https://launchpad.net/ubuntu/+source/r-base/3.4.4-1/+build/14757513 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos02-arm64-034 4.4.0-119-generic #143-Ubuntu SMP Mon Apr 2 16:10:02 UTC 2018 aarch64 Buildd toolchain package versions: launchpad-buildd_160 python-lpbuildd_160 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_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.3 dpkg-dev_1.18.4ubuntu1.4 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 14 Apr 02:27:44 ntpdate[1827]: adjust time server 10.211.37.1 offset 0.015261 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-14757513 /home/buildd/filecache-default/b70461af4419c13dbae7acd6fe74d075a1a9550f Creating target for build PACKAGEBUILD-14757513 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-14757513 Starting target for build PACKAGEBUILD-14757513 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-14757513 'deb http://ftpmaster.internal/ubuntu bionic main universe' 'deb http://ftpmaster.internal/ubuntu bionic-security main universe' 'deb http://ftpmaster.internal/ubuntu bionic-updates main universe' 'deb http://ftpmaster.internal/ubuntu bionic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-14757513 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-14757513 Updating target for build PACKAGEBUILD-14757513 Get:1 http://ftpmaster.internal/ubuntu bionic InRelease [235 kB] Get:2 http://ftpmaster.internal/ubuntu bionic-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu bionic-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu bionic-proposed InRelease [235 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main armhf Packages [973 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main Translation-en [517 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/universe armhf Packages [8262 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/universe Translation-en [4941 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf Packages [17.5 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-proposed/main Translation-en [11.3 kB] Get:11 http://ftpmaster.internal/ubuntu bionic-proposed/universe armhf Packages [49.3 kB] Get:12 http://ftpmaster.internal/ubuntu bionic-proposed/universe Translation-en [31.3 kB] Fetched 15.4 MB in 8s (1888 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: gnupg-agent libcryptsetup4 libcurl3-gnutls libgdbm3 libgssapi-krb5-2 libisl15 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmpfr4 libnghttp2-14 libpsl5 librtmp1 libssl1.0.0 libunistring0 libustr-1.0-1 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: dirmngr gcc-8-base gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpg-wks-server gpgconf gpgsm libargon2-0 libcom-err2 libcryptsetup12 libext2fs2 libgdbm-compat4 libgdbm5 libisl19 libjson-c3 libmpfr6 libnghttp2-14 libssl1.1 libunistring2 The following packages will be upgraded: adduser advancecomp apt apt-transport-https base-files base-passwd bash binutils binutils-arm-linux-gnueabihf binutils-common bsdutils build-essential ca-certificates coreutils cpp cpp-7 dash debconf debianutils dmsetup dpkg dpkg-dev e2fslibs e2fsprogs fakeroot fdisk findutils g++ g++-7 gcc gcc-7 gcc-7-base gnupg gnupg-agent gpgv hostname init init-system-helpers libapparmor1 libapt-pkg5.0 libasan4 libasn1-8-heimdal libassuan0 libatomic1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcilkrts5 libcomerr2 libcurl3-gnutls libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi6 libgcc-7-dev libgcc1 libgcrypt20 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhogweed4 libhx509-5-heimdal libidn11 libidn2-0 libip4tc0 libisl15 libk5crypto3 libkeyutils1 libkmod2 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblockfile-bin liblockfile1 liblz4-1 libmount1 libmpc3 libncurses5 libncursesw5 libnettle6 libnpth0 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre3 libperl5.26 libpng16-16 libprocps6 libpsl5 libreadline7 libroken18-heimdal libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage1 libslang2 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-7-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo5 libubsan0 libudev1 libuuid1 libwind0-heimdal linux-libc-dev login lsb-base mawk mount multiarch-support ncurses-base ncurses-bin openssl optipng passwd patch perl perl-base perl-modules-5.26 pinentry-curses pkgbinarymangler procps readline-common sed sensible-utils systemd systemd-sysv sysvinit-utils tzdata ubuntu-keyring util-linux 155 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. Need to get 61.4 MB of archives. After this operation, 6240 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu bionic/main armhf base-files armhf 10.1ubuntu1 [58.2 kB] Get:2 http://ftpmaster.internal/ubuntu bionic/main armhf debianutils armhf 4.8.4 [84.5 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main armhf bash armhf 4.4.18-2ubuntu1 [552 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main armhf bsdutils armhf 1:2.31.1-0.4ubuntu3 [55.2 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main armhf coreutils armhf 8.28-1ubuntu1 [1128 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main armhf dpkg armhf 1.19.0.5ubuntu1 [1095 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main armhf dash armhf 0.5.8-2.10 [80.4 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/main armhf libcom-err2 armhf 1.44.1-1 [9076 B] Get:9 http://ftpmaster.internal/ubuntu bionic/main armhf libcomerr2 armhf 1.44.1-1 [2696 B] Get:10 http://ftpmaster.internal/ubuntu bionic/main armhf perl-modules-5.26 all 5.26.1-5 [2761 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main armhf libgdbm5 armhf 1.14.1-6 [23.4 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/main armhf libgdbm-compat4 armhf 1.14.1-6 [5764 B] Get:13 http://ftpmaster.internal/ubuntu bionic/main armhf libperl5.26 armhf 5.26.1-5 [2886 kB] Get:14 http://ftpmaster.internal/ubuntu bionic/main armhf perl armhf 5.26.1-5 [202 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main armhf perl-base armhf 5.26.1-5 [1289 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main armhf libc6-dev armhf 2.27-0ubuntu3 [1900 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main armhf libc-dev-bin armhf 2.27-0ubuntu3 [59.4 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main armhf linux-libc-dev armhf 4.15.0-15.16 [988 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main armhf libc6 armhf 2.27-0ubuntu3 [2211 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main armhf libc-bin armhf 2.27-0ubuntu3 [459 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main armhf gcc-8-base armhf 8-20180408-0ubuntu1 [18.1 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main armhf libgcc1 armhf 1:8-20180408-0ubuntu1 [37.0 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main armhf libext2fs2 armhf 1.44.1-1 [145 kB] Get:24 http://ftpmaster.internal/ubuntu bionic/main armhf e2fslibs armhf 1.44.1-1 [2700 B] Get:25 http://ftpmaster.internal/ubuntu bionic/main armhf e2fsprogs armhf 1.44.1-1 [369 kB] Get:26 http://ftpmaster.internal/ubuntu bionic/main armhf findutils armhf 4.6.0+git+20170828-2 [277 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main armhf hostname armhf 3.20 [10.4 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main armhf login armhf 1:4.5-1ubuntu1 [303 kB] Get:29 http://ftpmaster.internal/ubuntu bionic/main armhf libncurses5 armhf 6.1-1ubuntu1 [74.8 kB] Get:30 http://ftpmaster.internal/ubuntu bionic/main armhf libtinfo5 armhf 6.1-1ubuntu1 [68.4 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/main armhf ncurses-bin armhf 6.1-1ubuntu1 [155 kB] Get:32 http://ftpmaster.internal/ubuntu bionic/main armhf libncursesw5 armhf 6.1-1ubuntu1 [95.7 kB] Get:33 http://ftpmaster.internal/ubuntu bionic/main armhf sed armhf 4.4-2 [175 kB] Get:34 http://ftpmaster.internal/ubuntu bionic/main armhf libuuid1 armhf 2.31.1-0.4ubuntu3 [19.2 kB] Get:35 http://ftpmaster.internal/ubuntu bionic/main armhf libblkid1 armhf 2.31.1-0.4ubuntu3 [112 kB] Get:36 http://ftpmaster.internal/ubuntu bionic/main armhf libsmartcols1 armhf 2.31.1-0.4ubuntu3 [74.3 kB] Get:37 http://ftpmaster.internal/ubuntu bionic/main armhf libfdisk1 armhf 2.31.1-0.4ubuntu3 [151 kB] Get:38 http://ftpmaster.internal/ubuntu bionic/main armhf libpcre3 armhf 2:8.39-9 [209 kB] Get:39 http://ftpmaster.internal/ubuntu bionic/main armhf libselinux1 armhf 2.7-2build2 [58.9 kB] Get:40 http://ftpmaster.internal/ubuntu bionic/main armhf libmount1 armhf 2.31.1-0.4ubuntu3 [122 kB] Get:41 http://ftpmaster.internal/ubuntu bionic/main armhf fdisk armhf 2.31.1-0.4ubuntu3 [97.6 kB] Get:42 http://ftpmaster.internal/ubuntu bionic/main armhf util-linux armhf 2.31.1-0.4ubuntu3 [845 kB] Get:43 http://ftpmaster.internal/ubuntu bionic/main armhf base-passwd armhf 3.5.44 [45.9 kB] Get:44 http://ftpmaster.internal/ubuntu bionic/main armhf init-system-helpers all 1.51 [37.3 kB] Get:45 http://ftpmaster.internal/ubuntu bionic/main armhf ncurses-base all 6.1-1ubuntu1 [17.3 kB] Get:46 http://ftpmaster.internal/ubuntu bionic/main armhf sysvinit-utils armhf 2.88dsf-59.10ubuntu1 [17.2 kB] Get:47 http://ftpmaster.internal/ubuntu bionic/main armhf liblz4-1 armhf 0.0~r131-2ubuntu3 [43.9 kB] Get:48 http://ftpmaster.internal/ubuntu bionic/main armhf libstdc++6 armhf 8-20180408-0ubuntu1 [349 kB] Get:49 http://ftpmaster.internal/ubuntu bionic/main armhf libudev1 armhf 237-3ubuntu8 [48.3 kB] Get:50 http://ftpmaster.internal/ubuntu bionic/main armhf libapt-pkg5.0 armhf 1.6~beta1 [726 kB] Get:51 http://ftpmaster.internal/ubuntu bionic/main armhf libaudit-common all 1:2.8.2-1ubuntu1 [4132 B] Get:52 http://ftpmaster.internal/ubuntu bionic/main armhf libcap-ng0 armhf 0.7.7-3.1 [9816 B] Get:53 http://ftpmaster.internal/ubuntu bionic/main armhf libaudit1 armhf 1:2.8.2-1ubuntu1 [35.5 kB] Get:54 http://ftpmaster.internal/ubuntu bionic/main armhf debconf all 1.5.66 [124 kB] Get:55 http://ftpmaster.internal/ubuntu bionic/main armhf libpam0g armhf 1.1.8-3.6ubuntu2 [49.5 kB] Get:56 http://ftpmaster.internal/ubuntu bionic/main armhf libsemanage-common all 2.7-2build2 [6904 B] Get:57 http://ftpmaster.internal/ubuntu bionic/main armhf libsemanage1 armhf 2.7-2build2 [72.1 kB] Get:58 http://ftpmaster.internal/ubuntu bionic/main armhf libpam-modules-bin armhf 1.1.8-3.6ubuntu2 [32.4 kB] Get:59 http://ftpmaster.internal/ubuntu bionic/main armhf libpam-modules armhf 1.1.8-3.6ubuntu2 [224 kB] Get:60 http://ftpmaster.internal/ubuntu bionic/main armhf passwd armhf 1:4.5-1ubuntu1 [769 kB] Get:61 http://ftpmaster.internal/ubuntu bionic/main armhf adduser all 3.116ubuntu1 [163 kB] Get:62 http://ftpmaster.internal/ubuntu bionic/main armhf libgpg-error0 armhf 1.27-6 [33.6 kB] Get:63 http://ftpmaster.internal/ubuntu bionic/main armhf libgcrypt20 armhf 1.8.1-4ubuntu1 [364 kB] Get:64 http://ftpmaster.internal/ubuntu bionic/main armhf gpgv armhf 2.2.4-1ubuntu1 [166 kB] Get:65 http://ftpmaster.internal/ubuntu bionic/main armhf ubuntu-keyring all 2018.02.28 [20.7 kB] Get:66 http://ftpmaster.internal/ubuntu bionic/main armhf libunistring2 armhf 0.9.9-0ubuntu1 [352 kB] Get:67 http://ftpmaster.internal/ubuntu bionic/main armhf libgmp10 armhf 2:6.1.2+dfsg-2 [182 kB] Get:68 http://ftpmaster.internal/ubuntu bionic/main armhf libnettle6 armhf 3.4-1 [123 kB] Get:69 http://ftpmaster.internal/ubuntu bionic/main armhf libhogweed4 armhf 3.4-1 [127 kB] Get:70 http://ftpmaster.internal/ubuntu bionic/main armhf libidn2-0 armhf 2.0.4-1.1build2 [46.1 kB] Get:71 http://ftpmaster.internal/ubuntu bionic/main armhf libffi6 armhf 3.2.1-8 [16.4 kB] Get:72 http://ftpmaster.internal/ubuntu bionic/main armhf libp11-kit0 armhf 0.23.9-2 [162 kB] Get:73 http://ftpmaster.internal/ubuntu bionic/main armhf libtasn1-6 armhf 4.13-2 [31.1 kB] Get:74 http://ftpmaster.internal/ubuntu bionic/main armhf libgnutls30 armhf 3.5.18-1ubuntu1 [585 kB] Get:75 http://ftpmaster.internal/ubuntu bionic/main armhf libseccomp2 armhf 2.3.1-2.1ubuntu4 [29.8 kB] Get:76 http://ftpmaster.internal/ubuntu bionic/main armhf apt armhf 1.6~beta1 [1112 kB] Get:77 http://ftpmaster.internal/ubuntu bionic/main armhf libargon2-0 armhf 0~20161029-1.1 [20.4 kB] Get:78 http://ftpmaster.internal/ubuntu bionic/main armhf libjson-c3 armhf 0.12.1-1.3 [19.6 kB] Get:79 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libdevmapper1.02.1 armhf 2:1.02.145-4.1ubuntu3 [117 kB] Get:80 http://ftpmaster.internal/ubuntu bionic/main armhf libcryptsetup12 armhf 2:2.0.2-1ubuntu1 [119 kB] Get:81 http://ftpmaster.internal/ubuntu bionic/main armhf libapparmor1 armhf 2.12-4ubuntu4 [27.8 kB] Get:82 