [2137] [2138] [2139] [2140] [2141] [2142] Underfull \hbox (badness 2134) in paragraph at lines 10614--10619 [][][]\T1/zi4/m/it/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/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/it/10 write. table[][][]\T1/ptm/m/n/10 ; Underfull \hbox (badness 10000) in paragraph at lines 10670--10675 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for Underfull \hbox (badness 10000) in paragraph at lines 10670--10675 \T1/zi4/m/it/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/zi4/m/it/10 HKEY_CLASSES _ROOT\T1/ptm/m/n/10 . \T1/zi4/m/it/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] Underfull \hbox (badness 2469) in paragraph at lines 11163--11167 []\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 11163--11167 [][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . 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[1] [2] Underfull \hbox (badness 6995) 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 . It Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1/pt m/m/n/10 if \T1/zi4/m/n/10 double.base Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth- er-wise, it is \T1/zi4/m/n/10 (double.base Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/zi4/m /n/10 1.110223e-16\T1/ptm/m/n/10 . As Underfull \hbox (badness 4995) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.neg.ulp.digits \T1/ptm/m/n/10 is bounded be-low by \T1/zi 4/m/n/10 -(double.digits + 3)\T1/ptm/m/n/10 , [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 297--301 []\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] [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 534--540 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/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 1178--1181 []\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] (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1966--1966 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] [34] [35] [36] [37] Underfull \hbox (badness 10000) in paragraph at lines 2402--2404 []\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci ently) by Underfull \hbox (badness 10000) in paragraph at lines 2405--2410 [][][]\T1/zi4/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le ngth re-sults, so at-tempt-ing to split via Underfull \hbox (badness 1102) in paragraph at lines 2405--2410 \T1/zi4/m/n/10 apply(x,MARGIN,identity) \T1/ptm/m/n/10 does not work (as it sim -ply gives \T1/zi4/m/n/10 x\T1/ptm/m/n/10 ). By chain-ing \T1/zi4/m/n/10 asplit [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] Underfull \hbox (badness 10000) in paragraph at lines 3784--3786 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [60] [61] [62] Overfull \hbox (6.42029pt too wide) in paragraph at lines 4025--4025 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 2521) in paragraph at lines 5046--5048 []\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 [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6202--6202 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [97] [98] [99] [100] [101] [102] Overfull \hbox (46.35893pt too wide) in paragraph at lines 6611--6613 []\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 : [103] [104] Underfull \hbox (badness 10000) in paragraph at lines 6759--6762 []\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 [105] [106] Underfull \hbox (badness 6063) in paragraph at lines 6941--6947 []\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- Underfull \hbox (badness 2343) in paragraph at lines 6941--6947 \T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files and web-pages gen-er- Underfull \hbox (badness 1708) in paragraph at lines 6941--6947 \T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it i s not rec-om-mended) when Underfull \hbox (badness 1831) in paragraph at lines 6941--6947 \T1/ptm/m/n/10 writ-ing it should be writ-ten ex-plic-itly, e.g. by \T1/zi4/m/n /10 writeChar("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or [107] Underfull \hbox (badness 3568) in paragraph at lines 7003--7010 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [108] [109] Underfull \vbox (badness 3803) has occurred while \output is active [110] Underfull \vbox (badness 10000) has occurred while \output is active [111] [112] Underfull \hbox (badness 1077) in paragraph at lines 7330--7336 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7330--7336 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [113] [114] [115] [116] [117] [118] Underfull \hbox (badness 2096) in paragraph at lines 7671--7675 \T1/zi4/m/n/10 status _ codes$[][] \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 . [119] [120] Underfull \hbox (badness 2351) in paragraph at lines 7789--7792 [][][]\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 , [121] [122] [123] [124] [125] Underfull \hbox (badness 4479) in paragraph at lines 8115--8125 [][][]\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), [126] [127] [128] [129] [130] [131] Underfull \hbox (badness 1629) in paragraph at lines 8562--8574 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 1609) in paragraph at lines 8562--8574 \T1/ptm/m/n/10 there is a prob-lem in the POSIX/C99 stan-dard with \T1/zi4/m/n/ 10 "1969-12-31 23:59:59 UTC"\T1/ptm/m/n/10 , which Underfull \hbox (badness 2426) in paragraph at lines 8562--8574 \T1/ptm/m/n/10 is \T1/zi4/m/n/10 -1 \T1/ptm/m/n/10 in cal-en-dar time and that value is on those OSes also used as an er-ror code. [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] Underfull \hbox (badness 1178) in paragraph at lines 9298--9302 []\T1/ptm/m/n/10 If true, [][]\T1/zi4/m/n/10 list[][][]\T1/ptm/m/n/10 s and ato mic vec-tors with non-[][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 names (see [][ ]\T1/zi4/m/n/10 names[][][]\T1/ptm/m/n/10 ) are de- [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] Underfull \hbox (badness 1735) in paragraph at lines 10446--10450 \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 . [161] [162] [163] [164] [165] [166] [167] Underfull \hbox (badness 6396) in paragraph at lines 10885--10893 []\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 1946) in paragraph at lines 10885--10893 \T1/zi4/m/n/10 duplicated \T1/ptm/m/n/10 and \T1/zi4/m/n/10 anyDuplicated\T1/pt m/m/n/10 , \T1/zi4/m/n/10 anyDuplicated(x,...) \T1/ptm/m/n/10 is a ``gen-er-al- ized'' short-cut for [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] Underfull \hbox (badness 4569) in paragraph at lines 12002--12006 []\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 12002--12006 \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 [184] Underfull \vbox (badness 10000) has occurred while \output is active [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] Underfull \hbox (badness 2253) in paragraph at lines 13665--13667 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [209] [210] Underfull \hbox (badness 1565) in paragraph at lines 13738--13742 [][][]\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 Underfull \hbox (badness 4927) in paragraph at lines 13782--13784 []\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 \T1/zi4 /m/n/10 fsep = [211] [212] Underfull \hbox (badness 3148) in paragraph at lines 13875--13880 [][][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[ ][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 help[][][]\T1/ptm/m/n/10 ; [][]\T1/zi4 /m/n/10 RShowDoc[][][] \T1/ptm/m/n/10 call \T1/zi4/m/n/10 file.show() \T1/ptm/m /n/10 for \T1/zi4/m/n/10 type = "text"\T1/ptm/m/n/10 . Con-sider [213] Underfull \hbox (badness 1466) in paragraph at lines 13922--13925 []\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 [214] Underfull \hbox (badness 10000) in paragraph at lines 14049--14053 [][][]\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 14060--14063 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [215] [216] [217] [218] [219] Underfull \hbox (badness 3965) in paragraph at lines 14352--14356 []\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, [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] Underfull \hbox (badness 4429) in paragraph at lines 15128--15131 []\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 [232] [233] Underfull \hbox (badness 10000) in paragraph at lines 15234--15236 []\T1/ptm/m/n/10 This works via \T1/zi4/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic h calls Underfull \hbox (badness 1215) in paragraph at lines 15234--15236 \T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times in this case, see Underfull \hbox (badness 10000) in paragraph at lines 15256--15261 []\T1/ptm/m/n/10 For num-bers, \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 calls \T 1/zi4/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls Underfull \hbox (badness 1558) in paragraph at lines 15256--15261 \T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero)\T1/ptm/m/n/10 . (\T1/ptm/m /it/10 ``when needed''\T1/ptm/m/n/10 : when \T1/zi4/m/n/10 zero.print \T1/ptm/m /n/10 is not Underfull \hbox (badness 10000) in paragraph at lines 15268--15272 []\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 Underfull \hbox (badness 2426) in paragraph at lines 15268--15272 \T1/zi4/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi ves \T1/zi4/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . If you want [234] Underfull \hbox (badness 2035) in paragraph at lines 15307--15311 []\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 within [235] Underfull \vbox (badness 10000) has occurred while \output is active [236] [237] [238] [239] [240] [241] [242] [243] Underfull \hbox (badness 2452) in paragraph at lines 15906--15910 []\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 15906--15910 \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 [244] [245] [246] Underfull \hbox (badness 1092) in paragraph at lines 16079--16084 [][]\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 [247] [248] [249] Underfull \hbox (badness 6741) in paragraph at lines 16329--16333 \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 , [250] [251] [252] [253] [254] [255] [256] [257] [258] Underfull \vbox (badness 3803) has occurred while \output is active [259] Underfull \vbox (badness 10000) has occurred while \output is active [260] [261] [262] [263] [264] [265] [266] [267] [268] [269] Underfull \hbox (badness 1478) in paragraph at lines 17622--17625 []\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 [270] [271] [272] [273] Underfull \hbox (badness 10000) in paragraph at lines 17877--17879 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [274] [275] [276] [277] [278] [279] [280] [281] [282] Underfull \hbox (badness 1442) in paragraph at lines 18477--18479 []\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 [283] Underfull \hbox (badness 2452) in paragraph at lines 18569--18585 [][][]\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 , [284] [285] [286] [287] [288] [289] [290] Underfull \hbox (badness 1248) in paragraph at lines 18988--18991 []\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 , [291] [292] [293] [294] Underfull \hbox (badness 4739) in paragraph at lines 19246--19248 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [295] [296] [297] [298] [299] [300] Underfull \hbox (badness 1596) in paragraph at lines 19665--19670 \T1/ptm/m/n/10 trix or, if \T1/zi4/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/zi4/m/n/10 simplify2array()\T1/ptm /m/n/10 . [301] [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] Underfull \hbox (badness 2469) in paragraph at lines 20269--20274 []\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 20283--20290 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [312] Underfull \hbox (badness 10000) in paragraph at lines 20357--20361 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 20357--20361 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$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 ' [313] [314] Underfull \hbox (badness 1014) in paragraph at lines 20527--20532 []\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 [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] Underfull \hbox (badness 1264) in paragraph at lines 21317--21322 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [327] Underfull \hbox (badness 4441) in paragraph at lines 21346--21349 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 , [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] Underfull \hbox (badness 6047) in paragraph at lines 22093--22095 []\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 \T1/zi4/m/n/10 make.unique(c(A,B)) == [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] Underfull \hbox (badness 1077) in paragraph at lines 23134--23140 \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 . [356] [357] [358] [359] [360] [361] [362] [363] Underfull \hbox (badness 2790) in paragraph at lines 23630--23633 []\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 23630--23633 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [364] [365] [366] [367] [368] Underfull \hbox (badness 1194) in paragraph at lines 23912--23915 []\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 [369] [370] [371] Underfull \hbox (badness 2368) in paragraph at lines 24118--24124 []\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 list, i.e., Underfull \hbox (badness 4981) in paragraph at lines 24118--24124 \T1/zi4/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are al so given by [][]\T1/zi4/m/n/10 ls[][][](env,all.names = [372] [373] [374] [375] [376] [377] Underfull \hbox (badness 10000) in paragraph at lines 24500--24503 []\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by [378] [379] [380] [381] [382] [383] [384] [385] [386] Underfull \hbox (badness 10000) in paragraph at lines 25105--25107 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than \T1/zi4/m/n/10 pkg %in% [387] [388] [389] [390] [391] [392] [393] [394] [395] [396] [397] [398] [399] Underfull \hbox (badness 1038) in paragraph at lines 25945--25953 []\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 1735) in paragraph at lines 25945--25953 \T1/ptm/m/n/10 set from value of the en-vi-ron-ment vari-able \T1/zi4/m/n/10 R_ DEFAULT_PACKAGES\T1/ptm/m/n/10 , or if that is un- Underfull \hbox (badness 1292) in paragraph at lines 25945--25953 \T1/ptm/m/n/10 set to \T1/zi4/m/n/10 c("datasets","utils","grDevices","graphics ","stats","methods")\T1/ptm/m/n/10 . (Set Underfull \hbox (badness 1881) in paragraph at lines 25954--25957 []\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 25973--25975 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [400] [401] Underfull \hbox (badness 2142) in paragraph at lines 26114--26118 []\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 26164--26169 []\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 [402] [403] [404] [405] Underfull \hbox (badness 10000) in paragraph at lines 26452--26458 []\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 26452--26458 \T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 26452--26458 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 26465--26468 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 26491--26493 []\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 26526--26531 []\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 2529) in paragraph at lines 26532--26543 \T1/ptm/m/n/10 in-di-rectly [][]\T1/zi4/m/n/10 update.packages[][][]\T1/ptm/m/n /10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si- Underfull \hbox (badness 2512) in paragraph at lines 26532--26543 \T1/ptm/m/n/10 ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi4/m /n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use and [406] Underfull \hbox (badness 7203) in paragraph at lines 26544--26547 []\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 10000) in paragraph at lines 26568--26573 []\T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma -cOS build), Underfull \hbox (badness 2057) in paragraph at lines 26568--26573 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). [407] [408] [409] [410] [411] [412] [413] [414] Underfull \hbox (badness 10000) in paragraph at lines 27086--27089 []\T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 str2lang(s ) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of [415] Underfull \hbox (badness 7925) in paragraph at lines 27165--27169 []\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 vec-to r \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n /10 cor-re-sponds to Underfull \hbox (badness 1622) in paragraph at lines 27165--27169 [][]\T1/zi4/m/n/10 parse[][][](text = s,keep.source=FALSE)\T1/ptm/m/n/10 , whic h is al-ways of type ([][]\T1/zi4/m/n/10 typeof[][][]\T1/ptm/m/n/10 ) and [][]\ T1/zi4/m/n/10 class[][][] Underfull \hbox (badness 6125) in paragraph at lines 27170--27179 []\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 string \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2lang(s) \T1/ptm/m/n/10 cor -re-sponds to [][]\T1/zi4/m/n/10 parse[][][](text = [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] Underfull \hbox (badness 2726) in paragraph at lines 27891--27894 []\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 [427] [428] [429] [430] [431] [432] [433] [434] [435] [436] [437] [438] [439] [440] [441] [442] [443] [444] Underfull \vbox (badness 3803) has occurred while \output is active [445] [446] [447] [448] [449] [450] [451] [452] Underfull \hbox (badness 1533) in paragraph at lines 29582--29585 []\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 [453] [454] [455] Underfull \hbox (badness 1163) in paragraph at lines 29745--29756 []\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 [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] [473] [474] [475] [476] [477] [478] [479] Underfull \hbox (badness 10000) in paragraph at lines 31291--31295 []\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 31291--31295 \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 31313--31315 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [480] [481] [482] [483] [484] [485] [486] [487] [488] Underfull \hbox (badness 1655) in paragraph at lines 31869--31871 []\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 [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] Underfull \hbox (badness 2261) in paragraph at lines 32988--32993 []\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 [506] Underfull \hbox (badness 10000) in paragraph at lines 33015--33021 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1484) in paragraph at lines 33015--33021 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal and hex-adec-i-mal rep-re-sen-ta-tions like [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551] [552] [553] [554] Underfull \hbox (badness 1072) in paragraph at lines 36157--36161 []\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 36162--36166 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 36190--36196 []\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 36190--36196 \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 36190--36196 \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 3009) in paragraph at lines 36202--36209 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 36202--36209 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 36202--36209 \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 36202--36209 \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 [555] [556] [557] [558] [559] [560] Underfull \hbox (badness 1142) in paragraph at lines 36556--36562 []\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 \T1/zi4/m/n/10 "%Y-%m-%d [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] Underfull \hbox (badness 1565) in paragraph at lines 37829--37831 []\T1/ptm/m/n/10 integer code used in \T1/zi4/m/n/10 quantile(*,type=quantile.t ype) \T1/ptm/m/n/10 for the de-fault [581] [582] [583] [584] [585] [586] [587] [588] [589] [590] Underfull \hbox (badness 4967) in paragraph at lines 38428--38433 []\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 [591] [592] Underfull \hbox (badness 1616) in paragraph at lines 38541--38546 \T1/zi4/m/n/10 system("id") \T1/ptm/m/n/10 is much more portable on Unix-alikes , pro-vided only the POSIX op-tions [593] [594] [595] [596] [597] [598] [599] [600] Underfull \hbox (badness 1472) in paragraph at lines 39067--39070 []\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 [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614] Underfull \hbox (badness 10000) in paragraph at lines 39981--39985 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/zi4/m/n/10 length(bin) > [615] [616] [617] [618] Underfull \hbox (badness 10000) in paragraph at lines 40232--40235 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [619] [620] [621] Underfull \hbox (badness 10000) in paragraph at lines 40416--40420 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [622] [623] [624] [625] [626] [627] [628] [629] [630] Underfull \hbox (badness 10000) in paragraph at lines 41029--41032 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[ ]zones / [631] [632] [633] [634] [635] [636] Underfull \vbox (badness 10000) has occurred while \output is active [637] [638] [639] [640] [641] [642] [643] [644] Underfull \hbox (badness 1990) in paragraph at lines 41933--41941 []\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 41933--41941 \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 [645] [646] [647] [648] [649] [650] [651] [652] Underfull \hbox (badness 1917) in paragraph at lines 42439--42446 []\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 [653] [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] Underfull \hbox (badness 3668) in paragraph at lines 43168--43170 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [664] [665] Underfull \hbox (badness 2401) in paragraph at lines 43296--43300 []\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 [666] [667] [668] Underfull \hbox (badness 2111) in paragraph at lines 43485--43490 \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 10000) in paragraph at lines 43506--43511 []\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 [669] [670] [671] [672] [673] [674] [675] [676] [677] Underfull \hbox (badness 5417) in paragraph at lines 44088--44092 []\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 [678] Underfull \hbox (badness 10000) in paragraph at lines 44149--44153 []\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 [679] [680]) (./compiler-pkg.tex Chapter 2. [681] [682] [683] [684]) (./datasets-pkg.tex Chapter 3. [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] Underfull \hbox (badness 1097) in paragraph at lines 1031--1035 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] Underfull \vbox (badness 1448) has occurred while \output is active [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] Overfull \vbox (19.74611pt too high) has occurred while \output is active [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] Underfull \vbox (badness 10000) has occurred while \output is active [753] [754] [755] [756] Underfull \vbox (badness 10000) has occurred while \output is active [757] [758] [759] [760] [761] [762] [763] [764] [765] [766]) (./grDevices-pkg.tex Chapter 4. [767] [768] [769] [770] [771] Underfull \hbox (badness 3158) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/zi4/m/n/10 c(mi,ma,n.)\T1/ptm /m/n/10 , with iden-ti-cal mean-ing to Underfull \hbox (badness 10000) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][]\T1/zi4/m/n/10 axisTicks[][][]() \T1/ptm/ m/n/10 just calls the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/ptm/m/n/1 0 in Underfull \hbox (badness 1852) in paragraph at lines 298--303 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 /src/main/plot.c\T1/ptm/m/n/10 ' which is also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t ion [772] [773] [774] [775] [776] [777] [778] [779] Underfull \hbox (badness 1424) in paragraph at lines 830--832 [][][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 (as in-te-ger or char-ac-ter) and \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 mean trans-par-ent, which can also be spec-i -fied as [780] [781] [782] [783] [784] Underfull \hbox (badness 5175) in paragraph at lines 1124--1126 []\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 [785] [786] [787] [788] Underfull \hbox (badness 1852) in paragraph at lines 1326--1329 []\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 [789] [790] [791] Underfull \hbox (badness 1490) in paragraph at lines 1532--1537 \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 [792] [793] [794] [795] [796] [797] Underfull \hbox (badness 1325) in paragraph at lines 1938--1948 \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 , [798] [799] Underfull \hbox (badness 10000) in paragraph at lines 2050--2052 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [800] [801] [802] Underfull \hbox (badness 6758) in paragraph at lines 2228--2231 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [803] [804] [805] [806] [807] [808] [809] [810] [811] [812] Underfull \hbox (badness 10000) in paragraph at lines 2832--2833 [813] [814] [815] [816] [817] [818] [819] [820] [821] Underfull \hbox (badness 10000) in paragraph at lines 3388--3393 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [822] [823] [824] [825] [826] Underfull \vbox (badness 10000) has occurred while \output is active [827] Underfull \hbox (badness 10000) in paragraph at lines 3789--3792 []\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 [828] [829] [830] [831] [832] [833] [834] [835] [836] [837] [838] Underfull \hbox (badness 10000) in paragraph at lines 4518--4523 [][][]$\T1/zi4/m/n/10 https : / / www . adobe . com / content / dam / acom / en / devnet / actionscript / articles / PLRM . pdf$[][] Underfull \hbox (badness 4181) in paragraph at lines 4518--4523 \T1/ptm/m/n/10 or PDF [][]$\T1/zi4/m/n/10 https : / / www . adobe . com / devne t / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in [839] Underfull \vbox (badness 10000) has occurred while \output is active [840] [841] Underfull \hbox (badness 1067) in paragraph at lines 4672--4679 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [842] [843] [844] [845] Underfull \hbox (badness 1377) in paragraph at lines 4975--4980 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [846] Underfull \hbox (badness 1418) in paragraph at lines 5051--5058 \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 1755) in paragraph at lines 5069--5071 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [847] [848] Underfull \hbox (badness 1377) in paragraph at lines 5180--5185 []\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 [849] Underfull \hbox (badness 7344) in paragraph at lines 5249--5251 []\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 [850] [851] Underfull \hbox (badness 2035) in paragraph at lines 5384--5393 []\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 5384--5393 \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 5384--5393 \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 , [852] Underfull \hbox (badness 10000) in paragraph at lines 5452--5459 []\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 5452--5459 \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 . [853] [854] [855] Underfull \hbox (badness 1546) in paragraph at lines 5594--5602 []\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 , [856] [857] [858] [859] [860] [861] [862] [863] Underfull \hbox (badness 10000) in paragraph at lines 6129--6132 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [864] [865] [866] [867] [868] [869] [870] [871] [872] [873] [874] [875] [876] Underfull \hbox (badness 1189) in paragraph at lines 6951--6953 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [877] Underfull \hbox (badness 10000) in paragraph at lines 7049--7051 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [878] [879] [880] [881] [882] Underfull \hbox (badness 3780) in paragraph at lines 7349--7355 []\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 , [883] [884] [885] Underfull \hbox (badness 2680) in paragraph at lines 7550--7552 []\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 [886] [887] [888]) (./graphics-pkg.tex Chapter 5. [889] [890] [891] [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] Underfull \hbox (badness 4634) in paragraph at lines 1351--1354 [][][]\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 , [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] Underfull \hbox (badness 1728) in paragraph at lines 2308--2310 []\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use \T1/zi4/m/n/10 "n " \T1/ptm/m/n/10 to sup-press and see also [927] [928] Underfull \hbox (badness 1009) in paragraph at lines 2399--2406 \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 [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] [947] [948] [949] [950] Underfull \vbox (badness 10000) has occurred while \output is active [951] [952] [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] Underfull \hbox (badness 3229) in paragraph at lines 4544--4549 []\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 [964] [965] [966] [967] [968] Underfull \hbox (badness 10000) in paragraph at lines 4901--4907 []\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 4901--4907 \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 [969] Underfull \hbox (badness 10000) in paragraph at lines 5032--5035 [970] Underfull \hbox (badness 10000) in paragraph at lines 5093--5095 [971 >/library/graphics/help/figures/ mai.pdf>] [972 >/library/graphics/hel p/figures/oma.pdf>] [973] Underfull \hbox (badness 10000) in paragraph at lines 5283--5285 []\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 [974] Underfull \vbox (badness 3803) has occurred while \output is active [975] [976] [977] [978] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] [995] [996] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6761--6762 [][] [997] [998 >/library/graphics/help/fi gures/pch.pdf>] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] Underfull \hbox (badness 2012) in paragraph at lines 7586--7589 []\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 poi nt [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] Underfull \hbox (badness 10000) in paragraph at lines 8846--8848 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8848--8850 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1032]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8928 \HeaderA{units}{Graphical Units}{units} [1033] [1034] [1035] [1036]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] Underfull \hbox (badness 2680) in paragraph at lines 483--486 []\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 [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] Underfull \hbox (badness 4279) in paragraph at lines 1064--1073 [][][]\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 , [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] Underfull \vbox (badness 10000) has occurred while \output is active [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] Underfull \hbox (badness 1067) in paragraph at lines 4486--4489 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1113] [1114] [1115] [1116] Underfull \hbox (badness 7256) in paragraph at lines 4731--4733 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \hbox (badness 1824) in paragraph at lines 6535--6538 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like \T1/zi4/m/n/10 depth [1148] [1149] [1150] [1151]) (./methods-pkg.tex [1152] Chapter 7. [1153] [1154] [1155] [1156] [1157] [1158] [1159] [1160] Underfull \vbox (badness 10000) has occurred while \output is active [1161] Underfull \vbox (badness 10000) has occurred while \output is active [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171] Underfull \hbox (badness 2237) in paragraph at lines 1385--1387 []\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 [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] Underfull \hbox (badness 2181) in paragraph at lines 1932--1939 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/zi4/m/n/10 is(x,"refClass") \T1/ptm/m/n/10 tests [1180] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\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 1981--1986 \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 [1181] [1182] [1183] Underfull \hbox (badness 2213) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/zi4/m/n/10 where = [1184] [1185] [1186] [1187] [1188] Underfull \hbox (badness 10000) in paragraph at lines 2574--2577 []\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 [1189] [1190] Underfull \hbox (badness 1132) in paragraph at lines 2714--2718 []\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 [1191] Underfull \hbox (badness 1033) in paragraph at lines 2746--2751 \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 [1192] [1193] [1194] [1195] [1196] [1197] [1198] Underfull \hbox (badness 1102) in paragraph at lines 3303--3305 []\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 [1199] [1200] [1201] [1202] [1203] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\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 [1204] Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1205] Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [] \T1/zi4/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude = "numeric",altitude [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] Underfull \hbox (badness 1769) in paragraph at lines 4472--4478 []\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 4472--4478 \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 [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] Underfull \vbox (badness 10000) has occurred while \output is active [1227] [1228] [1229] Underfull \hbox (badness 4036) in paragraph at lines 5437--5440 []\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 [1230] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1231] [1232] [1233] [1234] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] Underfull \hbox (badness 1675) in paragraph at lines 6451--6457 \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 [1243] [1244] [1245] [1246] Underfull \vbox (badness 10000) has occurred while \output is active [1247] [1248] [1249] [1250]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1251] [1252] [1253]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} [1254] Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1255] [1256] [1257] Underfull \hbox (badness 1286) in paragraph at lines 7484--7486 []\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 [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] Underfull \vbox (badness 10000) has occurred while \output is active [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] Underfull \hbox (badness 1137) in paragraph at lines 10011--10019 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/n/10 ne w("signature",functionDef,...)\T1/ptm/m/n/10 . The [1293] [1294] [1295] [1296] [1297] [1298] [1299] Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., [1300] [1301] [1302] [1303]) (./parallel-pkg.tex [1304] Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\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 [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] [1324] [1325] Underfull \hbox (badness 3386) in paragraph at lines 1365--1368 []\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 [1326] [1327] [1328]) (./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 [1329] [1330] [1331] [1332] [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344]) (./stats-pkg.tex Chapter 10. [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] Underfull \hbox (badness 1412) in paragraph at lines 875--877 []\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 [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] Underfull \hbox (badness 2503) in paragraph at lines 1356--1359 []\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 , [1367] [1368] [1369] Underfull \hbox (badness 10000) in paragraph at lines 1536--1540 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov","lm") \T1/ptm/m/n/1 0 or for mul-ti-ple re-sponses of class [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] Underfull \hbox (badness 2503) in paragraph at lines 3437--3440 []\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 , [1400] [1401] [1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] Underfull \hbox (badness 1127) in paragraph at lines 4351--4354 []\T1/ptm/m/n/10 standardized resid-u-als, \T1/zi4/m/n/10 (observed -expected) / sqrt(V)\T1/ptm/m/n/10 , where \T1/zi4/m/n/10 V \T1/ptm/m/n/10 is the [1415] [1416] [1417] [1418] [1419] Underfull \hbox (badness 3989) in paragraph at lines 4681--4688 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] Underfull \hbox (badness 2556) in paragraph at lines 5317--5320 []\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 5334--5336 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/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 [1430] [1431] [1432] [1433] [1434] [1435] [1436] Underfull \hbox (badness 2503) in paragraph at lines 5726--5730 []\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 , [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] Underfull \hbox (badness 7081) in paragraph at lines 6520--6523 []\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 6524--6526 []\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 [1450] [1451] [1452] [1453] [1454] Underfull \vbox (badness 3803) has occurred while \output is active [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] Underfull \hbox (badness 10000) in paragraph at lines 7369--7372 []\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 [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] Underfull \vbox (badness 10000) has occurred while \output is active [1485] [1486] [1487] [1488] [1489] Underfull \hbox (badness 2626) in paragraph at lines 9048--9051 []\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 [1490] [1491] Underfull \hbox (badness 2503) in paragraph at lines 9155--9159 []\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 , [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] [1509] [1510] [1511] Underfull \hbox (badness 4518) in paragraph at lines 10469--10474 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1512] [1513] [1514] [1515] [1516] Underfull \hbox (badness 2142) in paragraph at lines 10830--10833 []\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 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10849--10852 []\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, [1517] Underfull \hbox (badness 1708) in paragraph at lines 10911--10915 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1518] [1519] [1520] [1521] [1522] [1523] Underfull \hbox (badness 1694) in paragraph at lines 11307--11310 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531]pdfTeX warning (ext4): d estination with the same identifier (name{Rfn.hat}) has been already used, dupl icate ignored \relax l.11791 \aliasA{hat}{influence.measures}{hat} [1532] [1533] Underfull \hbox (badness 1484) in paragraph at lines 11926--11928 []\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 [1534] [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] Underfull \hbox (badness 10000) in paragraph at lines 12519--12521 []\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 \T1/zi4/m/n/10 SSinit = [1544] [1545] [1546] [1547] [1548] [1549] Underfull \hbox (badness 2894) in paragraph at lines 12855--12859 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] Underfull \hbox (badness 4518) in paragraph at lines 13605--13610 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] Underfull \hbox (badness 4518) in paragraph at lines 14257--14262 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1572] [1573] Underfull \hbox (badness 8151) in paragraph at lines 14395--14399 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = "interp olate",statistics = Underfull \hbox (badness 1199) in paragraph at lines 14402--14404 []\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 [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] Underfull \hbox (badness 2503) in paragraph at lines 15473--15477 []\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 , [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] Underfull \hbox (badness 4621) in paragraph at lines 15985--15991 []\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 [1600] [1601] [1602] [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] [1623] [1624] [1625] [1626] [1627] Underfull \vbox (badness 10000) has occurred while \output is active [1628] Underfull \vbox (badness 10000) has occurred while \output is active [1629] [1630] [1631] [1632] [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] Underfull \hbox (badness 1377) in paragraph at lines 18588--18593 []\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 18593--18596 []\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 [1642] Underfull \hbox (badness 2343) in paragraph at lines 18606--18610 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 3471) in paragraph at lines 18606--18610 \T1/ptm/m/n/10 the value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + re ltol) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18614--18618 []\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 [1643] [1644] [1645] Overfull \hbox (15.73795pt too wide) in paragraph at lines 18839--18839 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 18842--18842 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] Underfull \vbox (badness 10000) has occurred while \output is active [1646] [1647] [1648] [1649] [1650] [1651] [1652] Underfull \hbox (badness 1337) in paragraph at lines 19264--19267 []\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 [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] Underfull \hbox (badness 3049) in paragraph at lines 19760--19764 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1662] [1663] [1664] [1665] Underfull \hbox (badness 1194) in paragraph at lines 20018--20021 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1666] [1667] [1668] [1669] [1670] [1671] [1672] Underfull \hbox (badness 2503) in paragraph at lines 20397--20400 []\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 , Underfull \hbox (badness 3919) in paragraph at lines 20424--20426 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or \T1/zi4/m/n/10 "Comparison of Poisson [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] [1688] [1689] [1690] Underfull \hbox (badness 10000) in paragraph at lines 21501--21507 []\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 , [1691] [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] Underfull \hbox (badness 1337) in paragraph at lines 22855--22861 []\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 [1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] Overfull \hbox (27.74408pt too wide) in paragraph at lines 23420--23420 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1722] [1723] [1724] [1725] [1726] Underfull \hbox (badness 10000) in paragraph at lines 23671--23674 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 4205) in paragraph at lines 23671--23674 \T1/zi4/m/n/10 cutree(hclust.obj,k = k)\T1/ptm/m/n/10 , can be spec-i-fied for ef-fi-ciency if al-ready [1727] [1728] [1729] [1730] [1731] [1732] [1733] [1734] [1735] Underfull \hbox (badness 1824) in paragraph at lines 24257--24263 []\T1/ptm/m/n/10 Here, all the NAs in \T1/zi4/m/n/10 x \T1/ptm/m/n/10 are first re-placed by al-ter- Underfull \hbox (badness 1033) in paragraph at lines 24257--24263 \T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/ m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where [1736] Underfull \hbox (badness 10000) in paragraph at lines 24278--24281 []\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 \T1/zi4/m/n/10 y[j] = Underfull \hbox (badness 3690) in paragraph at lines 24347--24351 [][][]\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 [1737] Underfull \vbox (badness 3803) has occurred while \output is active [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] Underfull \hbox (badness 2165) in paragraph at lines 24856--24861 []\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm /m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1 0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [1746] [1747] [1748] [1749] Underfull \hbox (badness 1867) in paragraph at lines 25061--25063 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 25074--25078 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u se.fallback) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 PP [1750] [1751] [1752] [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] Underfull \vbox (badness 3803) has occurred while \output is active [1761] [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] [1771] [1772] [1773] Underfull \vbox (badness 10000) has occurred while \output is active [1774] Underfull \hbox (badness 3514) in paragraph at lines 26634--26639 []\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 [1775] [1776] [1777] [1778] Overfull \hbox (2.23795pt too wide) in paragraph at lines 26868--26868 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1779] Underfull \hbox (badness 3514) in paragraph at lines 26904--26910 []\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 [1780] [1781] [1782] [1783] Underfull \hbox (badness 3514) in paragraph at lines 27118--27123 []\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 [1784] Underfull \hbox (badness 3514) in paragraph at lines 27205--27210 []\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 [1785] Underfull \hbox (badness 3514) in paragraph at lines 27270--27275 []\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 [1786] [1787] Underfull \hbox (badness 3514) in paragraph at lines 27364--27369 []\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 [1788] [1789] Underfull \hbox (badness 6691) in paragraph at lines 27456--27461 []\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 [1790] [1791] [1792] [1793] [1794] [1795] [1796] [1797] Underfull \hbox (badness 4024) in paragraph at lines 27984--27987 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion , which [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] Underfull \hbox (badness 5431) in paragraph at lines 28590--28592 []\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 [1808] [1809] [1810] [1811] Underfull \hbox (badness 5431) in paragraph at lines 28800--28803 []\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 [1812] [1813] [1814] [1815] [1816] Underfull \hbox (badness 1337) in paragraph at lines 29114--29118 []\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 [1817] [1818] [1819] [1820] [1821] Underfull \hbox (badness 1616) in paragraph at lines 29416--29419 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1822] [1823] [1824] [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] [1835] [1836] [1837] [1838] [1839] [1840] Underfull \hbox (badness 3557) in paragraph at lines 30546--30550 []\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 \T1/zi4 /m/n/10 interval = [1841] [1842] [1843] Underfull \vbox (badness 10000) has occurred while \output is active [1844] [1845] [1846] Underfull \hbox (badness 1337) in paragraph at lines 30910--30914 []\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 [1847] [1848] [1849] [1850] [1851] [1852] [1853] [1854] [1855] Underfull \hbox (badness 1337) in paragraph at lines 31437--31441 []\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 [1856] [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865]) (./stats4-pkg.tex [1866] Chapter 11. [1867] [1868] [1869] [1870] [1871] [1872]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} [1873] [1874] [1875]) (./tcltk-pkg.tex [1876] Chapter 12. [1877] [1878] [1879] [1880] [1881] [1882] [1883] Underfull \vbox (badness 10000) has occurred while \output is active [1884] Underfull \vbox (badness 10000) has occurred while \output is active [1885] 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 [1886] [1887] [1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897]) (./tools-pkg.tex [1898] Chapter 13. [1899] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1900] 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 [1901] [1902] 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 [1903] [1904] 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 [1905] [1906] [1907] [1908] [1909] [1910] [1911] [1912] [1913] [1914] [1915] [1916] [1917] Underfull \hbox (badness 4441) in paragraph at lines 1139--1149 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- Underfull \hbox (badness 1014) in paragraph at lines 1163--1165 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1169--1171 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous [1918] Underfull \hbox (badness 10000) in paragraph at lines 1206--1209 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1206--1209 \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 , [1919] [1920] [1921] [1922] [1923] Underfull \hbox (badness 2293) in paragraph at lines 1558--1560 []\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with its func-tion-al-ity in-te-grated into that of [1924] [1925] [1926] Underfull \hbox (badness 7981) in paragraph at lines 1696--1701 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 1082) in paragraph at lines 1703--1705 []\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 [1927] [1928] [1929]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1930] [1931] [1932] [1933] [1934] [1935] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2202--2202 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1936] [1937] [1938] Underfull \hbox (badness 7981) in paragraph at lines 2371--2377 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1939] [1940] [1941] [1942] [1943] [1944] [1945] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2846. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2847. LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 2847. [1946] [1947] [1948] [1949] [1950] Underfull \hbox (badness 1424) in paragraph at lines 3128--3130 []\T1/zi4/m/it/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 [1951] [1952] [1953] [1954] [1955] [1956] [1957] [1958] [1959] [1960] [1961] Underfull \hbox (badness 10000) in paragraph at lines 3832--3834 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1962] [1963] Underfull \hbox (badness 10000) in paragraph at lines 3971--3974 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/it/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/it/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1964] [1965] Underfull \hbox (badness 1137) in paragraph at lines 4073--4075 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1966] [1967] [1968] [1969] [1970] Underfull \hbox (badness 1796) in paragraph at lines 4381--4386 []\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over \T 1/zi4/m/it/10 write_PACKAGES \T1/ptm/m/n/10 in the \T1/zi4/m/it/10 type == [1971] Underfull \hbox (badness 1838) in paragraph at lines 4455--4461 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/it/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/it/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4455--4461 \T1/ptm/m/n/10 `\T1/zi4/m/it/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 [1972] [1973] [1974] Underfull \hbox (badness 2197) in paragraph at lines 4671--4681 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/it/10 available.packages[][][]\T1/ptm/m/n/10 : [1975] Underfull \hbox (badness 1571) in paragraph at lines 4734--4738 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [1976] [1977] [1978]) (./utils-pkg.tex Chapter 14. [1979] 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/it/10 insertions\T1/ptm/m/n/10 ', [1980] [1981] [1982] [1983] [1984] Underfull \hbox (badness 10000) in paragraph at lines 376--381 \T1/zi4/m/it/10 c("vertical","horizontal","cascade","minimize","restore") \T1/p tm/m/n/10 with [1985] [1986] [1987] [1988] [1989] Underfull \hbox (badness 10000) in paragraph at lines 717--723 []\T1/ptm/m/n/10 Functions \T1/zi4/m/it/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/it/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 717--723 \T1/zi4/m/it/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/it/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1990] [1991] Underfull \hbox (badness 5847) in paragraph at lines 850--856 []\T1/ptm/m/n/10 Argument \T1/zi4/m/it/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 850--856 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/it/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1992] Underfull \hbox (badness 3861) in paragraph at lines 918--923 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/it/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/it/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/it/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1993] [1994] Underfull \hbox (badness 3323) in paragraph at lines 1089--1097 []\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/zi4/m/it/1 0 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1 /ptm/m/n/10 , in-di-cat- Underfull \hbox (badness 2961) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f or-mat- Underfull \hbox (badness 3919) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 3735) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/it/10 getOption[][][]("citation.bibtex.ma x",1) \T1/ptm/m/n/10 which is \T1/zi4/m/it/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by [1995] Underfull \hbox (badness 10000) in paragraph at lines 1101--1103 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1996] [1997] Underfull \vbox (badness 3803) has occurred while \output is active [1998] [1999] [2000] [2001] [2002] Underfull \hbox (badness 1371) in paragraph at lines 1606--1608 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/it/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/it/10 ccaddress \T1/ptm/m/n/10 to pass to [2003] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 1676. [2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] [2012] Underfull \hbox (badness 2057) in paragraph at lines 2215--2217 []\T1/ptm/m/n/10 None for \T1/zi4/m/it/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [2013] [2014] [2015] [2016] [2017] [2018]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.clipboard}) has been already used, duplicate ig nored \relax l.2566 ... the Clipboard in MS Windows}{clipboard} [2019] [2020] Underfull \hbox (badness 1748) in paragraph at lines 2733--2736 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/it/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/it/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/it/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [2021] [2022] [2023] [2024] [2025] [2026] [2027] Underfull \hbox (badness 5388) in paragraph at lines 3142--3146 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/it/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/it/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/it/10 .TXT\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/it/10 read.table[][][](...,header = Underfull \hbox (badness 2285) in paragraph at lines 3147--3150 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/it/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/it/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/it/10 read.table[] [][](...,header = TRUE,sep = [2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] Underfull \hbox (badness 1430) in paragraph at lines 3906--3914 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/it/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [2039] Underfull \hbox (badness 1231) in paragraph at lines 3983--3995 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [2040] [2041] Underfull \hbox (badness 10000) in paragraph at lines 4141--4143 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/it/10 dow nload.file[][][] \T1/ptm/m/n/10 and [2042] [2043] [2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.4839 ...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.4839 ...mat Unordered and Ordered Lists}{format} [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] Underfull \hbox (badness 1622) in paragraph at lines 5358--5362 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/it' instead on input line 5990. Underfull \hbox (badness 1371) in paragraph at lines 5994--5996 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/it/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/it/10 ccaddress \T1/ptm/m/n/10 to pass to [2072] Underfull \hbox (badness 1502) in paragraph at lines 6083--6088 []\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 6083--6088 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2073] [2074] [2075] Underfull \hbox (badness 10000) in paragraph at lines 6256--6265 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2076] Underfull \hbox (badness 2150) in paragraph at lines 6320--6323 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2077] [2078] Underfull \hbox (badness 3118) in paragraph at lines 6458--6460 []\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 [2079] [2080] [2081] Underfull \hbox (badness 1325) in paragraph at lines 6630--6634 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/it/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able Underfull \hbox (badness 4726) in paragraph at lines 6642--6648 \T1/ptm/m/n/10 used if \T1/zi4/m/it/10 repos = NULL\T1/ptm/m/n/10 . Can also be a char-ac-ter vec-tor, a sub-set of [2082] Underfull \hbox (badness 10000) in paragraph at lines 6714--6717 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be Underfull \hbox (badness 10000) in paragraph at lines 6714--6717 \T1/ptm/m/n/10 passed to \T1/zi4/m/it/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou rce pack-age in-stall. E.g., [2083] Underfull \hbox (badness 3219) in paragraph at lines 6790--6797 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/it/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6790--6797 \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 6790--6797 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1596) in paragraph at lines 6790--6797 [][]\T1/zi4/m/it/10 getOption[][][]("install.packages.compile.from.source")\T1/ ptm/m/n/10 . \T1/zi4/m/it/10 type = "both" \T1/ptm/m/n/10 will be silently Underfull \hbox (badness 2932) in paragraph at lines 6798--6801 []\T1/ptm/m/n/10 Using pack-ages with \T1/zi4/m/it/10 type = "source" \T1/ptm/m /n/10 al-ways works pro-vided the pack-age con-tains no [2084] Underfull \hbox (badness 10000) in paragraph at lines 6934--6939 [][][]\T1/zi4/m/it/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [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] Underfull \hbox (badness 10000) in paragraph at lines 8434--8436 []\T1/ptm/m/n/10 for \T1/zi4/m/it/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi 4/m/it/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 2310) in paragraph at lines 8456--8461 []\T1/ptm/m/n/10 If a `\T1/zi4/m/it/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2110] [2111] [2112] [2113] [2114] [2115] [2116] [2117] Underfull \hbox (badness 1248) in paragraph at lines 8980--8984 []\T1/zi4/m/it/10 R CMD build \T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/m/ n/10 source tar-balls. The name(s) of the pack-ages are taken from the [2118] Underfull \hbox (badness 1789) in paragraph at lines 9058--9060 []\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 [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131] Underfull \hbox (badness 1097) in paragraph at lines 9895--9898 []\T1/ptm/m/n/10 The name \T1/zi4/m/it/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2132] [2133] Underfull \hbox (badness 3000) in paragraph at lines 10031--10036 [][][]\T1/zi4/m/it/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/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/it/10 read.t able[][][]\T1/ptm/m/n/10 ; [2134] [2135] [2136] [2137] [2138] [2139] [2140] [2141] [2142] Underfull \hbox (badness 2134) in paragraph at lines 10614--10619 [][][]\T1/zi4/m/it/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/it/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/it/10 write. table[][][]\T1/ptm/m/n/10 ; Underfull \hbox (badness 10000) in paragraph at lines 10670--10675 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for Underfull \hbox (badness 10000) in paragraph at lines 10670--10675 \T1/zi4/m/it/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/zi4/m/it/10 HKEY_CLASSES _ROOT\T1/ptm/m/n/10 . \T1/zi4/m/it/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] Underfull \hbox (badness 2469) in paragraph at lines 11163--11167 []\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 11163--11167 [][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2152] [2153] [2154] [2155] [2156] Underfull \hbox (badness 4060) in paragraph at lines 11494--11497 []\T1/ptm/m/n/10 If `\T1/zi4/m/it/10 --default-packages\T1/ptm/m/n/10 ' is not used, then \T1/zi4/m/it/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var i-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 11517--11517 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [2157] [2158] [2159] [2160] Underfull \hbox (badness 2150) in paragraph at lines 11756--11758 [][][]$\T1/zi4/m/it/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/it/10 https : / / www . gnu . org / software / emac s / manual / [2161] [2162] [2163] [2164] Underfull \hbox (badness 10000) in paragraph at lines 11975--11979 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/it/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12006--12012 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2165] [2166] Underfull \hbox (badness 1009) in paragraph at lines 12200--12212 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. 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'/<>/src/library/grDevices/src/cairo' make[10]: Entering directory '/<>/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[9]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[8]: Leaving directory '/<>/src/library/grDevices/src/cairo' make[7]: Leaving directory '/<>/src/library/grDevices/src' make[6]: Leaving directory '/<>/src/library/grDevices/src' make[5]: Leaving directory '/<>/src/library/grDevices' make[5]: Entering directory '/<>/src/library/grDevices' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/grDevices' make[4]: Leaving directory '/<>/src/library/grDevices' make[4]: Entering directory '/<>/src/library/graphics' building package 'graphics' make[5]: Entering directory '/<>/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/<>/src/library/graphics' make[5]: Entering directory '/<>/src/library/graphics' make[6]: Entering directory '/<>/src/library/graphics/src' make[7]: Entering directory '/<>/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/<>/src/library/graphics/src' make[6]: Leaving directory '/<>/src/library/graphics/src' make[5]: Leaving directory '/<>/src/library/graphics' make[5]: Entering directory '/<>/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/graphics' make[4]: Leaving directory '/<>/src/library/graphics' make[4]: Entering directory '/<>/src/library/stats' building package 'stats' make[5]: Entering directory '/<>/src/library/stats' all.R is unchanged make[5]: Leaving directory '/<>/src/library/stats' make[5]: Entering directory '/<>/src/library/stats' make[6]: Entering directory '/<>/src/library/stats/src' make[7]: Entering directory '/<>/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/<>/src/library/stats/src' make[6]: Leaving directory '/<>/src/library/stats/src' make[5]: Leaving directory '/<>/src/library/stats' make[5]: Entering directory '/<>/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/stats' make[4]: Leaving directory '/<>/src/library/stats' make[4]: Entering directory '/<>/src/library/datasets' building package 'datasets' make[5]: Entering directory '/<>/src/library/datasets' make[5]: Leaving directory '/<>/src/library/datasets' make[4]: Leaving directory '/<>/src/library/datasets' make[4]: Entering directory '/<>/src/library/methods' building package 'methods' make[5]: Entering directory '/<>/src/library/methods' all.R is unchanged make[5]: Leaving directory '/<>/src/library/methods' make[5]: Entering directory '/<>/src/library/methods' make[6]: Entering directory '/<>/src/library/methods/src' make[7]: Entering directory '/<>/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/<>/src/library/methods/src' make[6]: Leaving directory '/<>/src/library/methods/src' make[5]: Leaving directory '/<>/src/library/methods' make[5]: Entering directory '/<>/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/<>/src/library/methods' make[4]: Leaving directory '/<>/src/library/methods' make[4]: Entering directory '/<>/src/library/grid' building package 'grid' make[5]: Entering directory '/<>/src/library/grid' all.R is unchanged make[5]: Leaving directory '/<>/src/library/grid' make[5]: Entering directory '/<>/src/library/grid' make[6]: Entering directory '/<>/src/library/grid/src' make[7]: Entering directory '/<>/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/<>/src/library/grid/src' make[6]: Leaving directory '/<>/src/library/grid/src' make[5]: Leaving directory '/<>/src/library/grid' make[5]: Entering directory '/<>/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/grid' make[4]: Leaving directory '/<>/src/library/grid' make[4]: Entering directory '/<>/src/library/splines' building package 'splines' make[5]: Entering directory '/<>/src/library/splines' all.R is unchanged make[5]: Leaving directory '/<>/src/library/splines' make[5]: Entering directory '/<>/src/library/splines' make[6]: Entering directory '/<>/src/library/splines/src' make[7]: Entering directory '/<>/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/<>/src/library/splines/src' make[6]: Leaving directory '/<>/src/library/splines/src' make[5]: Leaving directory '/<>/src/library/splines' make[5]: Entering directory '/<>/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/splines' make[4]: Leaving directory '/<>/src/library/splines' make[4]: Entering directory '/<>/src/library/stats4' building package 'stats4' make[5]: Entering directory '/<>/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/<>/src/library/stats4' make[5]: Entering directory '/<>/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/stats4' make[4]: Leaving directory '/<>/src/library/stats4' make[4]: Entering directory '/<>/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/<>/src/library/tcltk' make[5]: Leaving directory '/<>/src/library/tcltk' make[5]: Entering directory '/<>/src/library/tcltk/src' make[6]: Entering directory '/<>/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/<>/src/library/tcltk/src' make[5]: Leaving directory '/<>/src/library/tcltk/src' make[5]: Entering directory '/<>/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/tcltk' make[4]: Leaving directory '/<>/src/library/tcltk' make[4]: Entering directory '/<>/src/library/parallel' building package 'parallel' make[5]: Entering directory '/<>/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/<>/src/library/parallel' make[5]: Entering directory '/<>/src/library/parallel' make[6]: Entering directory '/<>/src/library/parallel/src' make[7]: Entering directory '/<>/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/<>/src/library/parallel/src' make[6]: Leaving directory '/<>/src/library/parallel/src' make[5]: Leaving directory '/<>/src/library/parallel' make[5]: Entering directory '/<>/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/<>/src/library/parallel' make[4]: Leaving directory '/<>/src/library/parallel' make[4]: Entering directory '/<>/src/library/base' make[4]: Leaving directory '/<>/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/<>/src/library' make[2]: Leaving directory '/<>/src' make[2]: Entering directory '/<>/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/<>/tests' make[2]: Entering directory '/<>/doc' make[3]: Entering directory '/<>/doc/manual' make[4]: Entering directory '/<>/doc/html' make[4]: Leaving directory '/<>/doc/html' make[3]: Leaving directory '/<>/doc/manual' make[2]: Leaving directory '/<>/doc' make[2]: Entering directory '/<>/src/library' make[3]: Entering directory '/<>/src/library' installing parsed Rd make[4]: Entering directory '/<>/src/library' base stats utils methods graphics grDevices datasets grid tools tcltk splines stats4 compiler parallel make[4]: Leaving directory '/<>/src/library' make[3]: Leaving directory '/<>/src/library' make[3]: Entering directory '/<>/src/library' building/updating package metadata ... make[3]: Leaving directory '/<>/src/library' make[3]: Entering directory '/<>/src/library' writing package indices make[4]: Entering directory '/<>/src/library' make[4]: Leaving directory '/<>/src/library' make[3]: Leaving directory '/<>/src/library' make[2]: Leaving directory '/<>/src/library' make[2]: Entering directory '/<>/src/library/Recommended' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/<>/src/library/Recommended' make[2]: Entering directory '/<>/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 '/<>/src/library' make[1]: Leaving directory '/<>' touch make-indep-stamp fakeroot debian/rules binary *** check *** xvfb-run make check-all make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/tests' make[3]: Entering directory '/<>/tests' make[4]: Entering directory '/<>/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 '/<>/tests/Examples' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running strict specific tests make[4]: Entering directory '/<>/tests' running code in 'eval-etc.R' ... OK comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ... OK running code in 'simple-true.R' ... OK comparing 'simple-true.Rout' to './simple-true.Rout.save' ... OK running code in 'arith-true.R' ... OK comparing 'arith-true.Rout' to './arith-true.Rout.save' ... OK running code in 'arith.R' ... OK comparing 'arith.Rout' to './arith.Rout.save' ... OK running code in 'lm-tests.R' ... OK comparing 'lm-tests.Rout' to './lm-tests.Rout.save' ... OK running code in 'ok-errors.R' ... OK comparing 'ok-errors.Rout' to './ok-errors.Rout.save' ... OK running code in 'method-dispatch.R' ... OK comparing 'method-dispatch.Rout' to './method-dispatch.Rout.save' ... OK running code in 'any-all.R' ... OK comparing 'any-all.Rout' to './any-all.Rout.save' ... OK running code in 'd-p-q-r-tests.R' ... OK comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save' ... OK make[4]: Leaving directory '/<>/tests' running sloppy specific tests make[4]: Entering directory '/<>/tests' running code in 'complex.R' ... OK comparing 'complex.Rout' to './complex.Rout.save' ... OK running code in 'eval-etc-2.R' ... OK comparing 'eval-etc-2.Rout' to './eval-etc-2.Rout.save' ...72,74c72,236 < Warning message: < In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : < there is no package called 'Matrix' --- > > cat("Trying some Matrix objects, too\n") > Trying some Matrix objects, too > > D5. <- Diagonal(x = 5:1) > > D5N <- D5. > > D5N[5, 5] <- NA > > example(Matrix) > > Matrix> Matrix(0, 3, 2) # 3 by 2 matrix of zeros -> sparse > 3 x 2 sparse Matrix of class "dgCMatrix" > > [1,] . . > [2,] . . > [3,] . . > > Matrix> Matrix(0, 3, 2, sparse=FALSE)# -> 'dense' > 3 x 2 Matrix of class "dgeMatrix" > [,1] [,2] > [1,] 0 0 > [2,] 0 0 > [3,] 0 0 > > Matrix> Matrix(0, 2, 2, sparse=FALSE)# diagonal ! > 2 x 2 diagonal matrix of class "ddiMatrix" > [,1] [,2] > [1,] 0 . > [2,] . 0 > > Matrix> Matrix(0, 2, 2, sparse=FALSE, doDiag=FALSE)# -> dense > 2 x 2 Matrix of class "dsyMatrix" > [,1] [,2] > [1,] 0 0 > [2,] 0 0 > > Matrix> Matrix(1:6, 3, 2) # a 3 by 2 matrix (+ integer warning) > 3 x 2 Matrix of class "dgeMatrix" > [,1] [,2] > [1,] 1 4 > [2,] 2 5 > [3,] 3 6 > > Matrix> Matrix(1:6 + 1, nrow=3) > 3 x 2 Matrix of class "dgeMatrix" > [,1] [,2] > [1,] 2 5 > [2,] 3 6 > [3,] 4 7 > > Matrix> ## logical ones: > Matrix> Matrix(diag(4) > 0)# -> "ldiMatrix" with diag = "U" > 4 x 4 diagonal matrix of class "ldiMatrix" > [,1] [,2] [,3] [,4] > [1,] TRUE . . . > [2,] . TRUE . . > [3,] . . TRUE . > [4,] . . . TRUE > > Matrix> Matrix(diag(4) > 0, sparse=TRUE)# -> sparse... > 4 x 4 sparse Matrix of class "lsCMatrix" > > [1,] | . . . > [2,] . | . . > [3,] . . | . > [4,] . . . | > > Matrix> Matrix(diag(4) >= 0)# -> "lsyMatrix" (of all 'TRUE') > 4 x 4 Matrix of class "lsyMatrix" > [,1] [,2] [,3] [,4] > [1,] TRUE TRUE TRUE TRUE > [2,] TRUE TRUE TRUE TRUE > [3,] TRUE TRUE TRUE TRUE > [4,] TRUE TRUE TRUE TRUE > > Matrix> ## triangular > Matrix> l3 <- upper.tri(matrix(,3,3)) > > Matrix> (M <- Matrix(l3)) # -> "ltCMatrix" > 3 x 3 sparse Matrix of class "ltCMatrix" > > [1,] . | | > [2,] . . | > [3,] . . . > > Matrix> Matrix(! l3)# -> "ltrMatrix" > 3 x 3 Matrix of class "ltrMatrix" > [,1] [,2] [,3] > [1,] TRUE . . > [2,] TRUE TRUE . > [3,] TRUE TRUE TRUE > > Matrix> as(l3, "CsparseMatrix") > 3 x 3 sparse Matrix of class "lgCMatrix" > > [1,] . | | > [2,] . . | > [3,] . . . > > Matrix> Matrix(1:9, nrow=3, > Matrix+ dimnames = list(c("a", "b", "c"), c("A", "B", "C"))) > 3 x 3 Matrix of class "dgeMatrix" > A B C > a 1 4 7 > b 2 5 8 > c 3 6 9 > > Matrix> (I3 <- Matrix(diag(3)))# identity, i.e., unit "diagonalMatrix" > 3 x 3 diagonal matrix of class "ddiMatrix" > [,1] [,2] [,3] > [1,] 1 . . > [2,] . 1 . > [3,] . . 1 > > Matrix> str(I3) # note the empty 'x' slot > Formal class 'ddiMatrix' [package "Matrix"] with 4 slots > ..@ diag : chr "U" > ..@ Dim : int [1:2] 3 3 > ..@ Dimnames:List of 2 > .. ..$ : NULL > .. ..$ : NULL > ..@ x : num(0) > > Matrix> (A <- cbind(a=c(2,1), b=1:2))# symmetric *apart* from dimnames > a b > [1,] 2 1 > [2,] 1 2 > > Matrix> Matrix(A) # hence 'dgeMatrix' > 2 x 2 Matrix of class "dgeMatrix" > a b > [1,] 2 1 > [2,] 1 2 > > Matrix> (As <- Matrix(A, dimnames = list(NULL,NULL)))# -> symmetric > 2 x 2 Matrix of class "dsyMatrix" > [,1] [,2] > [1,] 2 1 > [2,] 1 2 > > Matrix> stopifnot(is(As, "symmetricMatrix"), > Matrix+ is(Matrix(0, 3,3), "sparseMatrix"), > Matrix+ is(Matrix(FALSE, 1,1), "sparseMatrix")) > > i <- c(1, 3:8) > > j <- c(2, 9, 6:10) > > x <- 7 * (1:7) > > A <- sparseMatrix(i, j, x = x) > > sA <- sparseMatrix(i, j, x = x, symmetric = TRUE) > > tA <- sparseMatrix(i, j, x = x, triangular = TRUE) > > AA <- sparseMatrix(c(1, 3:8), c(2, 9, 6:10), x = 7 * (1:7), dims = c(10, > + 20)) > > set.seed(1) > > (perm <- sample(1:7)) > [1] 1 4 7 2 5 3 6 > > A1 <- sparseMatrix(i[perm], j[perm], x = x[perm]) > > args <- data.frame(i = c(i, 1), j = c(j, 2), x = c(x, 2)) > > Aa <- do.call(sparseMatrix, args) > > A. <- do.call(sparseMatrix, c(args, list(use.last.ij = TRUE))) > > nA <- do.call(sparseMatrix, args[c("i", "j")]) > > dn <- list(LETTERS[1:3], letters[1:5]) > > m <- sparseMatrix(i = c(3, 1, 3:2, 2:1), p = c(0:2, 4, 4, 6), x = 1:6, > + dimnames = dn) > > n <- sparseMatrix(i = 1:6, j = rev(2:7)) > > e <- sparseMatrix(dims = c(4, 6), i = { > + }, j = { > + }) > > sy <- sparseMatrix(i = c(2, 4, 3:5), j = c(4, 7:5, 5), x = 1:5, dims = c(7, > + 7), symmetric = TRUE) 76a239,290 > A: new("dgCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, > 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(8L, 10L), Dimnames = list( > NULL, NULL), x = c(7, 21, 28, 35, 14, 42, 49), factors = list()) > --> checking list(*): Ok > --=--=--=--=-- > A.: new("dgCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, > 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(8L, 10L), Dimnames = list( > NULL, NULL), x = c(2, 21, 28, 35, 14, 42, 49), factors = list()) > --> checking list(*): Ok > --=--=--=--=-- > A1: new("dgCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, > 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(8L, 10L), Dimnames = list( > NULL, NULL), x = c(7, 21, 28, 35, 14, 42, 49), factors = list()) > --> checking list(*): Ok > --=--=--=--=-- > AA: new("dgCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, > 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, > 7L, 7L, 7L, 7L), Dim = c(10L, 20L), Dimnames = list(NULL, NULL), > x = c(7, 21, 28, 35, 14, 42, 49), factors = list()) > --> checking list(*): Ok > --=--=--=--=-- > Aa: new("dgCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, > 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(8L, 10L), Dimnames = list( > NULL, NULL), x = c(9, 21, 28, 35, 14, 42, 49), factors = list()) > --> checking list(*): Ok > --=--=--=--=-- > As: new("dsyMatrix", x = c(2, 1, 1, 2), Dim = c(2L, 2L), Dimnames = list( > NULL, NULL), uplo = "U", factors = list()) > --> checking list(*): Ok > --=--=--=--=-- > D5.: new("ddiMatrix", diag = "N", Dim = c(5L, 5L), Dimnames = list( > NULL, NULL), x = c(5, 4, 3, 2, 1)) > --> checking list(*): Ok > --=--=--=--=-- > D5N: new("ddiMatrix", diag = "N", Dim = c(5L, 5L), Dimnames = list( > NULL, NULL), x = c(5, 4, 3, 2, NA)) > --> checking list(*): Ok > --=--=--=--=-- > I3: new("ddiMatrix", diag = "U", Dim = c(3L, 3L), Dimnames = list( > NULL, NULL), x = numeric(0)) > --> checking list(*): Ok > --=--=--=--=-- > M: new("ltCMatrix", i = c(0L, 0L, 1L), p = c(0L, 0L, 1L, 3L), Dim = c(3L, > 3L), Dimnames = list(NULL, NULL), x = c(TRUE, TRUE, TRUE), uplo = "U", > diag = "N") > --> checking list(*): Ok > --=--=--=--=-- > args: structure(list(i = c(1, 3, 4, 5, 6, 7, 8, 1), j = c(2, 9, 6, > 7, 8, 9, 10, 2), x = c(7, 14, 21, 28, 35, 42, 49, 2)), class = "data.frame", row.names = c(NA, > -8L)) > --> checking list(*): Ok > --=--=--=--=-- 178a393,399 > dn: list(c("A", "B", "C"), c("a", "b", "c", "d", "e")) > --> checking list(*): Ok > --=--=--=--=-- > e: new("ngCMatrix", i = integer(0), p = c(0L, 0L, 0L, 0L, 0L, 0L, > 0L), Dim = c(4L, 6L), Dimnames = list(NULL, NULL), factors = list()) > --> checking list(*): Ok > --=--=--=--=-- 240a462,464 > i: c(1, 3, 4, 5, 6, 7, 8) > --> checking list(*): Ok > --=--=--=--=-- 260a485,505 > j: c(2, 9, 6, 7, 8, 9, 10) > --> checking list(*): Ok > --=--=--=--=-- > l3: structure(c(FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, TRUE, TRUE, > FALSE), .Dim = c(3L, 3L)) > --> checking list(*): Ok > --=--=--=--=-- > m: new("dgCMatrix", i = c(2L, 0L, 1L, 2L, 0L, 1L), p = c(0L, 1L, > 2L, 4L, 4L, 6L), Dim = c(3L, 5L), Dimnames = list(c("A", "B", > "C"), c("a", "b", "c", "d", "e")), x = c(1, 2, 4, 3, 6, 5), factors = list()) > --> checking list(*): Ok > --=--=--=--=-- > n: new("ngCMatrix", i = 5:0, p = c(0L, 0L, 1L, 2L, 3L, 4L, 5L, 6L > ), Dim = 6:7, Dimnames = list(NULL, NULL), factors = list()) > --> checking list(*): Ok > --=--=--=--=-- > nA: new("ngCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, > 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(8L, 10L), Dimnames = list( > NULL, NULL), factors = list()) > --> checking list(*): Ok > --=--=--=--=-- 270a516,518 > perm: c(1L, 4L, 7L, 2L, 5L, 3L, 6L) > --> checking list(*): Ok > --=--=--=--=-- 312a561,580 > sA: new("dsCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, > 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(10L, 10L), Dimnames = list( > NULL, NULL), x = c(7, 21, 28, 35, 14, 42, 49), uplo = "U", > factors = list()) > --> checking list(*): Ok > --=--=--=--=-- > sy: new("dsCMatrix", i = c(1L, 3L, 4L, 2L, 3L), p = c(0L, 0L, 0L, > 0L, 1L, 3L, 4L, 5L), Dim = c(7L, 7L), Dimnames = list(NULL, NULL), > x = c(1, 4, 5, 3, 2), uplo = "U", factors = list()) > --> checking list(*): Ok > --=--=--=--=-- > tA: new("dtCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, > 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(10L, 10L), Dimnames = list( > NULL, NULL), x = c(7, 21, 28, 35, 14, 42, 49), uplo = "U", > diag = "N") > --> checking list(*): Ok > --=--=--=--=-- > x: c(7, 14, 21, 28, 35, 42, 49) > --> checking list(*): Ok > --=--=--=--=-- 315,317c583,584 < 1 identical warnings: < In library(package, lib.loc = lib.loc, character.only = TRUE, ... : < there is no package called 'Matrix' --- > Length Class Mode > 0 NULL NULL 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 '/<>/tests' make[4]: Entering directory '/<>/tests' checking Sys.timezone ... make[5]: Entering directory '/<>/tests' running code in 'timezone.R' ... OK make[5]: Leaving directory '/<>/tests' make[4]: Leaving directory '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running regression tests ... make[4]: Entering directory '/<>/tests' running code in 'array-subset.R' ... OK running code in 'reg-tests-1a.R' ... OK running code in 'reg-tests-1b.R' ... OK running code in 'reg-tests-1c.R' ... OK running code in 'reg-tests-1d.R' ... OK running code in 'reg-tests-2.R' ... OK comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ... OK running code in 'reg-examples1.R' ... OK running code in 'reg-examples2.R' ... OK running code in 'reg-packages.R' ... OK running code in 'p-qbeta-strict-tst.R' ... OK running code in 'r-strict-tst.R' ... OK running code in 'reg-IO.R' ... OK comparing 'reg-IO.Rout' to './reg-IO.Rout.save' ... OK running code in 'reg-IO2.R' ... OK comparing 'reg-IO2.Rout' to './reg-IO2.Rout.save' ... OK running code in 'reg-plot.R' ... OK comparing 'reg-plot.pdf' to './reg-plot.pdf.save' ... OK running code in 'reg-S4-examples.R' ... OK running code in 'reg-BLAS.R' ... OK make[4]: Leaving directory '/<>/tests' make[4]: Entering directory '/<>/tests' running tests of plotting Latin-1 expect failure or some differences if not in a Latin-1 or UTF-8 locale running code in 'reg-plot-latin1.R' ... OK comparing 'reg-plot-latin1.pdf' to './reg-plot-latin1.pdf.save' ... OK running code in 'reg-S4.R' ... OK comparing 'reg-S4.Rout' to './reg-S4.Rout.save' ...606,608c606 < Warning message: < In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : < there is no package called 'Matrix' --- > [ ] : .M.sub.i.logical() maybe inefficient 1249,1251c1247,1269 < Warning message: < In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : < there is no package called 'Matrix' --- > > setClass("Z", representation(zz = "list")) > > setClass("C", contains = c("Z", "dgCMatrix")) > > setClass("C2", contains = "C") > > setClass("C3", contains = "C2") > > m <- matrix(c(0, 0, 2:0), 3, 5, dimnames = list(NULL, NULL)) > > (mC <- as(m, "dgCMatrix")) > 3 x 5 sparse Matrix of class "dgCMatrix" > > [1,] . 