http://ftpmaster.internal/ubuntu bionic/main armhf libcap2 armhf 1:2.25-1.2 [11.7 kB] Get:83 http://ftpmaster.internal/ubuntu bionic/main armhf libidn11 armhf 1.33-2.1ubuntu1 [43.4 kB] Get:84 http://ftpmaster.internal/ubuntu bionic/main armhf libip4tc0 armhf 1.6.1-2ubuntu2 [17.8 kB] Get:85 http://ftpmaster.internal/ubuntu bionic/main armhf libkmod2 armhf 24-1ubuntu3 [34.4 kB] Get:86 http://ftpmaster.internal/ubuntu bionic/main armhf mount armhf 2.31.1-0.4ubuntu3 [99.7 kB] Get:87 http://ftpmaster.internal/ubuntu bionic/main armhf libprocps6 armhf 2:3.3.12-3ubuntu1 [28.4 kB] Get:88 http://ftpmaster.internal/ubuntu bionic/main armhf lsb-base all 9.20170808ubuntu1 [12.5 kB] Get:89 http://ftpmaster.internal/ubuntu bionic/main armhf procps armhf 2:3.3.12-3ubuntu1 [214 kB] Get:90 http://ftpmaster.internal/ubuntu bionic/main armhf systemd armhf 237-3ubuntu8 [2720 kB] Get:91 http://ftpmaster.internal/ubuntu bionic/main armhf libsystemd0 armhf 237-3ubuntu8 [185 kB] Get:92 http://ftpmaster.internal/ubuntu bionic/main armhf mawk armhf 1.3.3-17ubuntu3 [72.5 kB] Get:93 http://ftpmaster.internal/ubuntu bionic/main armhf init armhf 1.51 [5864 B] Get:94 http://ftpmaster.internal/ubuntu bionic/main armhf systemd-sysv armhf 237-3ubuntu8 [11.6 kB] Get:95 http://ftpmaster.internal/ubuntu bionic/main armhf libpam-runtime all 1.1.8-3.6ubuntu2 [37.0 kB] Get:96 http://ftpmaster.internal/ubuntu bionic/main armhf libss2 armhf 1.44.1-1 [9380 B] Get:97 http://ftpmaster.internal/ubuntu bionic/main armhf sensible-utils all 0.0.12 [14.8 kB] Get:98 http://ftpmaster.internal/ubuntu bionic/main armhf libssl1.1 armhf 1.1.0g-2ubuntu3 [911 kB] Get:99 http://ftpmaster.internal/ubuntu bionic/main armhf openssl armhf 1.1.0g-2ubuntu3 [510 kB] Get:100 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf ca-certificates all 20180409 [151 kB] Get:101 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf dmsetup armhf 2:1.02.145-4.1ubuntu3 [73.7 kB] Get:102 http://ftpmaster.internal/ubuntu bionic/main armhf readline-common all 7.0-3 [52.9 kB] Get:103 http://ftpmaster.internal/ubuntu bionic/main armhf libreadline7 armhf 7.0-3 [103 kB] Get:104 http://ftpmaster.internal/ubuntu bionic/main armhf libslang2 armhf 2.3.1a-3ubuntu1 [381 kB] Get:105 http://ftpmaster.internal/ubuntu bionic/main armhf libsqlite3-0 armhf 3.22.0-1 [421 kB] Get:106 http://ftpmaster.internal/ubuntu bionic/main armhf tzdata all 2018d-1 [188 kB] Get:107 http://ftpmaster.internal/ubuntu bionic/main armhf libgssapi-krb5-2 armhf 1.16-2build1 [101 kB] Get:108 http://ftpmaster.internal/ubuntu bionic/main armhf libkrb5-3 armhf 1.16-2build1 [233 kB] Get:109 http://ftpmaster.internal/ubuntu bionic/main armhf libk5crypto3 armhf 1.16-2build1 [83.2 kB] Get:110 http://ftpmaster.internal/ubuntu bionic/main armhf libkrb5support0 armhf 1.16-2build1 [27.5 kB] Get:111 http://ftpmaster.internal/ubuntu bionic/main armhf libkeyutils1 armhf 1.5.9-9.2ubuntu1 [8380 B] Get:112 http://ftpmaster.internal/ubuntu bionic/main armhf libpng16-16 armhf 1.6.34-1 [159 kB] Get:113 http://ftpmaster.internal/ubuntu bionic/main armhf libpsl5 armhf 0.19.1-5build1 [40.5 kB] Get:114 http://ftpmaster.internal/ubuntu bionic/main armhf libssl1.0.0 armhf 1.0.2n-1ubuntu5 [710 kB] Get:115 http://ftpmaster.internal/ubuntu bionic/main armhf multiarch-support armhf 2.27-0ubuntu3 [6916 B] Get:116 http://ftpmaster.internal/ubuntu bionic/main armhf advancecomp armhf 2.1-1 [166 kB] Get:117 http://ftpmaster.internal/ubuntu bionic/universe armhf apt-transport-https all 1.6~beta1 [1692 B] Get:118 http://ftpmaster.internal/ubuntu bionic/main armhf libbinutils armhf 2.30-15ubuntu1 [309 kB] Get:119 http://ftpmaster.internal/ubuntu bionic/main armhf binutils armhf 2.30-15ubuntu1 [3360 B] Get:120 http://ftpmaster.internal/ubuntu bionic/main armhf binutils-common armhf 2.30-15ubuntu1 [193 kB] Get:121 http://ftpmaster.internal/ubuntu bionic/main armhf binutils-arm-linux-gnueabihf armhf 2.30-15ubuntu1 [2175 kB] Get:122 http://ftpmaster.internal/ubuntu bionic/main armhf libgomp1 armhf 8-20180408-0ubuntu1 [66.6 kB] Get:123 http://ftpmaster.internal/ubuntu bionic/main armhf libatomic1 armhf 8-20180408-0ubuntu1 [7068 B] Get:124 http://ftpmaster.internal/ubuntu bionic/main armhf libasan4 armhf 7.3.0-16ubuntu2 [328 kB] Get:125 http://ftpmaster.internal/ubuntu bionic/main armhf libubsan0 armhf 7.3.0-16ubuntu2 [108 kB] Get:126 http://ftpmaster.internal/ubuntu bionic/main armhf libcilkrts5 armhf 7.3.0-16ubuntu2 [36.0 kB] Get:127 http://ftpmaster.internal/ubuntu bionic/main armhf g++-7 armhf 7.3.0-16ubuntu2 [6047 kB] Get:128 http://ftpmaster.internal/ubuntu bionic/main armhf gcc-7 armhf 7.3.0-16ubuntu2 [5946 kB] Get:129 http://ftpmaster.internal/ubuntu bionic/main armhf libstdc++-7-dev armhf 7.3.0-16ubuntu2 [1535 kB] Get:130 http://ftpmaster.internal/ubuntu bionic/main armhf libgcc-7-dev armhf 7.3.0-16ubuntu2 [706 kB] Get:131 http://ftpmaster.internal/ubuntu bionic/main armhf libcc1-0 armhf 8-20180408-0ubuntu1 [32.7 kB] Get:132 http://ftpmaster.internal/ubuntu bionic/main armhf cpp-7 armhf 7.3.0-16ubuntu2 [5295 kB] Get:133 http://ftpmaster.internal/ubuntu bionic/main armhf gcc-7-base armhf 7.3.0-16ubuntu2 [19.2 kB] Get:134 http://ftpmaster.internal/ubuntu bionic/main armhf libisl19 armhf 0.19-1 [426 kB] Get:135 http://ftpmaster.internal/ubuntu bionic/main armhf libmpc3 armhf 1.1.0-1 [33.2 kB] Get:136 http://ftpmaster.internal/ubuntu bionic/main armhf libmpfr6 armhf 4.0.1-1 [194 kB] Get:137 http://ftpmaster.internal/ubuntu bionic/main armhf cpp armhf 4:7.3.0-3ubuntu2 [27.5 kB] Get:138 http://ftpmaster.internal/ubuntu bionic/main armhf gcc armhf 4:7.3.0-3ubuntu2 [5208 B] Get:139 http://ftpmaster.internal/ubuntu bionic/main armhf g++ armhf 4:7.3.0-3ubuntu2 [1576 B] Get:140 http://ftpmaster.internal/ubuntu bionic/main armhf dpkg-dev all 1.19.0.5ubuntu1 [607 kB] Get:141 http://ftpmaster.internal/ubuntu bionic/main armhf libdpkg-perl all 1.19.0.5ubuntu1 [211 kB] Get:142 http://ftpmaster.internal/ubuntu bionic/main armhf patch armhf 2.7.6-2ubuntu1 [98.9 kB] Get:143 http://ftpmaster.internal/ubuntu bionic/main armhf build-essential armhf 12.4ubuntu1 [4752 B] Get:144 http://ftpmaster.internal/ubuntu bionic/main armhf gnupg-l10n all 2.2.4-1ubuntu1 [48.6 kB] Get:145 http://ftpmaster.internal/ubuntu bionic/main armhf libassuan0 armhf 2.5.1-2 [28.3 kB] Get:146 http://ftpmaster.internal/ubuntu bionic/main armhf gnupg armhf 2.2.4-1ubuntu1 [249 kB] Get:147 http://ftpmaster.internal/ubuntu bionic/universe armhf gnupg-agent all 2.2.4-1ubuntu1 [4544 B] Get:148 http://ftpmaster.internal/ubuntu bionic/main armhf gpgconf armhf 2.2.4-1ubuntu1 [105 kB] Get:149 http://ftpmaster.internal/ubuntu bionic/main armhf pinentry-curses armhf 1.1.0-1 [31.4 kB] Get:150 http://ftpmaster.internal/ubuntu bionic/main armhf libnpth0 armhf 1.5-3 [6632 B] Get:151 http://ftpmaster.internal/ubuntu bionic/main armhf gpg-agent armhf 2.2.4-1ubuntu1 [189 kB] Get:152 http://ftpmaster.internal/ubuntu bionic/main armhf gnupg-utils armhf 2.2.4-1ubuntu1 [106 kB] Get:153 http://ftpmaster.internal/ubuntu bionic/main armhf gpg armhf 2.2.4-1ubuntu1 [409 kB] Get:154 http://ftpmaster.internal/ubuntu bionic/main armhf gpg-wks-client armhf 2.2.4-1ubuntu1 [76.8 kB] Get:155 http://ftpmaster.internal/ubuntu bionic/main armhf gpg-wks-server armhf 2.2.4-1ubuntu1 [71.8 kB] Get:156 http://ftpmaster.internal/ubuntu bionic/main armhf gpgsm armhf 2.2.4-1ubuntu1 [183 kB] Get:157 http://ftpmaster.internal/ubuntu bionic/main armhf dirmngr armhf 2.2.4-1ubuntu1 [275 kB] Get:158 http://ftpmaster.internal/ubuntu bionic/main armhf libfakeroot armhf 1.22-2ubuntu1 [21.6 kB] Get:159 http://ftpmaster.internal/ubuntu bionic/main armhf fakeroot armhf 1.22-2ubuntu1 [60.3 kB] Get:160 http://ftpmaster.internal/ubuntu bionic/main armhf libroken18-heimdal armhf 7.5.0+dfsg-1 [34.1 kB] Get:161 http://ftpmaster.internal/ubuntu bionic/main armhf libasn1-8-heimdal armhf 7.5.0+dfsg-1 [136 kB] Get:162 http://ftpmaster.internal/ubuntu bionic/main armhf libnghttp2-14 armhf 1.30.0-1ubuntu1 [67.4 kB] Get:163 http://ftpmaster.internal/ubuntu bionic/main armhf libcurl3-gnutls armhf 7.58.0-2ubuntu3 [182 kB] Get:164 http://ftpmaster.internal/ubuntu bionic/main armhf libheimbase1-heimdal armhf 7.5.0+dfsg-1 [24.1 kB] Get:165 http://ftpmaster.internal/ubuntu bionic/main armhf libhcrypto4-heimdal armhf 7.5.0+dfsg-1 [76.5 kB] Get:166 http://ftpmaster.internal/ubuntu bionic/main armhf libwind0-heimdal armhf 7.5.0+dfsg-1 [47.2 kB] Get:167 http://ftpmaster.internal/ubuntu bionic/main armhf libhx509-5-heimdal armhf 7.5.0+dfsg-1 [87.9 kB] Get:168 http://ftpmaster.internal/ubuntu bionic/main armhf libkrb5-26-heimdal armhf 7.5.0+dfsg-1 [168 kB] Get:169 http://ftpmaster.internal/ubuntu bionic/main armhf libheimntlm0-heimdal armhf 7.5.0+dfsg-1 [13.1 kB] Get:170 http://ftpmaster.internal/ubuntu bionic/main armhf libgssapi3-heimdal armhf 7.5.0+dfsg-1 [78.8 kB] Get:171 http://ftpmaster.internal/ubuntu bionic/universe armhf libisl15 armhf 0.18-4 [423 kB] Get:172 http://ftpmaster.internal/ubuntu bionic/main armhf liblockfile-bin armhf 1.14-1.1 [10.9 kB] Get:173 http://ftpmaster.internal/ubuntu bionic/main armhf liblockfile1 armhf 1.14-1.1 [5784 B] Get:174 http://ftpmaster.internal/ubuntu bionic/main armhf libsasl2-modules-db armhf 2.1.27~101-g0780600+dfsg-3ubuntu2 [13.0 kB] Get:175 http://ftpmaster.internal/ubuntu bionic/main armhf libsasl2-2 armhf 2.1.27~101-g0780600+dfsg-3ubuntu2 [42.0 kB] Get:176 http://ftpmaster.internal/ubuntu bionic/main armhf optipng armhf 0.7.6-1.1 [80.6 kB] Get:177 http://ftpmaster.internal/ubuntu bionic/main armhf pkgbinarymangler all 136 [52.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 61.4 MB in 4s (14.6 MB/s) (Reading database ... 12457 files and directories currently installed.) 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Setting up libcc1-0:armhf (8-20180408-0ubuntu1) ... Setting up apt-transport-https (1.6~beta1) ... Setting up libssl1.0.0:armhf (1.0.2n-1ubuntu5) ... Setting up libnghttp2-14:armhf (1.30.0-1ubuntu1) ... Setting up e2fslibs:armhf (1.44.1-1) ... Setting up libpng16-16:armhf (1.6.34-1) ... Setting up libreadline7:armhf (7.0-3) ... Setting up libpsl5:armhf (0.19.1-5build1) ... Setting up multiarch-support (2.27-0ubuntu3) ... Setting up tzdata (2018d-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Apr 14 02:29:39 UTC 2018. Universal Time is now: Sat Apr 14 02:29:39 UTC 2018. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (237-3ubuntu8) ... Setting up mawk (1.3.3-17ubuntu3) ... Setting up liblockfile1:armhf (1.14-1.1) ... Setting up libsasl2-modules-db:armhf (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up linux-libc-dev:armhf (4.15.0-15.16) ... Setting up libmpfr6:armhf (4.0.1-1) ... Setting up advancecomp (2.1-1) ... Setting up libsasl2-2:armhf (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up libroken18-heimdal:armhf (7.5.0+dfsg-1) ... Setting up perl-modules-5.26 (5.26.1-5) ... Setting up libgdbm5:armhf (1.14.1-6) ... Setting up libkrb5support0:armhf (1.16-2build1) ... Setting up optipng (0.7.6-1.1) ... Setting up gnupg-l10n (2.2.4-1ubuntu1) ... Setting up gcc-7-base:armhf (7.3.0-16ubuntu2) ... Setting up binutils-common:armhf (2.30-15ubuntu1) ... Setting up libisl15:armhf (0.18-4) ... Setting up sensible-utils (0.0.12) ... Setting up patch (2.7.6-2ubuntu1) ... Processing triggers for libc-bin (2.27-0ubuntu3) ... Setting up libssl1.1:armhf (1.1.0g-2ubuntu3) ... Setting up libheimbase1-heimdal:armhf (7.5.0+dfsg-1) ... Setting up libfakeroot:armhf (1.22-2ubuntu1) ... Setting up openssl (1.1.0g-2ubuntu3) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up libsqlite3-0:armhf (3.22.0-1) ... Setting up dmsetup (2:1.02.145-4.1ubuntu3) ... Setting up libmpc3:armhf (1.1.0-1) ... Setting up libc-dev-bin (2.27-0ubuntu3) ... Setting up libcomerr2:armhf (1.44.1-1) ... Setting up libgdbm-compat4:armhf (1.14.1-6) ... Setting up libkeyutils1:armhf (1.5.9-9.2ubuntu1) ... Setting up ca-certificates (20180409) ... Updating certificates in /etc/ssl/certs... 8 added, 23 removed; done. Setting up libc6-dev:armhf (2.27-0ubuntu3) ... Setting up libslang2:armhf (2.3.1a-3ubuntu1) ... Setting up libassuan0:armhf (2.5.1-2) ... Setting up libisl19:armhf (0.19-1) ... Setting up libk5crypto3:armhf (1.16-2build1) ... Setting up pkgbinarymangler (136) ... Setting up libwind0-heimdal:armhf (7.5.0+dfsg-1) ... Setting up libasan4:armhf (7.3.0-16ubuntu2) ... Setting up libbinutils:armhf (2.30-15ubuntu1) ... Setting up libcilkrts5:armhf (7.3.0-16ubuntu2) ... Setting up init (1.51) ... Setting up libasn1-8-heimdal:armhf (7.5.0+dfsg-1) ... Setting up libubsan0:armhf (7.3.0-16ubuntu2) ... Setting up gpgconf (2.2.4-1ubuntu1) ... Setting up libhcrypto4-heimdal:armhf (7.5.0+dfsg-1) ... Setting up binutils-arm-linux-gnueabihf (2.30-15ubuntu1) ... Setting up fakeroot (1.22-2ubuntu1) ... Setting up libhx509-5-heimdal:armhf (7.5.0+dfsg-1) ... Setting up libgcc-7-dev:armhf (7.3.0-16ubuntu2) ... Setting up cpp-7 (7.3.0-16ubuntu2) ... Setting up libstdc++-7-dev:armhf (7.3.0-16ubuntu2) ... Setting up libperl5.26:armhf (5.26.1-5) ... Setting up gpgsm (2.2.4-1ubuntu1) ... Setting up gnupg-utils (2.2.4-1ubuntu1) ... Setting up pinentry-curses (1.1.0-1) ... Setting up libkrb5-3:armhf (1.16-2build1) ... Setting up binutils (2.30-15ubuntu1) ... Setting up libkrb5-26-heimdal:armhf (7.5.0+dfsg-1) ... Setting up dirmngr (2.2.4-1ubuntu1) ... Setting up libheimntlm0-heimdal:armhf (7.5.0+dfsg-1) ... Setting up gpg (2.2.4-1ubuntu1) ... Setting up cpp (4:7.3.0-3ubuntu2) ... Setting up gcc-7 (7.3.0-16ubuntu2) ... Setting up g++-7 (7.3.0-16ubuntu2) ... Setting up gpg-agent (2.2.4-1ubuntu1) ... Installing new version of config file /etc/X11/Xsession.d/90gpg-agent ... Setting up gcc (4:7.3.0-3ubuntu2) ... Setting up gpg-wks-server (2.2.4-1ubuntu1) ... Setting up gpg-wks-client (2.2.4-1ubuntu1) ... Setting up libgssapi-krb5-2:armhf (1.16-2build1) ... Setting up perl (5.26.1-5) ... Setting up g++ (4:7.3.0-3ubuntu2) ... Setting up gnupg-agent (2.2.4-1ubuntu1) ... Setting up libgssapi3-heimdal:armhf (7.5.0+dfsg-1) ... Setting up libcurl3-gnutls:armhf (7.58.0-2ubuntu3) ... Setting up gnupg (2.2.4-1ubuntu1) ... Setting up libdpkg-perl (1.19.0.5ubuntu1) ... Setting up dpkg-dev (1.19.0.5ubuntu1) ... Setting up build-essential (12.4ubuntu1) ... Processing triggers for libc-bin (2.27-0ubuntu3) ... Processing triggers for ca-certificates (20180409) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-14757513 armhf bionic-proposed -c chroot:build-PACKAGEBUILD-14757513 --arch=armhf --dist=bionic-proposed --nolog r-base_3.4.4-1.dsc Initiating build PACKAGEBUILD-14757513 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-119-generic #143-Ubuntu SMP Mon Apr 2 16:10:02 UTC 2018 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-034.buildd +==============================================================================+ | r-base 3.4.4-1 (armhf) 14 Apr 2018 02:30 | +==============================================================================+ Package: r-base Version: 3.4.4-1 Source Version: 3.4.4-1 Distribution: bionic-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/r-base-91nxmN/r-base-3.4.4' with '<>' I: NOTICE: Log filtering will replace 'build/r-base-91nxmN' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-14757513/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- r-base_3.4.4-1.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-WhO3f7/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-WhO3f7/apt_archive ./ InRelease Get:2 copy:/<>/resolver-WhO3f7/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-WhO3f7/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-WhO3f7/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-WhO3f7/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (22.2 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: gnupg-agent libcryptsetup4 libcurl3-gnutls libgdbm3 libgssapi-krb5-2 libisl15 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmpfr4 libnghttp2-14 libpsl5 librtmp1 libssl1.0.0 libunistring0 libustr-1.0-1 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-WhO3f7/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 (34.5 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12725 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.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, libpcre3-dev, libcurl4-openssl-dev | libcurl4-dev, xdg-utils, zlib1g-dev, libpng-dev, libjpeg-dev, libx11-dev, libxt-dev, x11proto-core-dev, libpango1.0-dev, libcairo2-dev, libtiff5-dev, xvfb, xauth, xfonts-base, texlive-base, texlive-latex-base, texlive-generic-recommended, texlive-fonts-recommended, texlive-fonts-extra, texlive-extra-utils, texlive-latex-recommended, texlive-latex-extra, openjdk-9-jdk | default-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, libpcre3-dev, libcurl4-openssl-dev | libcurl4-dev, xdg-utils, zlib1g-dev, libpng-dev, libjpeg-dev, libx11-dev, libxt-dev, x11proto-core-dev, libpango1.0-dev, libcairo2-dev, libtiff5-dev, xvfb, xauth, xfonts-base, texlive-base, texlive-latex-base, texlive-generic-recommended, texlive-fonts-recommended, texlive-fonts-extra, texlive-extra-utils, texlive-latex-recommended, texlive-latex-extra, openjdk-9-jdk | default-jdk, mpack, bash-completion dpkg-deb: building package 'sbuild-build-depends-r-base-dummy' in '/<>/resolver-bfpn5Z/apt_archive/sbuild-build-depends-r-base-dummy.deb'. Ign:1 copy:/<>/resolver-bfpn5Z/apt_archive ./ InRelease Get:2 copy:/<>/resolver-bfpn5Z/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-bfpn5Z/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-bfpn5Z/apt_archive ./ Sources [515 B] Get:5 copy:/<>/resolver-bfpn5Z/apt_archive ./ Packages [808 B] Fetched 3442 B in 0s (31.7 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: gnupg-agent libcryptsetup4 libcurl3-gnutls libgdbm3 libisl15 libmpfr4 libssl1.0.0 libunistring0 libustr-1.0-1 Use 'apt autoremove' to remove them. The following additional packages will be installed: adwaita-icon-theme autoconf automake autopoint autotools-dev bash-completion bison bsdmainutils ca-certificates-java dconf-gsettings-backend dconf-service debhelper dh-autoreconf dh-strip-nondeterminism file fontconfig fontconfig-config fonts-dejavu-core fonts-lmodern gettext gettext-base gfortran gfortran-7 gir1.2-freedesktop gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 gir1.2-pango-1.0 glib-networking glib-networking-common glib-networking-services groff-base gsettings-desktop-schemas gtk-update-icon-cache hicolor-icon-theme humanity-icon-theme icu-devtools intltool-debian java-common libarchive-zip-perl libasound2 libasound2-data libatk-bridge2.0-0 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 libatk1.0-data libatspi2.0-0 libavahi-client3 libavahi-common-data libavahi-common3 libbison-dev libblas-dev libblas3 libbsd0 libbz2-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev libcolord2 libcroco3 libcups2 libcupsimage2 libcurl4 libcurl4-openssl-dev libdatrie1 libdbus-1-3 libdconf1 libdrm-amdgpu1 libdrm-common libdrm-etnaviv1 libdrm-freedreno1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libegl-mesa0 libegl1 libelf1 libepoxy0 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfontconfig1-dev libfontenc1 libfreetype6 libfreetype6-dev libgbm1 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgfortran-7-dev libgfortran4 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 libgs9 libgs9-common libgtk-3-0 libgtk-3-common libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libice-dev libice6 libicu-dev libicu-le-hb-dev libicu-le-hb0 libicu60 libiculx60 libijs-0.35 libjbig-dev libjbig0 libjbig2dec0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjson-glib-1.0-0 libjson-glib-1.0-common libkpathsea6 liblapack-dev liblapack3 liblcms2-2 libllvm6.0 liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libmime-charset-perl libmpdec2 libncurses5-dev libnspr4 libnss3 libpango-1.0-0 libpango1.0-dev libpangocairo-1.0-0 libpangoft2-1.0-0 libpangoxft-1.0-0 libpaper-utils libpaper1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpcsclite1 libpipeline1 libpixman-1-0 libpixman-1-dev libpng-dev libpoppler73 libpotrace0 libproxy1v5 libptexenc1 libpthread-stubs0-dev libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.6-minimal libpython3.6-stdlib libreadline-dev librest-0.7-0 librsvg2-2 librsvg2-common libsensors4 libsigsegv2 libsm-dev libsm6 libsombok3 libsoup-gnome2.4-1 libsoup2.4-1 libsynctex1 libtcl8.6 libtexlua52 libtexluajit2 libtext-unidecode-perl libthai-data libthai0 libtiff5 libtiff5-dev libtiffxx5 libtimedate-perl libtinfo-dev libtk8.6 libtool libunicode-linebreak-perl libwayland-client0 libwayland-cursor0 libwayland-egl1-mesa libwayland-server0 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-render0-dev libxcb-shape0 libxcb-shm0 libxcb-shm0-dev libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev libxcomposite1 libxcursor1 libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes3 libxfont2 libxft-dev libxft2 libxi6 libxinerama1 libxkbcommon0 libxkbfile1 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml2 libxmu6 libxmuu1 libxpm4 libxrandr2 libxrender-dev libxrender1 libxshmfence1 libxss-dev libxss1 libxt-dev libxt6 libxtst6 libxv1 libxxf86dga1 libxxf86vm1 libzzip-0-13 m4 man-db mime-support mpack openjdk-9-jdk openjdk-9-jdk-headless openjdk-9-jre openjdk-9-jre-headless pkg-config po-debconf poppler-data preview-latex-style python python-minimal python2.7 python2.7-minimal python3 python3-distutils python3-lib2to3 python3-minimal python3.6 python3.6-minimal shared-mime-info t1utils tcl8.6 tcl8.6-dev tex-common texinfo texlive-base texlive-binaries texlive-extra-utils texlive-fonts-extra texlive-fonts-recommended texlive-generic-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures texlive-plain-generic tk8.6 tk8.6-dev ubuntu-mono ucf x11-common x11-utils 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 dwz gettext-doc libasprintf-dev libgettextpo-dev gfortran-multilib gfortran-doc gfortran-7-multilib gfortran-7-doc libgfortran4-dbg libcoarrays-dev groff default-jre libasound2-plugins alsa-utils liblapack-doc libcairo2-doc colord cups-common libcurl4-doc libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev libssl-dev libglib2.0-doc libgraphite2-utils gvfs libice-doc icu-doc liblcms2-utils liblzma-doc libencode-hanextra-perl libpod2-base-perl ncurses-doc imagemagick libpango1.0-doc pcscd readline-doc librsvg2-bin lm-sensors libsm-doc libtool-doc gcj-jdk libxcb-doc libxext-doc libxt-doc m4-doc apparmor less www-browser mail-transport-agent inews openjdk-9-demo openjdk-9-source visualvm icedtea-8-plugin libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic libmail-box-perl poppler-utils ghostscript fonts-japanese-mincho | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-nanum python-doc python-tk python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3.6-venv python3.6-doc tcl-tclreadline tcl8.6-doc texinfo-doc-nonfree gv | postscript-viewer perl-tk xpdf-reader | pdf-viewer chktex dvidvi dvipng fragmaster lacheck latexdiff latexmk purifyeps xindy cm-super texlive-fonts-extra-doc texlive-fonts-recommended-doc texlive-latex-base-doc python-pygments icc-profiles libfile-which-perl libspreadsheet-parseexcel-perl texlive-latex-extra-doc texlive-latex-recommended-doc texlive-pstricks dot2tex prerex ruby-tcltk | libtcltk-ruby texlive-pictures-doc vprerex tk8.6-doc mesa-utils Recommended packages: curl | wget | lynx at-spi2-core bzip2-doc libcupsfilters1 dbus libarchive-cpio-perl libgdk-pixbuf2.0-bin xdg-user-dirs fonts-droid-fallback libgtk-3-bin libpng-tools libltdl-dev libx11-doc libxml-sax-expat-perl fonts-dejavu-extra libmail-sendmail-perl lmodern ghostscript libfile-homedir-perl libyaml-tiny-perl ruby | ruby-interpreter fonts-adf-accanthis fonts-adf-berenis fonts-adf-gillius fonts-adf-universalis fonts-cabin 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-hinted fonts-noto-mono fonts-oflb-asana-math fonts-open-sans fonts-roboto-hinted 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-xserver-utils The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: adwaita-icon-theme autoconf automake autopoint autotools-dev bash-completion bison bsdmainutils ca-certificates-java dconf-gsettings-backend dconf-service debhelper dh-autoreconf dh-strip-nondeterminism file fontconfig fontconfig-config fonts-dejavu-core fonts-lmodern gettext gettext-base gfortran gfortran-7 gir1.2-freedesktop gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 gir1.2-pango-1.0 glib-networking glib-networking-common glib-networking-services groff-base gsettings-desktop-schemas gtk-update-icon-cache hicolor-icon-theme humanity-icon-theme icu-devtools intltool-debian java-common libarchive-zip-perl libasound2 libasound2-data libatk-bridge2.0-0 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 libatk1.0-data libatspi2.0-0 libavahi-client3 libavahi-common-data libavahi-common3 libbison-dev libblas-dev libblas3 libbsd0 libbz2-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev libcolord2 libcroco3 libcups2 libcupsimage2 libcurl4 libcurl4-openssl-dev libdatrie1 libdbus-1-3 