1 . . 2 > [2,] . . 2 . 1 > [3,] 2 . 1 . . > > (cc <- as(mC, "C")) > 3 x 5 sparse Matrix of class "C" > > [1,] . 1 . . 2 > [2,] . . 2 . 1 > [3,] 2 . 1 . . > > c2 <- as(mC, "C2") > > c3 <- as(mC, "C3") > > stopifnot(identical(capture.output(c2), sub("C3", "C2", capture.output(c3))), > + identical(as(cc, "matrix"), m), identical(as(c2, "matrix"), m), identical(as(c3, > + "matrix"), m)) > > invisible(lapply(c("Z", "C", "C2", "C3"), removeClass)) OK make[4]: Leaving directory '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running tests of Internet functions make[4]: Entering directory '/<>/tests' running code in 'internet.R' ... OK comparing 'internet.Rout' to './internet.Rout.save' ...8,10c8,247 < Warning message: < In nsl("cran.r-project.org") : < nsl() was unable to resolve host 'cran.r-project.org' --- > > > > # test do_download (and "record" #{packages}): > > ap <- available.packages(contrib.url("http://cran.r-project.org")) > > ## IGNORE_RDIFF_END > > > > # test url connections on http > > zz <- url("http://cran.r-project.org/") > > readLines(zz) > [1] "" > [2] "" > [3] "" > [4] "The Comprehensive R Archive Network" > [5] "" > [6] "" > [7] "" > [8] "" > [9] "" > [10] "" > [11] "" > [12] "" > [13] "" > [14] "" > [15] "" > [16] "" > [17] "" > [18] "<h1>The Comprehensive R Archive Network</h1>" > [19] "" > [20] "Your browser seems not to support frames," > [21] "here is the <A href=\"navbar.html\">contents page</A> of CRAN." > [22] "" > [23] "" > > close(zz) > > > > # and via read.table, test http and ftp. > > > > read.table("http://www.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat") > V1 V2 V3 V4 V5 > 1 1 307 930 36.58 0 > 2 2 307 940 36.73 0 > 3 3 307 950 36.93 0 > 4 4 307 1000 37.15 0 > 5 5 307 1010 37.23 0 > 6 6 307 1020 37.24 0 > 7 7 307 1030 37.24 0 > 8 8 307 1040 36.90 0 > 9 9 307 1050 36.95 0 > 10 10 307 1100 36.89 0 > 11 11 307 1110 36.95 0 > 12 12 307 1120 37.00 0 > 13 13 307 1130 36.90 0 > 14 14 307 1140 36.99 0 > 15 15 307 1150 36.99 0 > 16 16 307 1200 37.01 0 > 17 17 307 1210 37.04 0 > 18 18 307 1220 37.04 0 > 19 19 307 1230 37.14 0 > 20 20 307 1240 37.07 0 > 21 21 307 1250 36.98 0 > 22 22 307 1300 37.01 0 > 23 23 307 1310 36.97 0 > 24 24 307 1320 36.97 0 > 25 25 307 1330 37.12 0 > 26 26 307 1340 37.13 0 > 27 27 307 1350 37.14 0 > 28 28 307 1400 37.15 0 > 29 29 307 1410 37.17 0 > 30 30 307 1420 37.12 0 > 31 31 307 1430 37.12 0 > 32 32 307 1440 37.17 0 > 33 33 307 1450 37.28 0 > 34 34 307 1500 37.28 0 > 35 35 307 1510 37.44 0 > 36 36 307 1520 37.51 0 > 37 37 307 1530 37.64 0 > 38 38 307 1540 37.51 0 > 39 39 307 1550 37.98 1 > 40 40 307 1600 38.02 1 > 41 41 307 1610 38.00 1 > 42 42 307 1620 38.24 1 > 43 43 307 1630 38.10 1 > 44 44 307 1640 38.24 1 > 45 45 307 1650 38.11 1 > 46 46 307 1700 38.02 1 > 47 47 307 1710 38.11 1 > 48 48 307 1720 38.01 1 > 49 49 307 1730 37.91 1 > 50 50 307 1740 37.96 1 > 51 51 307 1750 38.03 1 > 52 52 307 1800 38.17 1 > 53 53 307 1810 38.19 1 > 54 54 307 1820 38.18 1 > 55 55 307 1830 38.15 1 > 56 56 307 1840 38.04 1 > 57 57 307 1850 37.96 1 > 58 58 307 1900 37.84 1 > 59 59 307 1910 37.83 1 > 60 60 307 1920 37.84 1 > 61 61 307 1930 37.74 1 > 62 62 307 1940 37.76 1 > 63 63 307 1950 37.76 1 > 64 64 307 2000 37.64 1 > 65 65 307 2010 37.63 1 > 66 66 307 2020 38.06 1 > 67 67 307 2030 38.19 1 > 68 68 307 2040 38.35 1 > 69 69 307 2050 38.25 1 > 70 70 307 2100 37.86 1 > 71 71 307 2110 37.95 1 > 72 72 307 2120 37.95 1 > 73 73 307 2130 37.76 1 > 74 74 307 2140 37.60 1 > 75 75 307 2150 37.89 1 > 76 76 307 2200 37.86 1 > 77 77 307 2210 37.71 1 > 78 78 307 2220 37.78 1 > 79 79 307 2230 37.82 1 > 80 80 307 2240 37.76 1 > 81 81 307 2250 37.81 1 > 82 82 307 2300 37.84 1 > 83 83 307 2310 38.01 1 > 84 84 307 2320 38.10 1 > 85 85 307 2330 38.15 1 > 86 86 307 2340 37.92 1 > 87 87 307 2350 37.64 1 > 88 88 308 0 37.70 1 > 89 89 308 10 37.46 1 > 90 90 308 20 37.41 1 > 91 91 308 30 37.46 1 > 92 92 308 40 37.56 1 > 93 93 308 50 37.55 1 > 94 94 308 100 37.75 1 > 95 95 308 110 37.76 1 > 96 96 308 120 37.73 1 > 97 97 308 130 37.77 1 > 98 98 308 140 38.01 1 > 99 99 308 150 38.04 1 > 100 100 308 200 38.07 1 > > read.table("ftp://ftp.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat") > V1 V2 V3 V4 V5 > 1 1 307 930 36.58 0 > 2 2 307 940 36.73 0 > 3 3 307 950 36.93 0 > 4 4 307 1000 37.15 0 > 5 5 307 1010 37.23 0 > 6 6 307 1020 37.24 0 > 7 7 307 1030 37.24 0 > 8 8 307 1040 36.90 0 > 9 9 307 1050 36.95 0 > 10 10 307 1100 36.89 0 > 11 11 307 1110 36.95 0 > 12 12 307 1120 37.00 0 > 13 13 307 1130 36.90 0 > 14 14 307 1140 36.99 0 > 15 15 307 1150 36.99 0 > 16 16 307 1200 37.01 0 > 17 17 307 1210 37.04 0 > 18 18 307 1220 37.04 0 > 19 19 307 1230 37.14 0 > 20 20 307 1240 37.07 0 > 21 21 307 1250 36.98 0 > 22 22 307 1300 37.01 0 > 23 23 307 1310 36.97 0 > 24 24 307 1320 36.97 0 > 25 25 307 1330 37.12 0 > 26 26 307 1340 37.13 0 > 27 27 307 1350 37.14 0 > 28 28 307 1400 37.15 0 > 29 29 307 1410 37.17 0 > 30 30 307 1420 37.12 0 > 31 31 307 1430 37.12 0 > 32 32 307 1440 37.17 0 > 33 33 307 1450 37.28 0 > 34 34 307 1500 37.28 0 > 35 35 307 1510 37.44 0 > 36 36 307 1520 37.51 0 > 37 37 307 1530 37.64 0 > 38 38 307 1540 37.51 0 > 39 39 307 1550 37.98 1 > 40 40 307 1600 38.02 1 > 41 41 307 1610 38.00 1 > 42 42 307 1620 38.24 1 > 43 43 307 1630 38.10 1 > 44 44 307 1640 38.24 1 > 45 45 307 1650 38.11 1 > 46 46 307 1700 38.02 1 > 47 47 307 1710 38.11 1 > 48 48 307 1720 38.01 1 > 49 49 307 1730 37.91 1 > 50 50 307 1740 37.96 1 > 51 51 307 1750 38.03 1 > 52 52 307 1800 38.17 1 > 53 53 307 1810 38.19 1 > 54 54 307 1820 38.18 1 > 55 55 307 1830 38.15 1 > 56 56 307 1840 38.04 1 > 57 57 307 1850 37.96 1 > 58 58 307 1900 37.84 1 > 59 59 307 1910 37.83 1 > 60 60 307 1920 37.84 1 > 61 61 307 1930 37.74 1 > 62 62 307 1940 37.76 1 > 63 63 307 1950 37.76 1 > 64 64 307 2000 37.64 1 > 65 65 307 2010 37.63 1 > 66 66 307 2020 38.06 1 > 67 67 307 2030 38.19 1 > 68 68 307 2040 38.35 1 > 69 69 307 2050 38.25 1 > 70 70 307 2100 37.86 1 > 71 71 307 2110 37.95 1 > 72 72 307 2120 37.95 1 > 73 73 307 2130 37.76 1 > 74 74 307 2140 37.60 1 > 75 75 307 2150 37.89 1 > 76 76 307 2200 37.86 1 > 77 77 307 2210 37.71 1 > 78 78 307 2220 37.78 1 > 79 79 307 2230 37.82 1 > 80 80 307 2240 37.76 1 > 81 81 307 2250 37.81 1 > 82 82 307 2300 37.84 1 > 83 83 307 2310 38.01 1 > 84 84 307 2320 38.10 1 > 85 85 307 2330 38.15 1 > 86 86 307 2340 37.92 1 > 87 87 307 2350 37.64 1 > 88 88 308 0 37.70 1 > 89 89 308 10 37.46 1 > 90 90 308 20 37.41 1 > 91 91 308 30 37.46 1 > 92 92 308 40 37.56 1 > 93 93 308 50 37.55 1 > 94 94 308 100 37.75 1 > 95 95 308 110 37.76 1 > 96 96 308 120 37.73 1 > 97 97 308 130 37.77 1 > 98 98 308 140 38.01 1 > 99 99 308 150 38.04 1 > 100 100 308 200 38.07 1 > > OK make[4]: Leaving directory '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running tests of date-time printing expect platform-specific differences make[4]: Entering directory '/<>/tests' running code in 'datetime2.R' ... OK comparing 'datetime2.Rout' to './datetime2.Rout.save' ... OK make[4]: Leaving directory '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running tests of documentation examples make[4]: Entering directory '/<>/tests' running code in 'R-intro.R' ... OK comparing 'R-intro.Rout' to './R-intro.Rout.save' ... OK make[4]: Leaving directory '/<>/tests' make[4]: Entering directory '/<>/tests' gcc -std=gnu99 -I"/<>/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R-exts.c -o R-exts.o gcc -std=gnu99 -shared -L/<>/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o R-exts.so R-exts.o -L/<>/lib -lR make[4]: Leaving directory '/<>/tests' make[4]: Entering directory '/<>/tests' running code in 'R-exts.R' ... OK make[4]: Leaving directory '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running tests of consistency of as/is.* make[4]: Entering directory '/<>/tests' creating 'isas-tests.R' running code in 'isas-tests.R' ... OK comparing 'isas-tests.Rout' to './isas-tests.Rout.save' ... OK rm isas-tests.R make[4]: Leaving directory '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running tests of random deviate generation make[4]: Entering directory '/<>/tests' running code in 'p-r-random-tests.R' ... OK comparing 'p-r-random-tests.Rout' to './p-r-random-tests.Rout.save' ... OK make[4]: Leaving directory '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running demos from base and stats make[4]: Entering directory '/<>/tests' running code in 'demos.R' ... OK comparing 'demos.Rout' to './demos.Rout.save' ... OK running code in 'demos2.R' ... OK make[4]: Leaving directory '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running tests of primitives make[4]: Entering directory '/<>/tests' running code in 'primitives.R' ... OK make[4]: Leaving directory '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running regexp regression tests make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running more Internet and socket tests make[4]: Entering directory '/<>/tests' running code in 'internet2.R' ... OK running code in 'libcurl.R' ... OK make[4]: Leaving directory '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>/tests' running tests of CRAN tools (can be slow unless mirror is local) make[4]: Entering directory '/<>/tests' running code in 'CRANtools.R' ...make[4]: *** [Makefile.common:106: CRANtools.Rout] Error 1 make[4]: Leaving directory '/<>/tests' make[3]: *** [Makefile.common:276: test-CRANtools] Error 2 make[3]: Leaving directory '/<>/tests' make[2]: *** [Makefile.common:180: test-all-devel] Error 1 make[2]: Leaving directory '/<>/tests' make[1]: *** [Makefile:241: check-all] Error 2 make[1]: Leaving directory '/<>' make: [debian/rules:389: check-stamp] Error 2 (ignored) touch check-stamp *** install-arch *** dh_testdir dh_testroot dh_prep -a dh_installdirs -A /<>/debian/r-base-core /usr/bin/make DESTDIR=/<>/debian/r-base-core install make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/m4' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/<>/m4' make[2]: Entering directory '/<>/tools' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/<>/tools' make[2]: Entering directory '/<>/doc' installing doc ... mkdir -p -- /<>/debian/r-base-core/usr/share/R/doc mkdir -p -- /<>/debian/r-base-core/usr/share/man/man1 make[3]: Entering directory '/<>/doc/html' installing doc/html ... mkdir -p -- /<>/debian/r-base-core/usr/share/R/doc/html make[3]: Leaving directory '/<>/doc/html' make[3]: Entering directory '/<>/doc/manual' installing doc/manual ... mkdir -p -- /<>/debian/r-base-core/usr/share/R/doc/manual mkdir -p -- /<>/debian/r-base-core/usr/share/R/doc/manual/images make[3]: Leaving directory '/<>/doc/manual' make[2]: Leaving directory '/<>/doc' make[2]: Entering directory '/<>/etc' mkdir -p -- /<>/debian/r-base-core/usr/lib/R/etc installing etc ... make[2]: Leaving directory '/<>/etc' make[2]: Entering directory '/<>/share' installing share ... mkdir -p -- /<>/debian/r-base-core/usr/share/R/share mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/R mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/dictionaries mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/encodings mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/java mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/licenses mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/make mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/Rd mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/Rd/macros mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/sh mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/texmf mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/texmf/bibtex/bib mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/texmf/bibtex/bst mkdir -p -- /<>/debian/r-base-core/usr/share/R/share/texmf/tex/latex make[2]: Leaving directory '/<>/share' make[2]: Entering directory '/<>/src' make[3]: Entering directory '/<>/src/scripts' mkdir -p -- /<>/debian/r-base-core/usr/lib/R/bin make[3]: Leaving directory '/<>/src/scripts' make[3]: Entering directory '/<>/src/include' make[4]: Entering directory '/<>/src/include/R_ext' mkdir -p -- /<>/debian/r-base-core/usr/share/R/include/R_ext make[4]: Leaving directory '/<>/src/include/R_ext' make[3]: Leaving directory '/<>/src/include' make[3]: Entering directory '/<>/src/extra' make[4]: Entering directory '/<>/src/extra/blas' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/<>/src/extra/blas' make[4]: Entering directory '/<>/src/extra/tre' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/<>/src/extra/tre' make[4]: Entering directory '/<>/src/extra/tzone' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/<>/src/extra/tzone' make[4]: Entering directory '/<>/src/extra/xdr' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/<>/src/extra/xdr' make[4]: Entering directory '/<>/src/extra/intl' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/<>/src/extra/intl' make[3]: Leaving directory '/<>/src/extra' make[3]: Entering directory '/<>/src/appl' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/<>/src/appl' make[3]: Entering directory '/<>/src/nmath' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/<>/src/nmath' make[3]: Entering directory '/<>/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/usr/lib/R"' \ -o Rscript ./Rscript.c mkdir -p -- /<>/debian/r-base-core/usr/lib/pkgconfig make[3]: Leaving directory '/<>/src/unix' make[3]: Entering directory '/<>/src/main' mkdir -p -- /<>/debian/r-base-core/usr/lib/R/bin/exec make[4]: Entering directory '/<>/src/main' make[4]: Leaving directory '/<>/src/main' make[4]: Entering directory '/<>/src/main' mkdir -p -- /<>/debian/r-base-core/usr/lib/R/lib make[4]: Leaving directory '/<>/src/main' make[3]: Leaving directory '/<>/src/main' make[3]: Entering directory '/<>/src/modules' make[4]: Entering directory '/<>/src/modules/internet' mkdir -p -- /<>/debian/r-base-core/usr/lib/R/modules make[4]: Leaving directory '/<>/src/modules/internet' make[4]: Entering directory '/<>/src/modules/lapack' make[4]: Leaving directory '/<>/src/modules/lapack' make[4]: Entering directory '/<>/src/modules/X11' make[4]: Leaving directory '/<>/src/modules/X11' make[3]: Leaving directory '/<>/src/modules' make[3]: Entering directory '/<>/src/library' mkdir -p -- /<>/debian/r-base-core/usr/lib/R/library installing packages ... building HTML index ... make[3]: Leaving directory '/<>/src/library' make[2]: Leaving directory '/<>/src' make[2]: Entering directory '/<>/tests' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/<>/tests' make[1]: Leaving directory '/<>' (cd src/unix; \ rm -vf Rscript /<>/debian/r-base-core/usr/bin/Rscript; \ /usr/bin/make CFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ CXXFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ FFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -D_REENTRANT" \ CC="gcc -std=gnu99" \ CXX=g++ \ F77=gfortran \ RHOME=/usr/lib/R \ DESTDIR=/<>/debian/r-base-core \ install-Rscript ) removed 'Rscript' removed '/<>/debian/r-base-core/usr/bin/Rscript' make[1]: Entering directory '/<>/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -Wl,-Bsymbolic-functions -Wl,-z,relro -DR_HOME='"/usr/lib/R"' \ -o Rscript ./Rscript.c make[1]: Leaving directory '/<>/src/unix' #ls -ltr /<>/debian/r-base-core/usr/bin/ #strings src/unix/Rscript cp -vax src/unix/Rscript /<>/debian/r-base-core/usr/bin/ 'src/unix/Rscript' -> '/<>/debian/r-base-core/usr/bin/Rscript' #ls -ltr /<>/debian/r-base-core/usr/bin/ #strings /<>/debian/r-base-core/usr/bin/Rscript (cd src/nmath/standalone; \ /usr/bin/make DESTDIR=/<>/debian/r-base-core install ) make[1]: Entering directory '/<>/src/nmath/standalone' make[2]: Entering directory '/<>/src/include' make[2]: 'Rmath.h' is up to date. make[2]: Leaving directory '/<>/src/include' /<>/debian/r-base-core/usr/share/R/include/Rmath.h is unchanged make[1]: Leaving directory '/<>/src/nmath/standalone' chmod a+x /<>/debian/r-base-core/usr/share/R/share/sh/echo.sh rm -v /<>/debian/r-base-core/usr/lib/R/COPYING removed '/<>/debian/r-base-core/usr/lib/R/COPYING' (cd /<>/debian/r-base-core/usr/lib/R/; \ ln -s ../../share/common-licenses/GPL-2 COPYING) rm -v /<>/debian/r-base-core/usr/share/R/doc/COPYING removed '/<>/debian/r-base-core/usr/share/R/doc/COPYING' (cd /<>/debian/r-base-core/usr/share/R/doc; \ ln -s ../../../share/common-licenses/GPL-2 COPYING) (cd /<>/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 make prefix=/<>/debian/r-base-core/usr \ rdocdir=/<>/debian/r-base-core/usr/share/R/doc \ install-pdf make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/doc/manual' installing R manuals in PDF format ... make[2]: Leaving directory '/<>/doc/manual' make[1]: Leaving directory '/<>' make prefix=/<>/debian/r-base-core/usr \ infodir=/<>/debian/r-base-core/usr/share/info install-info make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/doc/manual' mkdir -p -- /<>/debian/r-base-core/usr/share/info /usr/bin/install -c -m 644 "./dir" "/<>/debian/r-base-core/usr/share/info" installing R info pages ... updating '/<>/debian/r-base-core/usr/share/info/dir' ... you need to adjust /<>/debian/r-base-core/usr/share/info/dir manually you need to adjust /<>/debian/r-base-core/usr/share/info/dir manually you need to adjust /<>/debian/r-base-core/usr/share/info/dir manually you need to adjust /<>/debian/r-base-core/usr/share/info/dir manually you need to adjust /<>/debian/r-base-core/usr/share/info/dir manually you need to adjust /<>/debian/r-base-core/usr/share/info/dir manually you need to adjust /<>/debian/r-base-core/usr/share/info/dir manually make[2]: Leaving directory '/<>/doc/manual' make[1]: Leaving directory '/<>' dh_movefiles --sourcedir=debian/r-base-core -pr-doc-pdf dh_movefiles --sourcedir=debian/r-base-core -pr-doc-html gunzip -9v /<>/debian/r-base-core/usr/share/info/*.gz /<>/debian/r-base-core/usr/share/info/R-FAQ.info.gz: 67.2% -- replaced with /<>/debian/r-base-core/usr/share/info/R-FAQ.info /<>/debian/r-base-core/usr/share/info/R-admin.info.gz: 68.0% -- replaced with /<>/debian/r-base-core/usr/share/info/R-admin.info /<>/debian/r-base-core/usr/share/info/R-data.info.gz: 70.6% -- replaced with /<>/debian/r-base-core/usr/share/info/R-data.info /<>/debian/r-base-core/usr/share/info/R-exts.info-1.gz: 66.6% -- replaced with /<>/debian/r-base-core/usr/share/info/R-exts.info-1 /<>/debian/r-base-core/usr/share/info/R-exts.info-2.gz: 67.5% -- replaced with /<>/debian/r-base-core/usr/share/info/R-exts.info-2 /<>/debian/r-base-core/usr/share/info/R-exts.info-3.gz: 85.7% -- replaced with /<>/debian/r-base-core/usr/share/info/R-exts.info-3 /<>/debian/r-base-core/usr/share/info/R-exts.info.gz: 70.1% -- replaced with /<>/debian/r-base-core/usr/share/info/R-exts.info /<>/debian/r-base-core/usr/share/info/R-intro.info.gz: 70.1% -- replaced with /<>/debian/r-base-core/usr/share/info/R-intro.info /<>/debian/r-base-core/usr/share/info/R-ints.info.gz: 68.0% -- replaced with /<>/debian/r-base-core/usr/share/info/R-ints.info /<>/debian/r-base-core/usr/share/info/R-lang.info.gz: 71.6% -- replaced with /<>/debian/r-base-core/usr/share/info/R-lang.info dh_movefiles --sourcedir=debian/r-base-core -pr-doc-info rm -vf /<>/debian/r-doc-info/usr/share/info/dir \ /<>/debian/r-doc-info/usr/share/info/dir.old removed '/<>/debian/r-doc-info/usr/share/info/dir' touch install-indep-stamp 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 /<>/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 3140 -rw-rw-r-- 1 root root 2118354 Feb 22 23:31 libRmath.a -rwxrwxr-x 1 root root 1086624 Feb 22 23:31 libRmath.so drwxr-xr-x 2 root root 4096 Feb 22 23:31 pkgconfig renamed '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 \ /<>/debian/r-mathlib/usr/include install -m 0644 debian/Rprofile.site /<>/debian/r-base-core/etc/R install -m 0644 debian/Renviron.site /<>/debian/r-base-core/etc/R (cd /<>/debian/r-base-core/usr/lib/R/etc; \ cat /<>/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 46 with fuzz 2 (offset 13 lines). done dh_bash-completion # edd 12 Jan 2016 new location #install -m 0644 debian/R.bash-completion \ # debian/r-base-core/usr/share/bash-completion/completions/R (cd /<>/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 /<>/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../../lib/R/doc .) (cd /<>/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../R/doc .) (cd /<>/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../../lib/R/library .) install -p -m 0644 debian/r-base-core.lintian \ /<>/debian/r-base-core/usr/share/lintian/overrides/r-base-core install -p -m 0644 debian/r-recommended.lintian \ /<>/debian/r-recommended/usr/share/lintian/overrides/r-recommended install -p -m 0644 debian/r-mathlib.lintian \ /<>/debian/r-mathlib/usr/share/lintian/overrides/r-mathlib dh_installchangelogs -a -k doc/NEWS dh_strip --dbg-package=r-base-core-dbg dh_compress -a dh_fixperms -a dh_link -a dh_makeshlibs -a dh_installdeb -a dh_perl -a dh_shlibdeps -a -l /<>/debian/r-base-core/usr/lib/R/lib 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' 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: substitution variable ${perl:Depends} used, but is not defined dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing r-base-core (in debian/r-base-core); do_strip: , oemstrip: pkgstriptranslations: processing r-base-core-dbg (in debian/r-base-core-dbg); do_strip: , oemstrip: pkgstriptranslations: processing r-mathlib (in debian/r-mathlib); do_strip: , oemstrip: debian/r-base-core/usr/share/applications/R.desktop: does not have gettext domain, not stripping pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " 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 INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... pkgstripfiles: processing control file: debian/r-base-core/DEBIAN/control, package r-base-core, directory debian/r-base-core .. removing usr/share/doc/r-base-core/changelog.gz pkgstripfiles: Truncating usr/share/doc/r-base-core/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-base-core ... WARNING: optipng failed on usr/lib/R/library/graphics/help/figures/pch.png, ignoring WARNING: optipng failed on usr/lib/R/library/graphics/help/figures/mai.png, ignoring WARNING: optipng failed on usr/lib/R/library/graphics/help/figures/oma.png, ignoring ..oINFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... ooINFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... oINFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... oooINFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... o pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: PNG optimization (8/0) for package r-base-core took 5 s dpkg-deb: building package 'r-base-core' in '../r-base-core_3.6.2.20200221-1_amd64.deb'. 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 INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-mathlib ... pkgstripfiles: No PNG files. dpkg-deb: building package 'r-mathlib' in '../r-mathlib_3.6.2.20200221-1_amd64.deb'. Searching for duplicated docs in dependency r-base-core... symlinking changelog.Debian.gz in r-base-core-dbg to file in r-base-core pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-base-core-dbg ... pkgstripfiles: No PNG files. dpkg-deb: building package 'r-base-core-dbg' in '../r-base-core-dbg_3.6.2.20200221-1_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.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.faq debian/r-doc-html/usr/share/doc-base/r-faq 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.ints debian/r-doc-html/usr/share/doc-base/r-ints 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 \ /<>/debian/r-base-dev/usr/share/R/debian dh_compress -i dh_fixperms -i dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing r-base (in debian/r-base); do_strip: , oemstrip: pkgstriptranslations: processing r-base-html (in debian/r-base-html); do_strip: , oemstrip: pkgstriptranslations: processing r-recommended (in debian/r-recommended); do_strip: , oemstrip: pkgstriptranslations: processing r-doc-html (in debian/r-doc-html); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " 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 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-recommended... INFO: pkgstripfiles: waiting for lock (r-base-html) ... pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-base ... pkgstripfiles: No PNG files. dpkg-deb: building package 'r-base' in '../r-base_3.6.2.20200221-1_all.deb'. pkgstripfiles: processing control file: debian/r-doc-html/DEBIAN/control, package r-doc-html, directory debian/r-doc-html INFO: pkgstripfiles: waiting for lock (r-doc-html) ... INFO: pkgstriptranslations version 144 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_3.6.2.20200221-1_all.deb'. Searching for duplicated docs in dependency r-base-core... symlinking changelog.Debian.gz in r-base-html to file in r-base-core INFO: pkgstripfiles: waiting for lock (r-doc-html) ... 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_3.6.2.20200221-1_all.deb'. INFO: pkgstriptranslations version 144 pkgstriptranslations: processing r-doc-pdf (in debian/r-doc-pdf); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " INFO: pkgstripfiles: waiting for lock (r-doc-html) ... 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_3.6.2.20200221-1_all.deb'. 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_3.6.2.20200221-1_all.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/r-recommended/DEBIAN/control, package r-recommended, directory debian/r-recommended INFO: pkgstripfiles: waiting for lock (r-recommended) ... INFO: pkgstriptranslations version 144 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_3.6.2.20200221-1_all.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-recommended ... pkgstripfiles: No PNG files. dpkg-deb: building package 'r-recommended' in '../r-recommended_3.6.2.20200221-1_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../r-base_3.6.2.20200221-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20200222-2332 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ r-base_3.6.2.20200221-1_amd64.changes: -------------------------------------- Format: 1.8 Date: Sat, 22 Feb 2020 07:25:19 -0600 Source: r-base Binary: r-base r-base-core r-base-core-dbg r-base-dev r-base-html r-doc-html r-doc-info r-doc-pdf r-mathlib r-recommended Architecture: amd64 all Version: 3.6.2.20200221-1 Distribution: focal-proposed Urgency: medium 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 (3.6.2.20200221-1) unstable; 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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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(>= 1.6.0), libcurl4 (>= 7.28.0), libglib2.0-0 (>= 2.12.0), libgomp1 (>= 4.9), libicu65 (>= 65.1-1~), libjpeg8 (>= 8c), liblapack3 | liblapack.so.3, liblzma5 (>= 5.1.1alpha+20120614), libpango-1.0-0 (>= 1.14.0), libpangocairo-1.0-0 (>= 1.14.0), libpcre3, libpng16-16 (>= 1.6.2-1), libreadline8 (>= 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: elpa-ess, r-doc-info | r-doc-pdf, r-mathlib, r-base-html Conflicts: r-base-latex, r-cran-rcompgen, r-gnome Breaks: r-bioc-graph (<< 1.62.0-1~), r-cran-bbmle (<< 1.0.20-5~), r-cran-biocmanager (<< 1.30.4+dfsg-2~), r-cran-caret (<< 6.0-84-2~), r-cran-cmprsk (<< 2.2-8-1~), r-cran-coin (<< 1.3-0-1~), r-cran-dendextend (<< 1.12.0+dfsg-1~), r-cran-fields (<< 9.8-3-1~), r-cran-filehash (<< 2.4-2-2~), r-cran-future (<< 1.14.0+dfsg-1~), r-cran-genetics (<< 1.3.8.1.2-1~), r-cran-haplo.stats (<< 1.7.9-4~), r-cran-igraph (<< 1.2.4.1-1~), r-cran-lava (<< 1.6.5-1~), r-cran-libcoin (<< 1.0-4-1~), r-cran-msm (<< 1.6.7-1~), r-cran-permute (<< 0.9-5-1~), r-cran-phangorn (<< 2.5.5-1~), r-cran-popepi (<< 0.4.7-1~), r-cran-recipes (<< 0.1.6-1~), r-cran-sp (<< 1:1.3-1-2~), r-cran-spam (<< 2.2-2-1~), r-cran-units (<< 0.6-3-1~), r-cran-vegan (<< 2.5-5+dfsg-1~), r-cran-zelig (<< 5.1.6.1-1~) 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-3.5, 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-'. . 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./usr/share/doc/r-base-core/copyright lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-base-core/doc -> ../../R/doc lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-base-core/library -> ../../../lib/R/library drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/icons/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/icons/hicolor/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/icons/hicolor/48x48/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/icons/hicolor/48x48/apps/ -rw-r--r-- root/root 4111 2020-02-22 13:25 ./usr/share/icons/hicolor/48x48/apps/rlogo_icon.png drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/info/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/lintian/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 7851 2019-03-05 11:56 ./usr/share/lintian/overrides/r-base-core drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/man/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/man/man1/ -rw-r--r-- root/root 2581 2020-02-22 13:25 ./usr/share/man/man1/R.1.gz -rw-r--r-- root/root 659 2020-02-22 13:25 ./usr/share/man/man1/Rscript.1.gz drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/texmf/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/texmf/tex/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/texmf/tex/latex/ lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/texmf/tex/latex/R -> ../../../R/share/texmf r-base-dev_3.6.2.20200221-1_all.deb ----------------------------------- new debian package, version 2.0. size 4532 bytes: control archive=1676 bytes. 2267 bytes, 40 lines control 63 bytes, 1 lines md5sums 425 bytes, 26 lines * preinst #!/bin/sh Package: r-base-dev Source: r-base Version: 3.6.2.20200221-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Dirk Eddelbuettel Installed-Size: 15 Depends: r-base-core (>= 3.6.2.20200221-1), build-essential, gcc, g++, gfortran, libblas-dev | libatlas-base-dev, liblapack-dev | libatlas-base-dev, libncurses5-dev, libreadline-dev, libjpeg-dev, libpcre2-dev, libpcre3-dev, libpng-dev, zlib1g-dev, libbz2-dev, liblzma-dev, libicu-dev, xauth, pkg-config Suggests: texlive-base, texlive-latex-base, texlive-plain-generic, 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 2020-02-22 13:25 ./ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/R/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/R/debian/ -rwxr-xr-x root/root 6083 2019-03-05 11:56 ./usr/share/R/debian/r-cran.mk drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/doc/ lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-base-dev -> r-base-core r-base-html_3.6.2.20200221-1_all.deb ------------------------------------ new debian package, version 2.0. size 55864 bytes: control archive=1864 bytes. 