libdconf1 libdrm-amdgpu1 libdrm-common libdrm-etnaviv1 libdrm-freedreno1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libegl-mesa0 libegl1 libelf1 libepoxy0 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfontconfig1-dev libfontenc1 libfreetype6 libfreetype6-dev libgbm1 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgfortran-7-dev libgfortran4 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 libgs9 libgs9-common libgtk-3-0 libgtk-3-common libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libice-dev libice6 libicu-dev libicu-le-hb-dev libicu-le-hb0 libicu60 libiculx60 libijs-0.35 libjbig-dev libjbig0 libjbig2dec0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjson-glib-1.0-0 libjson-glib-1.0-common libkpathsea6 liblapack-dev liblapack3 liblcms2-2 libllvm6.0 liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libmime-charset-perl libmpdec2 libncurses5-dev libnspr4 libnss3 libpango-1.0-0 libpango1.0-dev libpangocairo-1.0-0 libpangoft2-1.0-0 libpangoxft-1.0-0 libpaper-utils libpaper1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpcsclite1 libpipeline1 libpixman-1-0 libpixman-1-dev libpng-dev libpoppler73 libpotrace0 libproxy1v5 libptexenc1 libpthread-stubs0-dev libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.6-minimal libpython3.6-stdlib libreadline-dev librest-0.7-0 librsvg2-2 librsvg2-common libsensors4 libsigsegv2 libsm-dev libsm6 libsombok3 libsoup-gnome2.4-1 libsoup2.4-1 libsynctex1 libtcl8.6 libtexlua52 libtexluajit2 libtext-unidecode-perl libthai-data libthai0 libtiff5 libtiff5-dev libtiffxx5 libtimedate-perl libtinfo-dev libtk8.6 libtool libunicode-linebreak-perl libwayland-client0 libwayland-cursor0 libwayland-egl1-mesa libwayland-server0 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-render0-dev libxcb-shape0 libxcb-shm0 libxcb-shm0-dev libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev libxcomposite1 libxcursor1 libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes3 libxfont2 libxft-dev libxft2 libxi6 libxinerama1 libxkbcommon0 libxkbfile1 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml2 libxmu6 libxmuu1 libxpm4 libxrandr2 libxrender-dev libxrender1 libxshmfence1 libxss-dev libxss1 libxt-dev libxt6 libxtst6 libxv1 libxxf86dga1 libxxf86vm1 libzzip-0-13 m4 man-db mime-support mpack openjdk-9-jdk openjdk-9-jdk-headless openjdk-9-jre openjdk-9-jre-headless pkg-config po-debconf poppler-data preview-latex-style python python-minimal python2.7 python2.7-minimal python3 python3-distutils python3-lib2to3 python3-minimal python3.6 python3.6-minimal sbuild-build-depends-r-base-dummy shared-mime-info t1utils tcl8.6 tcl8.6-dev tex-common texinfo texlive-base texlive-binaries texlive-extra-utils texlive-fonts-extra texlive-fonts-recommended texlive-generic-recommended texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures texlive-plain-generic tk8.6 tk8.6-dev ubuntu-mono ucf x11-common x11-utils 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, 323 newly installed, 1 to remove and 0 not upgraded. Need to get 680 MB of archives. After this operation, 1976 MB of additional disk space will be used. Get:1 copy:/<>/resolver-bfpn5Z/apt_archive ./ sbuild-build-depends-r-base-dummy 0.invalid.0 [1136 B] Get:2 http://ftpmaster.internal/ubuntu bionic/main armhf libpython3.6-minimal armhf 3.6.5-3 [524 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main armhf libexpat1 armhf 2.2.5-3 [59.7 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main armhf python3.6-minimal armhf 3.6.5-3 [1216 kB] Get:5 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf python3-minimal armhf 3.6.5-3 [23.8 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main armhf mime-support all 3.60ubuntu1 [30.1 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main armhf libmpdec2 armhf 2.4.2-1 [66.9 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/main armhf libpython3.6-stdlib armhf 3.6.5-3 [1595 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/main armhf python3.6 armhf 3.6.5-3 [186 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf libpython3-stdlib armhf 3.6.5-3 [7276 B] Get:11 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf python3 armhf 3.6.5-3 [10.2 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/main armhf libxau6 armhf 1:1.0.8-1 [7324 B] Get:13 http://ftpmaster.internal/ubuntu bionic/main armhf libbsd0 armhf 0.8.7-1 [40.4 kB] Get:14 http://ftpmaster.internal/ubuntu bionic/main armhf libxdmcp6 armhf 1:1.1.2-3 [9316 B] Get:15 http://ftpmaster.internal/ubuntu bionic/main armhf libxcb1 armhf 1.13-1 [41.2 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main armhf libx11-data all 2:1.6.4-3 [114 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main armhf libx11-6 armhf 2:1.6.4-3 [515 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main armhf libxext6 armhf 2:1.3.3-1 [25.1 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main armhf bsdmainutils armhf 11.1.2ubuntu1 [177 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main armhf groff-base armhf 1.22.3-10 [1013 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main armhf libpipeline1 armhf 1.5.0-1 [21.1 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main armhf man-db armhf 2.8.3-2 [993 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main armhf libfreetype6 armhf 2.8.1-2ubuntu2 [280 kB] Get:24 http://ftpmaster.internal/ubuntu bionic/main armhf ucf all 3.0038 [50.5 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main armhf fonts-dejavu-core all 2.37-1 [1041 kB] Get:26 http://ftpmaster.internal/ubuntu bionic/main armhf fontconfig-config all 2.12.6-0ubuntu2 [55.8 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main armhf libfontconfig1 armhf 2.12.6-0ubuntu2 [120 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main armhf fontconfig armhf 2.12.6-0ubuntu2 [167 kB] Get:29 http://ftpmaster.internal/ubuntu bionic/main armhf libjpeg-turbo8 armhf 1.5.2-0ubuntu5 [87.2 kB] Get:30 http://ftpmaster.internal/ubuntu bionic/main armhf liblzo2-2 armhf 2.08-1.2 [44.2 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/main armhf x11-common all 1:7.7+19ubuntu6 [21.9 kB] Get:32 http://ftpmaster.internal/ubuntu bionic/main armhf libice6 armhf 2:1.0.9-2 [33.5 kB] Get:33 http://ftpmaster.internal/ubuntu bionic/main armhf libsm6 armhf 2:1.2.2-1 [13.9 kB] Get:34 http://ftpmaster.internal/ubuntu bionic/main armhf libxrender1 armhf 1:0.9.10-1 [15.6 kB] Get:35 http://ftpmaster.internal/ubuntu bionic/main armhf libxft2 armhf 2.3.2-1 [30.5 kB] Get:36 http://ftpmaster.internal/ubuntu bionic/main armhf libxinerama1 armhf 2:1.1.3-1 [7278 B] Get:37 http://ftpmaster.internal/ubuntu bionic/main armhf libxshmfence1 armhf 1.2-1 [4848 B] Get:38 http://ftpmaster.internal/ubuntu bionic/main armhf libxss1 armhf 1:1.2.2-1 [7652 B] Get:39 http://ftpmaster.internal/ubuntu bionic/main armhf libxxf86dga1 armhf 2:1.1.4-1 [11.9 kB] Get:40 http://ftpmaster.internal/ubuntu bionic/main armhf libxxf86vm1 armhf 1:1.1.4-1 [9770 B] Get:41 http://ftpmaster.internal/ubuntu bionic/main armhf poppler-data all 0.4.8-2 [1479 kB] Get:42 http://ftpmaster.internal/ubuntu bionic/main armhf 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http://ftpmaster.internal/ubuntu bionic/main armhf libdbus-1-3 armhf 1.12.2-1ubuntu1 [153 kB] Get:54 http://ftpmaster.internal/ubuntu bionic/main armhf libelf1 armhf 0.170-0.4 [42.2 kB] Get:55 http://ftpmaster.internal/ubuntu bionic/main armhf libglib2.0-0 armhf 2.56.1-2ubuntu1 [1014 kB] Get:56 http://ftpmaster.internal/ubuntu bionic/main armhf libglib2.0-data all 2.56.1-2ubuntu1 [4220 B] Get:57 http://ftpmaster.internal/ubuntu bionic/main armhf libicu60 armhf 60.2-3ubuntu3 [7797 kB] Get:58 http://ftpmaster.internal/ubuntu bionic/main armhf libxml2 armhf 2.9.4+dfsg1-6.1ubuntu1 [567 kB] Get:59 http://ftpmaster.internal/ubuntu bionic/main armhf shared-mime-info armhf 1.9-2 [424 kB] Get:60 http://ftpmaster.internal/ubuntu bionic/main armhf xkb-data all 2.23.1-1ubuntu1 [325 kB] Get:61 http://ftpmaster.internal/ubuntu bionic/main armhf bash-completion all 1:2.8-1ubuntu1 [168 kB] Get:62 http://ftpmaster.internal/ubuntu bionic/main armhf gettext-base armhf 0.19.8.1-6 [46.2 kB] Get:63 http://ftpmaster.internal/ubuntu bionic/main armhf libgirepository-1.0-1 armhf 1.56.0-2 [69.5 kB] Get:64 http://ftpmaster.internal/ubuntu bionic/main armhf gir1.2-glib-2.0 armhf 1.56.0-2 [131 kB] Get:65 http://ftpmaster.internal/ubuntu bionic/main armhf libdrm-common all 2.4.91-2 [4916 B] Get:66 http://ftpmaster.internal/ubuntu bionic/main armhf libdrm2 armhf 2.4.91-2 [27.0 kB] Get:67 http://ftpmaster.internal/ubuntu bionic/main armhf libedit2 armhf 3.1-20170329-1 [61.9 kB] Get:68 http://ftpmaster.internal/ubuntu bionic/main armhf libxmuu1 armhf 2:1.1.2-2 [9130 B] Get:69 http://ftpmaster.internal/ubuntu bionic/main armhf xauth armhf 1:1.0.10-1 [21.7 kB] Get:70 http://ftpmaster.internal/ubuntu bionic/main armhf hicolor-icon-theme all 0.17-2 [9976 B] Get:71 http://ftpmaster.internal/ubuntu bionic/main armhf libjpeg8 armhf 8c-2ubuntu8 [2202 B] Get:72 http://ftpmaster.internal/ubuntu bionic/main armhf libjbig0 armhf 2.1-3.1build1 [23.9 kB] Get:73 http://ftpmaster.internal/ubuntu bionic/main armhf libtiff5 armhf 4.0.9-4ubuntu1 [134 kB] Get:74 http://ftpmaster.internal/ubuntu bionic/main armhf libgdk-pixbuf2.0-common all 2.36.11-2 [4536 B] Get:75 http://ftpmaster.internal/ubuntu bionic/main armhf libgdk-pixbuf2.0-0 armhf 2.36.11-2 [149 kB] Get:76 http://ftpmaster.internal/ubuntu bionic/main armhf gtk-update-icon-cache armhf 3.22.29-3ubuntu1 [26.9 kB] Get:77 http://ftpmaster.internal/ubuntu bionic/main armhf libpixman-1-0 armhf 0.34.0-2 [157 kB] Get:78 http://ftpmaster.internal/ubuntu bionic/main armhf libxcb-render0 armhf 1.13-1 [13.9 kB] Get:79 http://ftpmaster.internal/ubuntu bionic/main armhf libxcb-shm0 armhf 1.13-1 [5404 B] Get:80 http://ftpmaster.internal/ubuntu bionic/main armhf libcairo2 armhf 1.15.10-2 [507 kB] Get:81 http://ftpmaster.internal/ubuntu bionic/main armhf libcroco3 armhf 0.6.12-2 [69.4 kB] Get:82 http://ftpmaster.internal/ubuntu bionic/main armhf libthai-data all 0.1.27-2 [133 kB] Get:83 http://ftpmaster.internal/ubuntu bionic/main armhf libdatrie1 armhf 0.2.10-7 [14.5 kB] Get:84 http://ftpmaster.internal/ubuntu bionic/main armhf libthai0 armhf 0.1.27-2 [14.7 kB] Get:85 http://ftpmaster.internal/ubuntu bionic/main armhf libpango-1.0-0 armhf 1.40.14-1 [137 kB] Get:86 http://ftpmaster.internal/ubuntu bionic/main armhf libgraphite2-3 armhf 1.3.11-2 [67.5 kB] Get:87 http://ftpmaster.internal/ubuntu bionic/main armhf libharfbuzz0b armhf 1.7.2-1ubuntu1 [205 kB] Get:88 http://ftpmaster.internal/ubuntu bionic/main armhf libpangoft2-1.0-0 armhf 1.40.14-1 [28.6 kB] Get:89 http://ftpmaster.internal/ubuntu bionic/main armhf libpangocairo-1.0-0 armhf 1.40.14-1 [17.5 kB] Get:90 http://ftpmaster.internal/ubuntu bionic/main armhf librsvg2-2 armhf 2.40.20-2 [83.8 kB] Get:91 http://ftpmaster.internal/ubuntu bionic/main armhf librsvg2-common armhf 2.40.20-2 [4720 B] Get:92 http://ftpmaster.internal/ubuntu bionic/main armhf humanity-icon-theme all 0.6.15 [1250 kB] Get:93 http://ftpmaster.internal/ubuntu bionic/main armhf ubuntu-mono all 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http://ftpmaster.internal/ubuntu bionic/main armhf libtimedate-perl all 2.3000-2 [37.5 kB] Get:124 http://ftpmaster.internal/ubuntu bionic/main armhf dh-strip-nondeterminism all 0.040-1.1~build1 [5208 B] Get:125 http://ftpmaster.internal/ubuntu bionic/main armhf gettext armhf 0.19.8.1-6 [833 kB] Get:126 http://ftpmaster.internal/ubuntu bionic/main armhf intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:127 http://ftpmaster.internal/ubuntu bionic/main armhf po-debconf all 1.0.20 [232 kB] Get:128 http://ftpmaster.internal/ubuntu bionic/main armhf debhelper all 11.1.6ubuntu1 [902 kB] Get:129 http://ftpmaster.internal/ubuntu bionic/main armhf fonts-lmodern all 2.004.5-3 [4551 kB] Get:130 http://ftpmaster.internal/ubuntu bionic/main armhf libgfortran4 armhf 7.3.0-16ubuntu2 [200 kB] Get:131 http://ftpmaster.internal/ubuntu bionic/main armhf libgfortran-7-dev armhf 7.3.0-16ubuntu2 [249 kB] Get:132 http://ftpmaster.internal/ubuntu bionic/main armhf gfortran-7 armhf 7.3.0-16ubuntu2 [5634 kB] Get:133 http://ftpmaster.internal/ubuntu bionic/main armhf gfortran armhf 4:7.3.0-3ubuntu2 [1352 B] Get:134 http://ftpmaster.internal/ubuntu bionic/main armhf gir1.2-freedesktop armhf 1.56.0-2 [9084 B] Get:135 http://ftpmaster.internal/ubuntu bionic/main armhf gir1.2-harfbuzz-0.0 armhf 1.7.2-1ubuntu1 [18.5 kB] Get:136 http://ftpmaster.internal/ubuntu bionic/main armhf libpangoxft-1.0-0 armhf 1.40.14-1 [12.7 kB] Get:137 http://ftpmaster.internal/ubuntu bionic/main armhf gir1.2-pango-1.0 armhf 1.40.14-1 [21.6 kB] Get:138 http://ftpmaster.internal/ubuntu bionic/main armhf libproxy1v5 armhf 0.4.15-1 [42.7 kB] Get:139 http://ftpmaster.internal/ubuntu bionic/main armhf glib-networking-common all 2.56.0-1 [3324 B] Get:140 http://ftpmaster.internal/ubuntu bionic/main armhf glib-networking-services armhf 2.56.0-1 [7860 B] Get:141 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf gsettings-desktop-schemas all 3.28.0-1ubuntu1 [27.8 kB] Get:142 http://ftpmaster.internal/ubuntu bionic/main armhf glib-networking armhf 2.56.0-1 [49.3 kB] Get:143 http://ftpmaster.internal/ubuntu bionic/main armhf icu-devtools armhf 60.2-3ubuntu3 [161 kB] Get:144 http://ftpmaster.internal/ubuntu bionic/main armhf libasound2-data all 1.1.3-5 [36.1 kB] Get:145 http://ftpmaster.internal/ubuntu bionic/main armhf libasound2 armhf 1.1.3-5 [306 kB] Get:146 http://ftpmaster.internal/ubuntu bionic/main armhf libatk1.0-data all 2.28.1-1 [2992 B] Get:147 http://ftpmaster.internal/ubuntu bionic/main armhf libatk1.0-0 armhf 2.28.1-1 [36.9 kB] Get:148 http://ftpmaster.internal/ubuntu bionic/main armhf libatspi2.0-0 armhf 2.28.0-1 [49.9 kB] Get:149 http://ftpmaster.internal/ubuntu bionic/main armhf libatk-bridge2.0-0 armhf 2.26.2-1 [48.9 kB] Get:150 http://ftpmaster.internal/ubuntu bionic/main armhf libfontenc1 armhf 1:1.1.3-1 [11.7 kB] Get:151 http://ftpmaster.internal/ubuntu bionic/main armhf libglvnd0 armhf 1.0.0-2ubuntu2 [47.1 kB] Get:152 http://ftpmaster.internal/ubuntu bionic/main armhf libglapi-mesa armhf 18.0.0~rc5-1ubuntu1 [28.7 kB] Get:153 http://ftpmaster.internal/ubuntu bionic/main armhf libx11-xcb1 armhf 2:1.6.4-3 [9578 B] Get:154 http://ftpmaster.internal/ubuntu bionic/main armhf libxcb-dri2-0 armhf 1.13-1 [6712 B] Get:155 http://ftpmaster.internal/ubuntu bionic/main armhf libxcb-dri3-0 armhf 1.13-1 [6320 B] Get:156 http://ftpmaster.internal/ubuntu bionic/main armhf libxcb-glx0 armhf 1.13-1 [20.1 kB] Get:157 http://ftpmaster.internal/ubuntu bionic/main armhf libxcb-present0 armhf 1.13-1 [5472 B] Get:158 http://ftpmaster.internal/ubuntu bionic/main armhf libxcb-sync1 armhf 1.13-1 [8272 B] Get:159 http://ftpmaster.internal/ubuntu bionic/main armhf libxdamage1 armhf 1:1.1.4-3 [6488 B] Get:160 http://ftpmaster.internal/ubuntu bionic/main armhf libxfixes3 armhf 1:5.0.3-1 [9390 B] Get:161 http://ftpmaster.internal/ubuntu bionic/main armhf libdrm-amdgpu1 armhf 2.4.91-2 [17.5 kB] Get:162 http://ftpmaster.internal/ubuntu bionic/main armhf libdrm-etnaviv1 armhf 2.4.91-2 [10.2 kB] Get:163 http://ftpmaster.internal/ubuntu bionic/main armhf libdrm-freedreno1 armhf 2.4.91-2 [16.2 kB] Get:164 http://ftpmaster.internal/ubuntu bionic/main armhf libdrm-nouveau2 armhf 2.4.91-2 [14.7 kB] Get:165 http://ftpmaster.internal/ubuntu bionic/main armhf libdrm-radeon1 armhf 2.4.91-2 [19.6 kB] Get:166 http://ftpmaster.internal/ubuntu bionic/main armhf libllvm6.0 armhf 1:6.0-1ubuntu2 [13.5 MB] Get:167 http://ftpmaster.internal/ubuntu bionic/main armhf libsensors4 armhf 1:3.4.0-4 [25.8 kB] Get:168 http://ftpmaster.internal/ubuntu bionic/main armhf libgl1-mesa-dri armhf 18.0.0~rc5-1ubuntu1 [3718 kB] Get:169 http://ftpmaster.internal/ubuntu bionic/main armhf libglx-mesa0 armhf 18.0.0~rc5-1ubuntu1 [116 kB] Get:170 http://ftpmaster.internal/ubuntu bionic/main armhf libglx0 armhf 1.0.0-2ubuntu2 [23.3 kB] Get:171 http://ftpmaster.internal/ubuntu bionic/main armhf libgl1 armhf 1.0.0-2ubuntu2 [94.2 kB] Get:172 http://ftpmaster.internal/ubuntu bionic/main armhf libxt6 armhf 1:1.1.5-1 [129 kB] Get:173 http://ftpmaster.internal/ubuntu bionic/main armhf libxmu6 armhf 2:1.1.2-2 [38.3 kB] Get:174 http://ftpmaster.internal/ubuntu bionic/main armhf libxpm4 armhf 1:3.5.12-1 [29.0 kB] Get:175 http://ftpmaster.internal/ubuntu bionic/main armhf libxaw7 armhf 2:1.0.13-1 [141 kB] Get:176 http://ftpmaster.internal/ubuntu bionic/main armhf libxcb-shape0 armhf 1.13-1 [5684 B] Get:177 http://ftpmaster.internal/ubuntu bionic/main armhf libxcomposite1 armhf 1:0.4.4-2 [7684 B] Get:178 http://ftpmaster.internal/ubuntu bionic/main armhf libxrandr2 armhf 2:1.5.1-1 [15.5 kB] Get:179 http://ftpmaster.internal/ubuntu bionic/main armhf libxv1 armhf 2:1.0.11-1 [9430 B] Get:180 http://ftpmaster.internal/ubuntu bionic/main armhf x11-utils armhf 7.7+3build1 [173 kB] Get:181 http://ftpmaster.internal/ubuntu bionic/main armhf libatk-wrapper-java all 0.33.3-20 [34.7 kB] Get:182 http://ftpmaster.internal/ubuntu bionic/main armhf libatk-wrapper-java-jni armhf 0.33.3-20 [23.4 kB] Get:183 http://ftpmaster.internal/ubuntu bionic/main armhf libblas3 armhf 3.7.1-4ubuntu1 [97.0 kB] Get:184 http://ftpmaster.internal/ubuntu bionic/main armhf libblas-dev armhf 3.7.1-4ubuntu1 [104 kB] Get:185 http://ftpmaster.internal/ubuntu bionic/main armhf libbz2-dev armhf 1.0.6-8.1 [27.6 kB] Get:186 http://ftpmaster.internal/ubuntu bionic/main armhf libcairo-gobject2 armhf 1.15.10-2 [16.2 kB] Get:187 http://ftpmaster.internal/ubuntu bionic/main armhf libcairo-script-interpreter2 armhf 1.15.10-2 [44.2 kB] Get:188 http://ftpmaster.internal/ubuntu bionic/main armhf libexpat1-dev armhf 2.2.5-3 [106 kB] Get:189 http://ftpmaster.internal/ubuntu bionic/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-0ubuntu2 [168 kB] Get:190 http://ftpmaster.internal/ubuntu bionic/main armhf libpng-dev armhf 1.6.34-1 [162 kB] Get:191 http://ftpmaster.internal/ubuntu bionic/main armhf libfreetype6-dev armhf 2.8.1-2ubuntu2 [2488 kB] Get:192 http://ftpmaster.internal/ubuntu bionic/main armhf pkg-config armhf 0.29.1-0ubuntu2 [42.0 kB] Get:193 http://ftpmaster.internal/ubuntu bionic/main armhf libfontconfig1-dev armhf 2.12.6-0ubuntu2 [675 kB] Get:194 http://ftpmaster.internal/ubuntu bionic/main armhf xorg-sgml-doctools all 1:1.11-1 [12.9 kB] Get:195 http://ftpmaster.internal/ubuntu bionic/main armhf x11proto-dev all 2018.4-4 [251 kB] Get:196 http://ftpmaster.internal/ubuntu bionic/main armhf x11proto-core-dev all 2018.4-4 [2620 B] Get:197 http://ftpmaster.internal/ubuntu bionic/main armhf libxau-dev armhf 1:1.0.8-1 [9438 B] Get:198 http://ftpmaster.internal/ubuntu bionic/main armhf libxdmcp-dev armhf 1:1.1.2-3 [23.6 kB] Get:199 http://ftpmaster.internal/ubuntu bionic/main armhf xtrans-dev all 1.3.5-1 [70.5 kB] Get:200 http://ftpmaster.internal/ubuntu bionic/main armhf libpthread-stubs0-dev armhf 0.3-4 [4084 B] Get:201 http://ftpmaster.internal/ubuntu bionic/main armhf libxcb1-dev armhf 1.13-1 [77.3 kB] Get:202 http://ftpmaster.internal/ubuntu bionic/main armhf libx11-dev armhf 2:1.6.4-3 [585 kB] Get:203 http://ftpmaster.internal/ubuntu bionic/main armhf libxrender-dev armhf 1:0.9.10-1 [21.7 kB] Get:204 http://ftpmaster.internal/ubuntu bionic/main armhf x11proto-xext-dev all 2018.4-4 [2620 B] Get:205 http://ftpmaster.internal/ubuntu bionic/main armhf libxext-dev armhf 2:1.3.3-1 [77.8 kB] Get:206 http://ftpmaster.internal/ubuntu bionic/main armhf libice-dev armhf 2:1.0.9-2 [40.4 kB] Get:207 http://ftpmaster.internal/ubuntu bionic/main armhf libsm-dev armhf 2:1.2.2-1 [14.8 kB] Get:208 http://ftpmaster.internal/ubuntu bionic/main armhf libpixman-1-dev armhf 0.34.0-2 [177 kB] Get:209 http://ftpmaster.internal/ubuntu bionic/main armhf libxcb-render0-dev armhf 1.13-1 [18.2 kB] Get:210 http://ftpmaster.internal/ubuntu bionic/main armhf libxcb-shm0-dev armhf 1.13-1 [6700 B] Get:211 http://ftpmaster.internal/ubuntu bionic/main armhf libglib2.0-bin armhf 2.56.1-2ubuntu1 [62.9 kB] Get:212 http://ftpmaster.internal/ubuntu bionic/main armhf python3-lib2to3 all 3.6.5-3 [76.6 kB] Get:213 http://ftpmaster.internal/ubuntu bionic/main armhf python3-distutils all 3.6.5-3 [141 kB] Get:214 http://ftpmaster.internal/ubuntu bionic/main armhf libglib2.0-dev-bin armhf 2.56.1-2ubuntu1 [99.7 kB] Get:215 http://ftpmaster.internal/ubuntu bionic/main armhf libpcre16-3 armhf 2:8.39-9 [128 kB] Get:216 http://ftpmaster.internal/ubuntu bionic/main armhf libpcre32-3 armhf 2:8.39-9 [120 kB] Get:217 http://ftpmaster.internal/ubuntu bionic/main armhf libpcrecpp0v5 armhf 2:8.39-9 [13.2 kB] Get:218 http://ftpmaster.internal/ubuntu bionic/main armhf libpcre3-dev armhf 2:8.39-9 [473 kB] Get:219 http://ftpmaster.internal/ubuntu bionic/main armhf libglib2.0-dev armhf 2.56.1-2ubuntu1 [1283 kB] Get:220 http://ftpmaster.internal/ubuntu bionic/main armhf libcairo2-dev armhf 1.15.10-2 [552 kB] Get:221 http://ftpmaster.internal/ubuntu bionic/main armhf libcolord2 armhf 1.3.3-2build1 [95.3 kB] Get:222 http://ftpmaster.internal/ubuntu bionic/main armhf libcupsimage2 armhf 2.2.7-1ubuntu2 [16.3 kB] Get:223 http://ftpmaster.internal/ubuntu bionic/main armhf libcurl4 armhf 7.58.0-2ubuntu3 [183 kB] Get:224 http://ftpmaster.internal/ubuntu bionic/main armhf libcurl4-openssl-dev armhf 7.58.0-2ubuntu3 [271 kB] Get:225 http://ftpmaster.internal/ubuntu bionic/main armhf libwayland-server0 armhf 1.14.0-2 [22.8 kB] Get:226 http://ftpmaster.internal/ubuntu bionic/main armhf libgbm1 armhf 18.0.0~rc5-1ubuntu1 [21.3 kB] Get:227 http://ftpmaster.internal/ubuntu bionic/main armhf libwayland-client0 armhf 1.14.0-2 [17.8 kB] Get:228 http://ftpmaster.internal/ubuntu bionic/main armhf libxcb-xfixes0 armhf 1.13-1 [9036 B] Get:229 http://ftpmaster.internal/ubuntu bionic/main armhf libegl-mesa0 armhf 18.0.0~rc5-1ubuntu1 [67.5 kB] Get:230 http://ftpmaster.internal/ubuntu bionic/main armhf libepoxy0 armhf 1.4.3-1 [161 kB] Get:231 http://ftpmaster.internal/ubuntu bionic/main armhf libgif7 armhf 5.1.4-2 [28.3 kB] Get:232 http://ftpmaster.internal/ubuntu bionic/main armhf libgraphite2-dev armhf 1.3.11-2 [14.5 kB] Get:233 http://ftpmaster.internal/ubuntu bionic/main armhf libijs-0.35 armhf 0.35-13 [13.9 kB] Get:234 http://ftpmaster.internal/ubuntu bionic/main armhf libjbig2dec0 armhf 0.13-6 [48.6 kB] Get:235 http://ftpmaster.internal/ubuntu bionic/main armhf libpaper1 armhf 1.1.24+nmu5ubuntu1 [12.9 kB] Get:236 http://ftpmaster.internal/ubuntu bionic/main armhf libgs9-common all 9.22~dfsg+1-0ubuntu1 [5197 kB] Get:237 http://ftpmaster.internal/ubuntu bionic/main armhf libgs9 armhf 9.22~dfsg+1-0ubuntu1 [1910 kB] Get:238 http://ftpmaster.internal/ubuntu bionic/main armhf libgtk-3-common all 3.22.29-3ubuntu1 [228 kB] Get:239 http://ftpmaster.internal/ubuntu bionic/main armhf libjson-glib-1.0-common all 1.4.2-3 [3464 B] Get:240 http://ftpmaster.internal/ubuntu bionic/main armhf libjson-glib-1.0-0 armhf 1.4.2-3 [51.2 kB] Get:241 http://ftpmaster.internal/ubuntu bionic/main armhf libsoup2.4-1 armhf 2.62.1-1 [249 kB] Get:242 http://ftpmaster.internal/ubuntu bionic/main armhf libsoup-gnome2.4-1 armhf 2.62.1-1 [4712 B] Get:243 http://ftpmaster.internal/ubuntu bionic/main armhf librest-0.7-0 armhf 0.8.0-2 [26.9 kB] Get:244 http://ftpmaster.internal/ubuntu bionic/main armhf libwayland-cursor0 armhf 1.14.0-2 [8860 B] Get:245 http://ftpmaster.internal/ubuntu bionic/main armhf libegl1 armhf 1.0.0-2ubuntu2 [26.5 kB] Get:246 http://ftpmaster.internal/ubuntu bionic/main armhf libwayland-egl1-mesa armhf 18.0.0~rc5-1ubuntu1 [6952 B] Get:247 http://ftpmaster.internal/ubuntu bionic/main armhf libxcursor1 armhf 1:1.1.15-1 [16.9 kB] Get:248 http://ftpmaster.internal/ubuntu bionic/main armhf libxkbcommon0 armhf 0.8.0-1 [86.1 kB] Get:249 http://ftpmaster.internal/ubuntu bionic/main armhf libgtk-3-0 armhf 3.22.29-3ubuntu1 [2134 kB] Get:250 http://ftpmaster.internal/ubuntu bionic/main armhf libharfbuzz-icu0 armhf 1.7.2-1ubuntu1 [5196 B] Get:251 http://ftpmaster.internal/ubuntu bionic/main armhf libharfbuzz-gobject0 armhf 1.7.2-1ubuntu1 [12.0 kB] Get:252 http://ftpmaster.internal/ubuntu bionic/main armhf libicu-le-hb0 armhf 1.0.3+git161113-4 [12.5 kB] Get:253 http://ftpmaster.internal/ubuntu bionic/main armhf libiculx60 armhf 60.2-3ubuntu3 [16.1 kB] Get:254 http://ftpmaster.internal/ubuntu bionic/main armhf libicu-le-hb-dev armhf 1.0.3+git161113-4 [27.8 kB] Get:255 http://ftpmaster.internal/ubuntu bionic/main armhf libicu-dev armhf 60.2-3ubuntu3 [8715 kB] Get:256 http://ftpmaster.internal/ubuntu bionic/main armhf libharfbuzz-dev armhf 1.7.2-1ubuntu1 [276 kB] Get:257 http://ftpmaster.internal/ubuntu bionic/main armhf libjpeg-turbo8-dev armhf 1.5.2-0ubuntu5 [199 kB] Get:258 http://ftpmaster.internal/ubuntu bionic/main armhf libjpeg8-dev armhf 8c-2ubuntu8 [1554 B] Get:259 http://ftpmaster.internal/ubuntu bionic/main armhf libjpeg-dev armhf 8c-2ubuntu8 [1554 B] Get:260 http://ftpmaster.internal/ubuntu bionic/main armhf libkpathsea6 armhf 2017.20170613.44572-8build1 [46.9 kB] Get:261 