2020 bytes, 43 lines control 2138 bytes, 29 lines md5sums Package: r-base-html Source: r-base Version: 3.6.2.20200221-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Dirk Eddelbuettel Installed-Size: 561 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: optional 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. It is not a required package as the same documentation is already included for on-line browsing. drwxr-xr-x root/root 0 2020-02-22 13:25 ./ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/lib/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/lib/R/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/lib/R/library/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/lib/R/library/base/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/lib/R/library/base/html/ -rw-r--r-- root/root 145750 2020-02-22 13:25 ./usr/lib/R/library/base/html/00Index.html -rw-r--r-- root/root 1335 2020-02-22 13:25 ./usr/lib/R/library/base/html/R.css drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/lib/R/library/compiler/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/lib/R/library/compiler/html/ -rw-r--r-- root/root 1859 2020-02-22 13:25 ./usr/lib/R/library/compiler/html/00Index.html -rw-r--r-- root/root 1335 2020-02-22 13:25 ./usr/lib/R/library/compiler/html/R.css drwxr-xr-x root/root 0 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2020-02-22 13:25 ./usr/lib/R/library/tcltk/html/00Index.html -rw-r--r-- root/root 1335 2020-02-22 13:25 ./usr/lib/R/library/tcltk/html/R.css drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/lib/R/library/tools/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/lib/R/library/tools/html/ -rw-r--r-- root/root 20720 2020-02-22 13:25 ./usr/lib/R/library/tools/html/00Index.html -rw-r--r-- root/root 1335 2020-02-22 13:25 ./usr/lib/R/library/tools/html/R.css drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/lib/R/library/utils/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/lib/R/library/utils/html/ -rw-r--r-- root/root 38570 2020-02-22 13:25 ./usr/lib/R/library/utils/html/00Index.html -rw-r--r-- root/root 1335 2020-02-22 13:25 ./usr/lib/R/library/utils/html/R.css drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/doc/r-base-html/ lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-base-html/changelog.Debian.gz -> ../r-base-core/changelog.Debian.gz -rw-r--r-- root/root 20761 2019-03-05 11:56 ./usr/share/doc/r-base-html/copyright r-base_3.6.2.20200221-1_all.deb ------------------------------- new debian package, version 2.0. size 9316 bytes: control archive=1476 bytes. 2139 bytes, 43 lines control 134 bytes, 2 lines md5sums Package: r-base Version: 3.6.2.20200221-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Dirk Eddelbuettel Installed-Size: 61 Depends: r-base-core (>= 3.6.2.20200221-1), r-recommended (= 3.6.2.20200221-1) Recommends: r-base-html, r-doc-html Suggests: elpa-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. Providing this package gives a way to users to then only install r-base-core if they so desire. drwxr-xr-x root/root 0 2020-02-22 13:25 ./ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/doc/r-base/ -rw-r--r-- root/root 463 2019-03-05 11:56 ./usr/share/doc/r-base/README.Debian lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-base/changelog.Debian.gz -> ../r-base-core/changelog.Debian.gz -rw-r--r-- root/root 20761 2019-03-05 11:56 ./usr/share/doc/r-base/copyright r-doc-html_3.6.2.20200221-1_all.deb ----------------------------------- new debian package, version 2.0. size 537292 bytes: control archive=2080 bytes. 1861 bytes, 40 lines control 1063 bytes, 16 lines md5sums 635 bytes, 32 lines * preinst #!/bin/sh Package: r-doc-html Source: r-base Version: 3.6.2.20200221-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Dirk Eddelbuettel Installed-Size: 3047 Suggests: r-base-core, mozilla | www-browser Replaces: r-base (<= 1.4.1-1) Section: doc Priority: optional Homepage: http://www.r-project.org/ Description: GNU R html manuals for statistical computing 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 R manuals in html format. The sibling packages r-doc-pdf and r-doc-info provides the same manuals. drwxr-xr-x root/root 0 2020-02-22 13:25 ./ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/R/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/R/doc/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/R/doc/manual/ -rw-r--r-- root/root 236637 2020-02-22 13:25 ./usr/share/R/doc/manual/R-FAQ.html -rw-r--r-- root/root 414008 2020-02-22 13:25 ./usr/share/R/doc/manual/R-admin.html -rw-r--r-- root/root 187050 2020-02-22 13:25 ./usr/share/R/doc/manual/R-data.html -rw-r--r-- root/root 983405 2020-02-22 13:25 ./usr/share/R/doc/manual/R-exts.html -rw-r--r-- root/root 509700 2020-02-22 13:25 ./usr/share/R/doc/manual/R-intro.html -rw-r--r-- root/root 357314 2020-02-22 13:25 ./usr/share/R/doc/manual/R-ints.html -rw-r--r-- root/root 346196 2020-02-22 13:25 ./usr/share/R/doc/manual/R-lang.html drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/doc-base/ -rw-r--r-- root/root 296 2019-03-05 11:56 ./usr/share/doc-base/r-admin -rw-r--r-- root/root 283 2019-03-05 11:56 ./usr/share/doc-base/r-data -rw-r--r-- root/root 398 2019-03-05 11:56 ./usr/share/doc-base/r-extensions -rw-r--r-- root/root 313 2019-03-05 11:56 ./usr/share/doc-base/r-faq -rw-r--r-- root/root 726 2019-03-05 11:56 ./usr/share/doc-base/r-intro -rw-r--r-- root/root 336 2019-03-05 11:56 ./usr/share/doc-base/r-ints -rw-r--r-- root/root 371 2019-03-05 11:56 ./usr/share/doc-base/r-language drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/doc/r-doc-html/ -rw-r--r-- root/root 893 2020-02-22 13:25 ./usr/share/doc/r-doc-html/changelog.Debian.gz -rw-r--r-- root/root 20761 2019-03-05 11:56 ./usr/share/doc/r-doc-html/copyright drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/doc/r-doc-html/manual/ lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-doc-html/manual/R-FAQ.html -> ../../../R/doc/manual/R-FAQ.html lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-doc-html/manual/R-admin.html -> ../../../R/doc/manual/R-admin.html lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-doc-html/manual/R-data.html -> ../../../R/doc/manual/R-data.html lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-doc-html/manual/R-exts.html -> ../../../R/doc/manual/R-exts.html lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-doc-html/manual/R-intro.html -> ../../../R/doc/manual/R-intro.html lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-doc-html/manual/R-ints.html -> ../../../R/doc/manual/R-ints.html lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-doc-html/manual/R-lang.html -> ../../../R/doc/manual/R-lang.html r-doc-info_3.6.2.20200221-1_all.deb ----------------------------------- new debian package, version 2.0. size 600892 bytes: control archive=1660 bytes. 1904 bytes, 41 lines control 795 bytes, 12 lines md5sums Package: r-doc-info Source: r-base Version: 3.6.2.20200221-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Dirk Eddelbuettel Installed-Size: 640 Depends: dpkg (>= 1.15.4) | install-info Suggests: r-base-core, info (>= 3.12) | info-browser Replaces: r-base (<= 1.4.1-1) Section: doc Priority: optional Homepage: http://www.r-project.org/ Description: GNU R info manuals statistical computing 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 R manuals in info format. The sibling packages r-doc-html and r-doc-pdf provide the same manuals. drwxr-xr-x root/root 0 2020-02-22 13:25 ./ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/doc/r-doc-info/ -rw-r--r-- root/root 893 2020-02-22 13:25 ./usr/share/doc/r-doc-info/changelog.Debian.gz -rw-r--r-- root/root 20761 2019-03-05 11:56 ./usr/share/doc/r-doc-info/copyright drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/info/ -rw-r--r-- root/root 46140 2020-02-22 13:25 ./usr/share/info/R-FAQ.info.gz -rw-r--r-- root/root 81935 2020-02-22 13:25 ./usr/share/info/R-admin.info.gz -rw-r--r-- root/root 32290 2020-02-22 13:25 ./usr/share/info/R-data.info.gz -rw-r--r-- root/root 100400 2020-02-22 13:25 ./usr/share/info/R-exts.info-1.gz -rw-r--r-- root/root 98425 2020-02-22 13:25 ./usr/share/info/R-exts.info-2.gz -rw-r--r-- root/root 7099 2020-02-22 13:25 ./usr/share/info/R-exts.info-3.gz -rw-r--r-- root/root 4371 2020-02-22 13:25 ./usr/share/info/R-exts.info.gz -rw-r--r-- root/root 89484 2020-02-22 13:25 ./usr/share/info/R-intro.info.gz -rw-r--r-- root/root 70974 2020-02-22 13:25 ./usr/share/info/R-ints.info.gz -rw-r--r-- root/root 54328 2020-02-22 13:25 ./usr/share/info/R-lang.info.gz r-doc-pdf_3.6.2.20200221-1_all.deb ---------------------------------- new debian package, version 2.0. size 9524508 bytes: control archive=1824 bytes. 1831 bytes, 39 lines control 763 bytes, 11 lines md5sums 422 bytes, 26 lines * preinst #!/bin/sh Package: r-doc-pdf Source: r-base Version: 3.6.2.20200221-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Dirk Eddelbuettel Installed-Size: 15898 Suggests: r-base-core, xdg-utils | pdf-viewer Section: doc Priority: optional Homepage: http://www.r-project.org/ Description: GNU R pdf manuals for statistical computing 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 R manuals in pdf format. The sibling packages r-doc-html and r-doc-info provides the same manuals. drwxr-xr-x root/root 0 2020-02-22 13:25 ./ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/R/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/R/doc/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/R/doc/manual/ -rw-r--r-- root/root 374487 2020-02-22 13:25 ./usr/share/R/doc/manual/R-FAQ.pdf -rw-r--r-- root/root 528971 2020-02-22 13:25 ./usr/share/R/doc/manual/R-admin.pdf -rw-r--r-- root/root 311811 2020-02-22 13:25 ./usr/share/R/doc/manual/R-data.pdf -rw-r--r-- root/root 986185 2020-02-22 13:25 ./usr/share/R/doc/manual/R-exts.pdf -rw-r--r-- root/root 633335 2020-02-22 13:25 ./usr/share/R/doc/manual/R-intro.pdf -rw-r--r-- root/root 452855 2020-02-22 13:25 ./usr/share/R/doc/manual/R-ints.pdf -rw-r--r-- root/root 379564 2020-02-22 13:25 ./usr/share/R/doc/manual/R-lang.pdf -rw-r--r-- root/root 6266446 2020-02-22 13:25 ./usr/share/R/doc/manual/fullrefman.pdf -rw-r--r-- root/root 6266446 2020-02-22 13:25 ./usr/share/R/doc/manual/refman.pdf drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/doc/r-doc-pdf/ -rw-r--r-- root/root 892 2020-02-22 13:25 ./usr/share/doc/r-doc-pdf/changelog.Debian.gz -rw-r--r-- root/root 20761 2019-03-05 11:56 ./usr/share/doc/r-doc-pdf/copyright drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/doc/r-doc-pdf/manual/ lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-doc-pdf/manual/R-FAQ.pdf -> ../../../R/doc/manual/R-FAQ.pdf lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-doc-pdf/manual/R-admin.pdf -> ../../../R/doc/manual/R-admin.pdf lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-doc-pdf/manual/R-data.pdf -> ../../../R/doc/manual/R-data.pdf lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-doc-pdf/manual/R-exts.pdf -> ../../../R/doc/manual/R-exts.pdf lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-doc-pdf/manual/R-intro.pdf -> ../../../R/doc/manual/R-intro.pdf lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-doc-pdf/manual/R-ints.pdf -> ../../../R/doc/manual/R-ints.pdf lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-doc-pdf/manual/R-lang.pdf -> ../../../R/doc/manual/R-lang.pdf lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-doc-pdf/manual/refman.pdf -> ../../../R/doc/manual/refman.pdf r-mathlib_3.6.2.20200221-1_amd64.deb ------------------------------------ new debian package, version 2.0. size 1857500 bytes: control archive=2088 bytes. 1866 bytes, 40 lines control 1148 bytes, 17 lines md5sums 369 bytes, 27 lines * postinst #!/bin/sh 21 bytes, 1 lines shlibs 72 bytes, 2 lines triggers Package: r-mathlib Source: r-base Version: 3.6.2.20200221-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Dirk Eddelbuettel Installed-Size: 2666 Depends: libc6 (>= 2.29) Recommends: r-base-core (= 3.6.2.20200221-1), r-base-dev (= 3.6.2.20200221-1) 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 2020-02-22 13:25 ./ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/include/ -rw-r--r-- root/root 17446 2020-02-22 13:25 ./usr/include/Rmath.h drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/lib/ -rw-r--r-- root/root 590466 2020-02-22 13:25 ./usr/lib/libRmath.a lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/lib/libRmath.so -> libRmath.so.1 lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/lib/libRmath.so.1 -> libRmath.so.1.0.0 -rw-r--r-- root/root 223640 2020-02-22 13:25 ./usr/lib/libRmath.so.1.0.0 drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/lib/pkgconfig/ -rw-r--r-- root/root 173 2020-02-22 13:25 ./usr/lib/pkgconfig/libRmath.pc drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/doc/r-mathlib/ -rw-r--r-- root/root 35933 2018-09-25 08:43 ./usr/share/doc/r-mathlib/NEWS.0.gz -rw-r--r-- root/root 108753 2018-09-25 08:43 ./usr/share/doc/r-mathlib/NEWS.1.gz -rw-r--r-- root/root 96630 2018-09-25 08:43 ./usr/share/doc/r-mathlib/NEWS.2.Rd.gz -rw-r--r-- root/root 229657 2018-09-25 08:43 ./usr/share/doc/r-mathlib/NEWS.2.gz -rw-r--r-- root/root 122167 2020-02-18 23:04 ./usr/share/doc/r-mathlib/NEWS.Rd.gz lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-mathlib/NEWS.gz -> changelog.gz -rw-r--r-- root/root 583739 2020-02-22 13:25 ./usr/share/doc/r-mathlib/NEWS.pdf.gz -rw-r--r-- root/root 516429 2020-02-22 13:25 ./usr/share/doc/r-mathlib/NEWS.rds.gz -rw-r--r-- root/root 2107 2018-09-25 08:47 ./usr/share/doc/r-mathlib/README.gz -rw-r--r-- root/root 3026 2019-03-05 11:56 ./usr/share/doc/r-mathlib/README.mathlib -rw-r--r-- root/root 892 2020-02-22 13:25 ./usr/share/doc/r-mathlib/changelog.Debian.gz -rw-r--r-- root/root 20761 2019-03-05 11:56 ./usr/share/doc/r-mathlib/copyright drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/doc/r-mathlib/examples/ -rw-r--r-- root/root 1371 2018-09-25 08:46 ./usr/share/doc/r-mathlib/examples/test.c drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/lintian/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 364 2019-03-05 11:56 ./usr/share/lintian/overrides/r-mathlib r-recommended_3.6.2.20200221-1_all.deb -------------------------------------- new debian package, version 2.0. size 2820 bytes: control archive=2172 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: 3.6.2.20200221-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Dirk Eddelbuettel Installed-Size: 13 Depends: r-base-core (>= 3.6.2.20200221-1), 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 2020-02-22 13:25 ./ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/lib/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/lib/R/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/lib/R/library/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/doc/ lrwxrwxrwx root/root 0 2020-02-22 13:25 ./usr/share/doc/r-recommended -> r-base-core drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/lintian/ drwxr-xr-x root/root 0 2020-02-22 13:25 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 542 2019-03-05 11:56 ./usr/share/lintian/overrides/r-recommended +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 412464 Build-Time: 858 Distribution: focal-proposed Host Architecture: amd64 Install-Time: 169 Job: r-base_3.6.2.20200221-1.dsc Machine Architecture: amd64 Package: r-base Package-Time: 1029 Source-Version: 3.6.2.20200221-1 Space: 412464 Status: successful Version: 3.6.2.20200221-1 -------------------------------------------------------------------------------- Finished at 20200222-2332 Build needed 00:17:09, 412464k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18748350 Scanning for processes to kill in build PACKAGEBUILD-18748350