http://ftpmaster.internal/ubuntu bionic/main armhf liblapack3 armhf 3.7.1-4ubuntu1 [1627 kB] Get:262 http://ftpmaster.internal/ubuntu bionic/main armhf liblapack-dev armhf 3.7.1-4ubuntu1 [1675 kB] Get:263 http://ftpmaster.internal/ubuntu bionic/universe armhf libmime-charset-perl all 1.012.2-1 [30.9 kB] Get:264 http://ftpmaster.internal/ubuntu bionic/main armhf libtinfo-dev armhf 6.1-1ubuntu1 [70.9 kB] Get:265 http://ftpmaster.internal/ubuntu bionic/main armhf libncurses5-dev armhf 6.1-1ubuntu1 [157 kB] Get:266 http://ftpmaster.internal/ubuntu bionic/main armhf libxft-dev armhf 2.3.2-1 [40.4 kB] Get:267 http://ftpmaster.internal/ubuntu bionic/main armhf libpango1.0-dev armhf 1.40.14-1 [267 kB] Get:268 http://ftpmaster.internal/ubuntu bionic/main armhf libpaper-utils armhf 1.1.24+nmu5ubuntu1 [8026 B] Get:269 http://ftpmaster.internal/ubuntu bionic/main armhf libpoppler73 armhf 0.62.0-2ubuntu1 [675 kB] Get:270 http://ftpmaster.internal/ubuntu bionic/main armhf libpotrace0 armhf 1.14-2 [15.0 kB] Get:271 http://ftpmaster.internal/ubuntu bionic/main armhf libptexenc1 armhf 2017.20170613.44572-8build1 [32.4 kB] Get:272 http://ftpmaster.internal/ubuntu bionic/main armhf libreadline-dev armhf 7.0-3 [121 kB] Get:273 http://ftpmaster.internal/ubuntu bionic/universe armhf libsombok3 armhf 2.4.0-1 [23.0 kB] Get:274 http://ftpmaster.internal/ubuntu bionic/main armhf libsynctex1 armhf 2017.20170613.44572-8build1 [35.2 kB] Get:275 http://ftpmaster.internal/ubuntu bionic/main armhf libtcl8.6 armhf 8.6.8+dfsg-3 [776 kB] Get:276 http://ftpmaster.internal/ubuntu bionic/main armhf libtexlua52 armhf 2017.20170613.44572-8build1 [68.5 kB] Get:277 http://ftpmaster.internal/ubuntu bionic/main armhf libtexluajit2 armhf 2017.20170613.44572-8build1 [179 kB] Get:278 http://ftpmaster.internal/ubuntu bionic/universe armhf libtext-unidecode-perl all 1.30-1 [99.0 kB] Get:279 http://ftpmaster.internal/ubuntu bionic/main armhf libjbig-dev armhf 2.1-3.1build1 [22.9 kB] Get:280 http://ftpmaster.internal/ubuntu bionic/main armhf liblzma-dev armhf 5.2.2-1.3 [138 kB] Get:281 http://ftpmaster.internal/ubuntu bionic/main armhf libtiffxx5 armhf 4.0.9-4ubuntu1 [5784 B] Get:282 http://ftpmaster.internal/ubuntu bionic/main armhf libtiff5-dev armhf 4.0.9-4ubuntu1 [257 kB] Get:283 http://ftpmaster.internal/ubuntu bionic/main armhf libtk8.6 armhf 8.6.8-4 [612 kB] Get:284 http://ftpmaster.internal/ubuntu bionic/universe armhf libunicode-linebreak-perl armhf 0.0.20160702-1build2 [93.8 kB] Get:285 http://ftpmaster.internal/ubuntu bionic/main armhf libxfont2 armhf 1:2.0.3-1 [75.4 kB] Get:286 http://ftpmaster.internal/ubuntu bionic/main armhf libxkbfile1 armhf 1:1.0.9-2 [55.9 kB] Get:287 http://ftpmaster.internal/ubuntu bionic/main armhf libxml-namespacesupport-perl all 1.12-1 [13.2 kB] Get:288 http://ftpmaster.internal/ubuntu bionic/main armhf libxml-sax-base-perl all 1.09-1 [18.8 kB] Get:289 http://ftpmaster.internal/ubuntu bionic/main armhf libxml-sax-perl all 0.99+dfsg-2ubuntu1 [64.6 kB] Get:290 http://ftpmaster.internal/ubuntu bionic/main armhf libxml-libxml-perl armhf 2.0128+dfsg-5 [298 kB] Get:291 http://ftpmaster.internal/ubuntu bionic/main armhf x11proto-scrnsaver-dev all 2018.4-4 [2628 B] Get:292 http://ftpmaster.internal/ubuntu bionic/main armhf libxss-dev armhf 1:1.2.2-1 [12.1 kB] Get:293 http://ftpmaster.internal/ubuntu bionic/main armhf libxt-dev armhf 1:1.1.5-1 [366 kB] Get:294 http://ftpmaster.internal/ubuntu bionic/main armhf libzzip-0-13 armhf 0.13.62-3.1 [22.0 kB] Get:295 http://ftpmaster.internal/ubuntu bionic/universe armhf mpack armhf 1.6-8.2 [31.9 kB] Get:296 http://ftpmaster.internal/ubuntu bionic/main armhf openjdk-9-jre armhf 9.0.4+12-4ubuntu2 [46.5 kB] Get:297 http://ftpmaster.internal/ubuntu bionic/main armhf openjdk-9-jdk-headless armhf 9.0.4+12-4ubuntu2 [70.7 MB] Get:298 http://ftpmaster.internal/ubuntu bionic/main armhf openjdk-9-jdk armhf 9.0.4+12-4ubuntu2 [70.1 kB] Get:299 http://ftpmaster.internal/ubuntu bionic/main armhf preview-latex-style all 11.91-1ubuntu1 [185 kB] Get:300 http://ftpmaster.internal/ubuntu bionic/main armhf t1utils armhf 1.41-2 [48.2 kB] Get:301 http://ftpmaster.internal/ubuntu bionic/main armhf tcl8.6 armhf 8.6.8+dfsg-3 [14.2 kB] Get:302 http://ftpmaster.internal/ubuntu bionic/main armhf tcl8.6-dev armhf 8.6.8+dfsg-3 [803 kB] Get:303 http://ftpmaster.internal/ubuntu bionic/universe armhf texinfo armhf 6.5.0.dfsg.1-2 [748 kB] Get:304 http://ftpmaster.internal/ubuntu bionic/main armhf texlive-binaries armhf 2017.20170613.44572-8build1 [6462 kB] Get:305 http://ftpmaster.internal/ubuntu bionic/main armhf xdg-utils all 1.1.2-1ubuntu2 [60.7 kB] Get:306 http://ftpmaster.internal/ubuntu bionic/main armhf texlive-base all 2017.20180305-1 [18.7 MB] Get:307 http://ftpmaster.internal/ubuntu bionic/main armhf texlive-latex-base all 2017.20180305-1 [951 kB] Get:308 http://ftpmaster.internal/ubuntu bionic/universe armhf texlive-extra-utils all 2017.20180305-2 [20.9 MB] Get:309 http://ftpmaster.internal/ubuntu bionic/universe armhf texlive-fonts-extra all 2017.20180305-2 [354 MB] Get:310 http://ftpmaster.internal/ubuntu bionic/universe armhf texlive-fonts-recommended all 2017.20180305-1 [5262 kB] Get:311 http://ftpmaster.internal/ubuntu bionic/universe armhf texlive-plain-generic all 2017.20180305-2 [23.6 MB] Get:312 http://ftpmaster.internal/ubuntu bionic/universe armhf texlive-generic-recommended all 2017.20180305-1 [15.9 kB] Get:313 http://ftpmaster.internal/ubuntu bionic/main armhf texlive-latex-recommended all 2017.20180305-1 [14.9 MB] Get:314 http://ftpmaster.internal/ubuntu bionic/universe armhf texlive-pictures all 2017.20180305-1 [4026 kB] Get:315 http://ftpmaster.internal/ubuntu bionic/universe armhf texlive-latex-extra all 2017.20180305-2 [10.6 MB] Get:316 http://ftpmaster.internal/ubuntu bionic/main armhf tk8.6 armhf 8.6.8-4 [12.1 kB] Get:317 http://ftpmaster.internal/ubuntu bionic/main armhf tk8.6-dev armhf 8.6.8-4 [621 kB] Get:318 http://ftpmaster.internal/ubuntu bionic/main armhf x11-xkb-utils armhf 7.7+3 [136 kB] Get:319 http://ftpmaster.internal/ubuntu bionic/main armhf xfonts-encodings all 1:1.0.4-2 [573 kB] Get:320 http://ftpmaster.internal/ubuntu bionic/main armhf xfonts-utils armhf 1:7.7+6 [83.0 kB] Get:321 http://ftpmaster.internal/ubuntu bionic/main armhf xfonts-base all 1:1.0.4+nmu1 [5914 kB] Get:322 http://ftpmaster.internal/ubuntu bionic-proposed/main armhf xserver-common all 2:1.19.6-1ubuntu4 [27.2 kB] Get:323 http://ftpmaster.internal/ubuntu bionic-proposed/universe armhf xvfb armhf 2:1.19.6-1ubuntu4 [652 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 680 MB in 38s (18.0 MB/s) (Reading database ... 12725 files and directories currently installed.) 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Unpacking sbuild-build-depends-r-base-dummy (0.invalid.0) ... Setting up libgs9-common (9.22~dfsg+1-0ubuntu1) ... Setting up libedit2:armhf (3.1-20170329-1) ... Setting up libkpathsea6:armhf (2017.20170613.44572-8build1) ... Setting up libtexlua52:armhf (2017.20170613.44572-8build1) ... Setting up libglvnd0:armhf (1.0.0-2ubuntu2) ... Setting up libicu60:armhf (60.2-3ubuntu3) ... Setting up libjson-glib-1.0-common (1.4.2-3) ... Setting up libbz2-dev:armhf (1.0.6-8.1) ... Setting up libsynctex1:armhf (2017.20170613.44572-8build1) ... Setting up libptexenc1:armhf (2017.20170613.44572-8build1) ... Setting up glib-networking-common (2.56.0-1) ... Setting up libarchive-zip-perl (1.60-1) ... Setting up mime-support (3.60ubuntu1) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up libgfortran4:armhf (7.3.0-16ubuntu2) ... Setting up libllvm6.0:armhf (1:6.0-1ubuntu2) ... Setting up libtimedate-perl (2.3000-2) ... Setting up liblcms2-2:armhf (2.9-1) ... Setting up libjbig0:armhf (2.1-3.1build1) ... Setting up libpcsclite1:armhf (1.8.23-1) ... Setting up libsigsegv2:armhf (2.12-1) ... Setting up libpthread-stubs0-dev:armhf (0.3-4) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up poppler-data (0.4.8-2) ... Setting up bash-completion (1:2.8-1ubuntu1) ... Setting up libelf1:armhf (0.170-0.4) ... Setting up groff-base (1.22.3-10) ... Setting up libglib2.0-0:armhf (2.56.1-2ubuntu1) ... Setting up libasound2-data (1.1.3-5) ... Setting up libxshmfence1:armhf (1.2-1) ... Setting up xorg-sgml-doctools (1:1.11-1) ... Setting up libtext-unidecode-perl (1.30-1) ... Setting up libwayland-client0:armhf (1.14.0-2) ... Setting up xkb-data (2.23.1-1ubuntu1) ... Setting up libcurl4:armhf (7.58.0-2ubuntu3) ... Setting up libproxy1v5:armhf (0.4.15-1) ... Setting up java-common (0.63ubuntu1~02) ... Setting up libtinfo-dev:armhf (6.1-1ubuntu1) ... Setting up libgdk-pixbuf2.0-common (2.36.11-2) ... Setting up glib-networking-services (2.56.0-1) ... Setting up libdatrie1:armhf (0.2.10-7) ... Setting up gettext-base (0.19.8.1-6) ... Setting up libgif7:armhf (5.1.4-2) ... Setting up libjpeg-turbo8:armhf (1.5.2-0ubuntu5) ... Setting up libpipeline1:armhf (1.5.0-1) ... Setting up libglapi-mesa:armhf (18.0.0~rc5-1ubuntu1) ... Setting up m4 (1.4.18-1) ... Setting up libbsd0:armhf (0.8.7-1) ... Setting up libnspr4:armhf (2:4.18-1ubuntu1) ... Setting up ucf (3.0038) ... Setting up libgirepository-1.0-1:armhf (1.56.0-2) ... Setting up libxml2:armhf (2.9.4+dfsg1-6.1ubuntu1) ... Setting up mpack (1.6-8.2) ... Setting up x11proto-dev (2018.4-4) ... Setting up libfreetype6:armhf (2.8.1-2ubuntu2) ... Setting up libmagic-mgc (1:5.32-2) ... Setting up libasound2:armhf (1.1.3-5) ... Setting up libmagic1:armhf (1:5.32-2) ... Setting up libdrm-common (2.4.91-2) ... Setting up libjson-glib-1.0-0:armhf (1.4.2-3) ... Setting up libgraphite2-3:armhf (1.3.11-2) ... Setting up libjbig-dev:armhf (2.1-3.1build1) ... Setting up libcroco3:armhf (0.6.12-2) ... Setting up libncurses5-dev:armhf (6.1-1ubuntu1) ... Setting up libatk1.0-data (2.28.1-1) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up pkg-config (0.29.1-0ubuntu2) ... Setting up libjbig2dec0:armhf (0.13-6) ... Setting up libx11-xcb1:armhf (2:1.6.4-3) ... Setting up libpixman-1-0:armhf (0.34.0-2) ... Setting up xtrans-dev (1.3.5-1) ... Setting up libmime-charset-perl (1.012.2-1) ... Setting up libblas3:armhf (3.7.1-4ubuntu1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up gir1.2-glib-2.0:armhf (1.56.0-2) ... Setting up x11proto-xext-dev (2018.4-4) ... Setting up libjpeg-turbo8-dev:armhf (1.5.2-0ubuntu5) ... Setting up libglib2.0-data (2.56.1-2ubuntu1) ... Processing triggers for libc-bin (2.27-0ubuntu3) ... Setting up libepoxy0:armhf (1.4.3-1) ... Setting up autotools-dev (20180224.1) ... Setting up libpixman-1-dev:armhf (0.34.0-2) ... Setting up t1utils (1.41-2) ... Setting up libatk1.0-0:armhf (2.28.1-1) ... Processing triggers for systemd (237-3ubuntu8) ... Setting up libgfortran-7-dev:armhf (7.3.0-16ubuntu2) ... Setting up libreadline-dev:armhf (7.0-3) ... Setting up libijs-0.35:armhf (0.35-13) ... Setting up libbison-dev:armhf (2:3.0.4.dfsg-1build1) ... Setting up libfontenc1:armhf (1:1.1.3-1) ... Setting up libdconf1:armhf (0.26.0-2ubuntu3) ... Setting up libexpat1-dev:armhf (2.2.5-3) ... Setting up libpotrace0 (1.14-2) ... Setting up libsensors4:armhf (1:3.4.0-4) ... Setting up shared-mime-info (1.9-2) ... Setting up libxkbcommon0:armhf (0.8.0-1) ... Setting up x11proto-scrnsaver-dev (2018.4-4) ... Setting up gfortran-7 (7.3.0-16ubuntu2) ... Setting up libpcrecpp0v5:armhf (2:8.39-9) ... Setting up libpcre32-3:armhf (2:8.39-9) ... Setting up icu-devtools (60.2-3ubuntu3) ... Setting up libpcre16-3:armhf (2:8.39-9) ... Setting up libtcl8.6:armhf (8.6.8+dfsg-3) ... Setting up libcolord2:armhf (1.3.3-2build1) ... Setting up libthai-data (0.1.27-2) ... Setting up liblzma-dev:armhf (5.2.2-1.3) ... Setting up bison (2:3.0.4.dfsg-1build1) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up libxdmcp6:armhf (1:1.1.2-3) ... Setting up bsdmainutils (11.1.2ubuntu1) ... 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 x11-common (1:7.7+19ubuntu6) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libzzip-0-13:armhf (0.13.62-3.1) ... Setting up xdg-utils (1.1.2-1ubuntu2) ... Processing triggers for ca-certificates (20180409) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Setting up hicolor-icon-theme (0.17-2) ... Setting up libglib2.0-bin (2.56.1-2ubuntu1) ... Setting up libgraphite2-dev:armhf (1.3.11-2) ... Setting up libwayland-cursor0:armhf (1.14.0-2) ... Setting up libtexluajit2:armhf (2017.20170613.44572-8build1) ... Setting up libcurl4-openssl-dev:armhf (7.58.0-2ubuntu3) ... Setting up libx11-data (2:1.6.4-3) ... Setting up libpython2.7-stdlib:armhf (2.7.14-8) ... Setting up libxau6:armhf (1:1.0.8-1) ... Setting up autopoint (0.19.8.1-6) ... Setting up libmpdec2:armhf (2.4.2-1) ... Setting up libdbus-1-3:armhf (1.12.2-1ubuntu1) ... Setting up liblzo2-2:armhf (2.08-1.2) ... Setting up fonts-lmodern (2.004.5-3) ... Setting up libavahi-common-data:armhf (0.7-3.1ubuntu1) ... Setting up libwayland-server0:armhf (1.14.0-2) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.040-1.1~build1) ... Setting up libxml-sax-perl (0.99+dfsg-2ubuntu1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libjpeg8:armhf (8c-2ubuntu8) ... Setting up libpaper1:armhf (1.1.24+nmu5ubuntu1) ... Creating config file /etc/papersize with new version Setting up gfortran (4:7.3.0-3ubuntu2) ... 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 libpython3.6-stdlib:armhf (3.6.5-3) ... Setting up libpaper-utils (1.1.24+nmu5ubuntu1) ... Setting up libpcre3-dev:armhf (2:8.39-9) ... Setting up fontconfig-config (2.12.6-0ubuntu2) ... Setting up python3.6 (3.6.5-3) ... Setting up tex-common (6.09) ... update-language: texlive-base not installed and configured, doing nothing! Setting up x11proto-core-dev (2018.4-4) ... Setting up dconf-service (0.26.0-2ubuntu3) ... Setting up gettext (0.19.8.1-6) ... Setting up libblas-dev:armhf (3.7.1-4ubuntu1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode Setting up gir1.2-freedesktop:armhf (1.56.0-2) ... Setting up liblapack3:armhf (3.7.1-4ubuntu1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up python2.7 (2.7.14-8) ... Setting up libnss3:armhf (2:3.35-2ubuntu2) ... Setting up libxfont2:armhf (1:2.0.3-1) ... Setting up libharfbuzz0b:armhf (1.7.2-1ubuntu1) ... Setting up libtiff5:armhf (4.0.9-4ubuntu1) ... Setting up libxau-dev:armhf (1:1.0.8-1) ... Setting up preview-latex-style (11.91-1ubuntu1) ... Setting up autoconf (2.69-11) ... Setting up libthai0:armhf (0.1.27-2) ... Setting up file (1:5.32-2) ... Setting up xfonts-encodings (1:1.0.4-2) ... Setting up libdrm2:armhf (2.4.91-2) ... Setting up libpython-stdlib:armhf (2.7.14-4) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libxdmcp-dev:armhf (1:1.1.2-3) ... Setting up libjpeg8-dev:armhf (8c-2ubuntu8) ... Setting up gir1.2-harfbuzz-0.0:armhf (1.7.2-1ubuntu1) ... Setting up libjpeg-dev:armhf (8c-2ubuntu8) ... Setting up tcl8.6 (8.6.8+dfsg-3) ... Setting up libdrm-etnaviv1:armhf (2.4.91-2) ... Setting up automake (1:1.15.1-3ubuntu2) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up libice6:armhf (2:1.0.9-2) ... Setting up libtiffxx5:armhf (4.0.9-4ubuntu1) ... Setting up man-db (2.8.3-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libavahi-common3:armhf (0.7-3.1ubuntu1) ... Setting up libdrm-radeon1:armhf (2.4.91-2) ... Setting up libxml-libxml-perl (2.0128+dfsg-5) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libpng-dev:armhf (1.6.34-1) ... Setting up libdrm-nouveau2:armhf (2.4.91-2) ... Setting up dconf-gsettings-backend:armhf (0.26.0-2ubuntu3) ... Setting up libxcb1:armhf (1.13-1) ... Setting up libharfbuzz-gobject0:armhf (1.7.2-1ubuntu1) ... Setting up python (2.7.14-4) ... Setting up tcl8.6-dev:armhf (8.6.8+dfsg-3) ... Setting up libsombok3:armhf (2.4.0-1) ... Setting up liblapack-dev:armhf (3.7.1-4ubuntu1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode Setting up libtool (2.4.6-2) ... Setting up libpython3-stdlib:armhf (3.6.5-3) ... Setting up libxcb-present0:armhf (1.13-1) ... Setting up libfontconfig1:armhf (2.12.6-0ubuntu2) ... Setting up libxcb-dri2-0:armhf (1.13-1) ... Setting up libsm6:armhf (2:1.2.2-1) ... Setting up libxcb-dri3-0:armhf (1.13-1) ... Setting up libxcb-glx0:armhf (1.13-1) ... Setting up libxcb-xfixes0:armhf (1.13-1) ... Setting up libxcb-render0:armhf (1.13-1) ... Setting up libharfbuzz-icu0:armhf (1.7.2-1ubuntu1) ... Setting up po-debconf (1.0.20) ... Setting up gsettings-desktop-schemas (3.28.0-1ubuntu1) ... Setting up python3 (3.6.5-3) ... Setting up libdrm-amdgpu1:armhf (2.4.91-2) ... Setting up libdrm-freedreno1:armhf (2.4.91-2) ... Setting up libgtk-3-common (3.22.29-3ubuntu1) ... Setting up libicu-le-hb0:armhf (1.0.3+git161113-4) ... Setting up libgbm1:armhf (18.0.0~rc5-1ubuntu1) ... Setting up libtiff5-dev:armhf (4.0.9-4ubuntu1) ... Setting up libx11-6:armhf (2:1.6.4-3) ... Setting up libgl1-mesa-dri:armhf (18.0.0~rc5-1ubuntu1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up libxmuu1:armhf (2:1.1.2-2) ... Setting up libxcb-sync1:armhf (1.13-1) ... Setting up libpoppler73:armhf (0.62.0-2ubuntu1) ... Setting up libfreetype6-dev:armhf (2.8.1-2ubuntu2) ... Setting up libice-dev:armhf (2:1.0.9-2) ... Setting up glib-networking:armhf (2.56.0-1) ... Setting up libiculx60:armhf (60.2-3ubuntu3) ... Setting up libunicode-linebreak-perl (0.0.20160702-1build2) ... Setting up libxcomposite1:armhf (1:0.4.4-2) ... Setting up libxcb-shm0:armhf (1.13-1) ... Setting up libxpm4:armhf (1:3.5.12-1) ... Setting up libxt6:armhf (1:1.1.5-1) ... Setting up libxcb-shape0:armhf (1.13-1) ... Setting up libxrender1:armhf (1:0.9.10-1) ... Setting up libxcb1-dev:armhf (1.13-1) ... Setting up libavahi-client3:armhf (0.7-3.1ubuntu1) ... Setting up libegl-mesa0:armhf (18.0.0~rc5-1ubuntu1) ... Setting up texinfo (6.5.0.dfsg.1-2) ... Running mktexlsr. This may take some time. ... done. Setting up libx11-dev:armhf (2:1.6.4-3) ... Setting up libxft2:armhf (2.3.2-1) ... Setting up python3-lib2to3 (3.6.5-3) ... Setting up python3-distutils (3.6.5-3) ... Setting up xfonts-base (1:1.0.4+nmu1) ... Setting up fontconfig (2.12.6-0ubuntu2) ... Regenerating fonts cache... done. Setting up libcups2:armhf (2.2.7-1ubuntu2) ... Setting up libxkbfile1:armhf (1:1.0.9-2) ... Setting up libfontconfig1-dev:armhf (2.12.6-0ubuntu2) ... Setting up libsm-dev:armhf (2:1.2.2-1) ... Setting up libxdamage1:armhf (1:1.1.4-3) ... Setting up libxext6:armhf (2:1.3.3-1) ... Setting up libxfixes3:armhf (1:5.0.3-1) ... Setting up libglib2.0-dev-bin (2.56.1-2ubuntu1) ... Setting up libatspi2.0-0:armhf (2.28.0-1) ... Setting up libxss1:armhf (1:1.2.2-1) ... Setting up libgdk-pixbuf2.0-0:armhf (2.36.11-2) ... Setting up libxcb-shm0-dev:armhf (1.13-1) ... Setting up libsoup2.4-1:armhf (2.62.1-1) ... Setting up libxrender-dev:armhf (1:0.9.10-1) ... Setting up libsoup-gnome2.4-1:armhf (2.62.1-1) ... Setting up libglib2.0-dev:armhf (2.56.1-2ubuntu1) ... Setting up libxtst6:armhf (2:1.2.3-1) ... Setting up libxmu6:armhf (2:1.1.2-2) ... Setting up xauth (1:1.0.10-1) ... Setting up libxcb-render0-dev:armhf (1.13-1) ... Setting up libcupsimage2:armhf (2.2.7-1ubuntu2) ... Setting up libegl1:armhf (1.0.0-2ubuntu2) ... Setting up libxft-dev (2.3.2-1) ... Setting up gtk-update-icon-cache (3.22.29-3ubuntu1) ... Setting up libxcursor1:armhf (1:1.1.15-1) ... Setting up libxxf86dga1:armhf (2:1.1.4-1) ... Setting up libxext-dev:armhf (2:1.3.3-1) ... Setting up libpango-1.0-0:armhf (1.40.14-1) ... Setting up libwayland-egl1-mesa:armhf (18.0.0~rc5-1ubuntu1) ... Setting up libatk-bridge2.0-0:armhf (2.26.2-1) ... Setting up libxv1:armhf (2:1.0.11-1) ... Setting up librest-0.7-0:armhf (0.8.0-2) ... Setting up libxxf86vm1:armhf (1:1.1.4-1) ... Setting up libgs9:armhf (9.22~dfsg+1-0ubuntu1) ... Setting up libxrandr2:armhf (2:1.5.1-1) ... Setting up libglx-mesa0:armhf (18.0.0~rc5-1ubuntu1) ... Setting up libxi6:armhf (2:1.7.9-1) ... Setting up libxaw7:armhf (2:1.0.13-1) ... Setting up libcairo2:armhf (1.15.10-2) ... Setting up libxinerama1:armhf (2:1.1.3-1) ... Setting up libxt-dev:armhf (1:1.1.5-1) ... Setting up x11-xkb-utils (7.7+3) ... Setting up libcairo-script-interpreter2:armhf (1.15.10-2) ... Setting up libtk8.6:armhf (8.6.8-4) ... Setting up libcairo-gobject2:armhf (1.15.10-2) ... Setting up texlive-binaries (2017.20170613.44572-8build1) ... 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 libxss-dev:armhf (1:1.2.2-1) ... Setting up libpangoft2-1.0-0:armhf (1.40.14-1) ... Setting up texlive-base (2017.20180305-1) ... 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 texlive-fonts-recommended (2017.20180305-1) ... Setting up texlive-plain-generic (2017.20180305-2) ... Setting up texlive-generic-recommended (2017.20180305-1) ... Setting up libglx0:armhf (1.0.0-2ubuntu2) ... Setting up texlive-latex-base (2017.20180305-1) ... Setting up texlive-latex-recommended (2017.20180305-1) ... Setting up texlive-extra-utils (2017.20180305-2) ... Setting up xserver-common (2:1.19.6-1ubuntu4) ... Setting up tk8.6 (8.6.8-4) ... Setting up texlive-fonts-extra (2017.20180305-2) ... Setting up libcairo2-dev:armhf (1.15.10-2) ... Setting up texlive-pictures (2017.20180305-1) ... Setting up tk8.6-dev:armhf (8.6.8-4) ... Setting up libpangoxft-1.0-0:armhf (1.40.14-1) ... Setting up libpangocairo-1.0-0:armhf (1.40.14-1) ... Setting up gir1.2-pango-1.0:armhf (1.40.14-1) ... Setting up libgl1:armhf (1.0.0-2ubuntu2) ... Setting up librsvg2-2:armhf (2.40.20-2) ... Setting up texlive-latex-extra (2017.20180305-2) ... Setting up xvfb (2:1.19.6-1ubuntu4) ... Setting up x11-utils (7.7+3build1) ... Setting up librsvg2-common:armhf (2.40.20-2) ... Setting up libatk-wrapper-java (0.33.3-20) ... Setting up libatk-wrapper-java-jni:armhf (0.33.3-20) ... Setting up adwaita-icon-theme (3.28.0-1ubuntu1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up openjdk-9-jre-headless:armhf (9.0.4+12-4ubuntu2) ... update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up ca-certificates-java (20170930ubuntu1) ... Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:SecureTrust_CA.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:LuxTrust_Global_Root_2.pem Adding debian:DST_Root_CA_X3.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:OpenTrust_Root_CA_G2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:TrustCor_ECA-1.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:OpenTrust_Root_CA_G3.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Visa_eCommerce_Root.pem Adding debian:TÃœRKTRUST_Elektronik_Sertifika_Hizmet_SaÄŸlayıcısı_H5.pem Adding debian:AffirmTrust_Networking.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:Izenpe.com.pem Adding debian:ACCVRAIZ1.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Certplus_Root_CA_G2.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:AddTrust_External_Root.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:ISRG_Root_X1.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:Certinomis_-_Root_CA.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Certplus_Root_CA_G1.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:Secure_Global_CA.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:Certigna.pem Adding debian:AffirmTrust_Premium.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_FÅ‘tanúsítvány.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:OpenTrust_Root_CA_G1.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:EC-ACC.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:Taiwan_GRCA.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:DigiCert_Global_Root_G3.pem done. Setting up dh-autoreconf (17) ... Setting up libicu-le-hb-dev:armhf (1.0.3+git161113-4) ... Setting up openjdk-9-jdk-headless:armhf (9.0.4+12-4ubuntu2) ... update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/idlj to provide /usr/bin/idlj (idlj) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/wsimport to provide /usr/bin/wsimport (wsimport) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/javah to provide /usr/bin/javah (javah) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/policytool to provide /usr/bin/policytool (policytool) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/schemagen to provide /usr/bin/schemagen (schemagen) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/xjc to provide /usr/bin/xjc (xjc) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/wsgen to provide /usr/bin/wsgen (wsgen) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode Setting up humanity-icon-theme (0.6.15) ... Setting up libicu-dev (60.2-3ubuntu3) ... Setting up libgtk-3-0:armhf (3.22.29-3ubuntu1) ... Setting up dh-strip-nondeterminism (0.040-1.1~build1) ... Setting up openjdk-9-jre:armhf (9.0.4+12-4ubuntu2) ... Setting up libharfbuzz-dev:armhf (1.7.2-1ubuntu1) ... Setting up debhelper (11.1.6ubuntu1) ... Setting up ubuntu-mono (16.10+18.04.20180328-0ubuntu1) ... Setting up openjdk-9-jdk:armhf (9.0.4+12-4ubuntu2) ... update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/appletviewer to provide /usr/bin/appletviewer (appletviewer) in auto mode update-alternatives: using /usr/lib/jvm/java-9-openjdk-armhf/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up libpango1.0-dev (1.40.14-1) ... Setting up sbuild-build-depends-r-base-dummy (0.invalid.0) ... (Reading database ... 119003 files and directories currently installed.) Purging configuration files for pkg-create-dbgsym (0.73) ... Processing triggers for tex-common (6.09) ... 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. Processing triggers for libgdk-pixbuf2.0-0:armhf (2.36.11-2) ... Processing triggers for libc-bin (2.27-0ubuntu3) ... Processing triggers for systemd (237-3ubuntu8) ... Processing triggers for ca-certificates (20180409) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-119-generic arm64 (armv7l) Toolchain package versions: binutils_2.30-15ubuntu1 dpkg-dev_1.19.0.5ubuntu1 g++-7_7.3.0-16ubuntu2 gcc-7_7.3.0-16ubuntu2 libc6-dev_2.27-0ubuntu3 libstdc++-7-dev_7.3.0-16ubuntu2 libstdc++6_8-20180408-0ubuntu1 linux-libc-dev_4.15.0-15.16 Package versions: adduser_3.116ubuntu1 advancecomp_2.1-1 adwaita-icon-theme_3.28.0-1ubuntu1 apt_1.6~beta1 apt-transport-https_1.6~beta1 autoconf_2.69-11 automake_1:1.15.1-3ubuntu2 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1ubuntu1 base-passwd_3.5.44 bash_4.4.18-2ubuntu1 bash-completion_1:2.8-1ubuntu1 binutils_2.30-15ubuntu1 binutils-arm-linux-gnueabihf_2.30-15ubuntu1 binutils-common_2.30-15ubuntu1 bison_2:3.0.4.dfsg-1build1 bsdmainutils_11.1.2ubuntu1 bsdutils_1:2.31.1-0.4ubuntu3 build-essential_12.4ubuntu1 bzip2_1.0.6-8.1 ca-certificates_20180409 ca-certificates-java_20170930ubuntu1 coreutils_8.28-1ubuntu1 cpp_4:7.3.0-3ubuntu2 cpp-7_7.3.0-16ubuntu2 dash_0.5.8-2.10 dconf-gsettings-backend_0.26.0-2ubuntu3 dconf-service_0.26.0-2ubuntu3 debconf_1.5.66 debhelper_11.1.6ubuntu1 debianutils_4.8.4 dh-autoreconf_17 dh-strip-nondeterminism_0.040-1.1~build1 diffutils_1:3.6-1 dirmngr_2.2.4-1ubuntu1 dmsetup_2:1.02.145-4.1ubuntu3 dpkg_1.19.0.5ubuntu1 dpkg-dev_1.19.0.5ubuntu1 e2fslibs_1.44.1-1 e2fsprogs_1.44.1-1 fakeroot_1.22-2ubuntu1 fdisk_2.31.1-0.4ubuntu3 file_1:5.32-2 findutils_4.6.0+git+20170828-2 fontconfig_2.12.6-0ubuntu2 fontconfig-config_2.12.6-0ubuntu2 fonts-dejavu-core_2.37-1 fonts-lmodern_2.004.5-3 g++_4:7.3.0-3ubuntu2 g++-7_7.3.0-16ubuntu2 gcc_4:7.3.0-3ubuntu2 gcc-7_7.3.0-16ubuntu2 gcc-7-base_7.3.0-16ubuntu2 gcc-8-base_8-20180408-0ubuntu1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gfortran_4:7.3.0-3ubuntu2 gfortran-7_7.3.0-16ubuntu2 gir1.2-freedesktop_1.56.0-2 gir1.2-glib-2.0_1.56.0-2 gir1.2-harfbuzz-0.0_1.7.2-1ubuntu1 gir1.2-pango-1.0_1.40.14-1 glib-networking_2.56.0-1 glib-networking-common_2.56.0-1 glib-networking-services_2.56.0-1 gnupg_2.2.4-1ubuntu1 gnupg-agent_2.2.4-1ubuntu1 gnupg-l10n_2.2.4-1ubuntu1 gnupg-utils_2.2.4-1ubuntu1 gpg_2.2.4-1ubuntu1 gpg-agent_2.2.4-1ubuntu1 gpg-wks-client_2.2.4-1ubuntu1 gpg-wks-server_2.2.4-1ubuntu1 gpgconf_2.2.4-1ubuntu1 gpgsm_2.2.4-1ubuntu1 gpgv_2.2.4-1ubuntu1 grep_3.1-2 groff-base_1.22.3-10 gsettings-desktop-schemas_3.28.0-1ubuntu1 gtk-update-icon-cache_3.22.29-3ubuntu1 gzip_1.6-5ubuntu1 hicolor-icon-theme_0.17-2 hostname_3.20 humanity-icon-theme_0.6.15 icu-devtools_60.2-3ubuntu3 init_1.51 init-system-helpers_1.51 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 java-common_0.63ubuntu1~02 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu4 libapt-pkg5.0_1.6~beta1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-1.1 libasan4_7.3.0-16ubuntu2 libasn1-8-heimdal_7.5.0+dfsg-1 libasound2_1.1.3-5 libasound2-data_1.1.3-5 libassuan0_2.5.1-2 libatk-bridge2.0-0_2.26.2-1 libatk-wrapper-java_0.33.3-20 libatk-wrapper-java-jni_0.33.3-20 libatk1.0-0_2.28.1-1 libatk1.0-data_2.28.1-1 libatomic1_8-20180408-0ubuntu1 libatspi2.0-0_2.28.0-1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.2-1ubuntu1 libaudit1_1:2.8.2-1ubuntu1 libavahi-client3_0.7-3.1ubuntu1 libavahi-common-data_0.7-3.1ubuntu1 libavahi-common3_0.7-3.1ubuntu1 libbinutils_2.30-15ubuntu1 libbison-dev_2:3.0.4.dfsg-1build1 libblas-dev_3.7.1-4ubuntu1 libblas3_3.7.1-4ubuntu1 libblkid1_2.31.1-0.4ubuntu3 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libbz2-dev_1.0.6-8.1 libc-bin_2.27-0ubuntu3 libc-dev-bin_2.27-0ubuntu3 libc6_2.27-0ubuntu3 libc6-dev_2.27-0ubuntu3 libcairo-gobject2_1.15.10-2 libcairo-script-interpreter2_1.15.10-2 libcairo2_1.15.10-2 libcairo2-dev_1.15.10-2 libcap-ng0_0.7.7-3.1 libcap2_1:2.25-1.2 libcc1-0_8-20180408-0ubuntu1 libcilkrts5_7.3.0-16ubuntu2 libcolord2_1.3.3-2build1 libcom-err2_1.44.1-1 libcomerr2_1.44.1-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1ubuntu1 libcryptsetup4_2:1.7.3-4ubuntu1 libcups2_2.2.7-1ubuntu2 libcupsimage2_2.2.7-1ubuntu2 libcurl3-gnutls_7.58.0-2ubuntu3 libcurl4_7.58.0-2ubuntu3 libcurl4-openssl-dev_7.58.0-2ubuntu3 libdatrie1_0.2.10-7 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.2-1ubuntu1 libdconf1_0.26.0-2ubuntu3 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu3 libdpkg-perl_1.19.0.5ubuntu1 libdrm-amdgpu1_2.4.91-2 libdrm-common_2.4.91-2 libdrm-etnaviv1_2.4.91-2 libdrm-freedreno1_2.4.91-2 libdrm-nouveau2_2.4.91-2 libdrm-radeon1_2.4.91-2 libdrm2_2.4.91-2 libedit2_3.1-20170329-1 libegl-mesa0_18.0.0~rc5-1ubuntu1 libegl1_1.0.0-2ubuntu2 libelf1_0.170-0.4 libepoxy0_1.4.3-1 libexpat1_2.2.5-3 libexpat1-dev_2.2.5-3 libext2fs2_1.44.1-1 libfakeroot_1.22-2ubuntu1 libfdisk1_2.31.1-0.4ubuntu3 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.040-1.1~build1 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systemd-sysv_237-3ubuntu8 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 t1utils_1.41-2 tar_1.29b-2 tcl8.6_8.6.8+dfsg-3 tcl8.6-dev_8.6.8+dfsg-3 tex-common_6.09 texinfo_6.5.0.dfsg.1-2 texlive-base_2017.20180305-1 texlive-binaries_2017.20170613.44572-8build1 texlive-extra-utils_2017.20180305-2 texlive-fonts-extra_2017.20180305-2 texlive-fonts-recommended_2017.20180305-1 texlive-generic-recommended_2017.20180305-1 texlive-latex-base_2017.20180305-1 texlive-latex-extra_2017.20180305-2 texlive-latex-recommended_2017.20180305-1 texlive-pictures_2017.20180305-1 texlive-plain-generic_2017.20180305-2 tk8.6_8.6.8-4 tk8.6-dev_8.6.8-4 tzdata_2018d-1 ubuntu-keyring_2018.02.28 ubuntu-mono_16.10+18.04.20180328-0ubuntu1 ucf_3.0038 util-linux_2.31.1-0.4ubuntu3 x11-common_1:7.7+19ubuntu6 x11-utils_7.7+3build1 x11-xkb-utils_7.7+3 x11proto-core-dev_2018.4-4 x11proto-dev_2018.4-4 x11proto-scrnsaver-dev_2018.4-4 x11proto-xext-dev_2018.4-4 xauth_1:1.0.10-1 xdg-utils_1.1.2-1ubuntu2 xfonts-base_1:1.0.4+nmu1 xfonts-encodings_1:1.0.4-2 xfonts-utils_1:7.7+6 xkb-data_2.23.1-1ubuntu1 xorg-sgml-doctools_1:1.11-1 xserver-common_2:1.19.6-1ubuntu4 xtrans-dev_1.3.5-1 xvfb_2:1.19.6-1ubuntu4 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Mar 15 11:37:14 2018 UTC gpgv: using RSA key A1489FE2AB99A21A gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./r-base_3.4.4-1.dsc dpkg-source: info: extracting r-base in r-base-3.4.4 dpkg-source: info: unpacking r-base_3.4.4.orig.tar.gz dpkg-source: info: unpacking r-base_3.4.4-1.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-14757513 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-14757513 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-14757513 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 3.4.4-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build r-base-3.4.4 dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean *** clean *** dh_testdir dh_testroot rm -f configure-stamp \ build-stamp build-indep-stamp build-arch-stamp \ make-stamp make-arch-stamp make-indep-stamp \ install-indep-stamp install-arch-stamp \ check-stamp [ ! -f Makefile ] || /usr/bin/make distclean rm -f `find . -name "*~"` rm -rf debian/tmp debian/files* core debian/substvars rm -f doc/html/function.html doc/html/packages.html rm -f modules/*.so src/unix/Rscript dh_clean debian/rules build-arch *** configure *** #automake #autoconf dh_testdir R_TEXI2DVICMD=emulation \ R_PAPERSIZE=letter \ R_BROWSER=xdg-open \ R_GZIPCMD="/bin/gzip -n" \ PAGER=/usr/bin/pager \ PERL=/usr/bin/perl \ JAVA_HOME=/usr/lib/jvm/default-java \ R_UNZIPCMD=/usr/bin/unzip \ R_ZIPCMD=/usr/bin/zip \ R_PRINTCMD=/usr/bin/lpr \ LIBnn=lib \ AWK=/usr/bin/awk \ CC="gcc -std=gnu99" \ CXX=g++ \ F77=gfortran \ FC=gfortran \ CFLAGS="-g -O2 -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 arm-linux-gnueabihf configure: WARNING: unrecognized options: --with-system-bzlib, --with-system-pcre, --with-system-zlib checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf loading site script './config.site' loading build-specific script './config.site' checking for pwd... /bin/pwd checking whether builddir is srcdir... yes checking for working aclocal... found checking for working autoconf... found checking for working automake... found checking for working autoheader... found checking whether ln -s works... yes checking for bison... bison -y 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 gtar... no checking for gnutar... no checking for 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... 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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 defining F77 to be gfortran checking whether we are using the GNU Fortran 77 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 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(cached) /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc -std=gnu99... /usr/bin/arm-linux-gnueabihf-ld checking if the linker (/usr/bin/arm-linux-gnueabihf-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 arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop checking for /usr/bin/arm-linux-gnueabihf-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... 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(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/arm-linux-gnueabihf-ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for cos in -lm... yes checking for sin in -lm... yes checking for dlopen in -ldl... yes checking readline/history.h usability... yes checking readline/history.h presence... yes checking for readline/history.h... yes checking readline/readline.h usability... yes checking readline/readline.h presence... yes checking for readline/readline.h... yes checking for rl_callback_read_char in -lreadline... yes checking for history_truncate_file... yes checking whether rl_callback_sigcleanup exists and is declared... yes checking whether rl_completion_matches exists and is declared... yes checking whether rl_resize_terminal exists and is declared... yes checking whether rl_sort_completion_matches exists and is declared... yes checking for ANSI C header files... (cached) yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for sys/wait.h that is POSIX.1 compatible... yes checking for dlfcn.h... (cached) yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking glob.h usability... yes checking glob.h presence... yes checking for glob.h... yes checking grp.h usability... yes checking grp.h presence... yes checking for grp.h... yes checking pwd.h usability... yes checking pwd.h presence... yes checking for pwd.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for strings.h... (cached) yes checking sys/resource.h usability... yes checking sys/resource.h presence... yes checking for sys/resource.h... yes checking sys/select.h usability... yes checking sys/select.h presence... yes checking for sys/select.h... yes checking sys/socket.h usability... yes checking sys/socket.h presence... yes checking for sys/socket.h... yes checking for sys/stat.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sys/times.h usability... yes checking sys/times.h presence... yes checking for sys/times.h... yes checking sys/utsname.h usability... yes checking sys/utsname.h presence... yes checking for sys/utsname.h... yes checking for unistd.h... (cached) yes checking utime.h usability... yes checking utime.h presence... yes checking for utime.h... yes checking arpa/inet.h usability... yes checking arpa/inet.h presence... yes checking for arpa/inet.h... yes checking dl.h usability... no checking dl.h presence... no checking for dl.h... no checking elf.h usability... yes checking elf.h presence... yes checking for elf.h... yes checking features.h usability... yes checking features.h presence... yes checking for features.h... yes checking floatingpoint.h usability... no checking floatingpoint.h presence... no checking for floatingpoint.h... no checking langinfo.h usability... yes checking langinfo.h presence... yes checking for langinfo.h... yes checking netdb.h usability... yes checking netdb.h presence... yes checking for netdb.h... yes checking netinet/in.h usability... yes checking netinet/in.h presence... yes checking for netinet/in.h... yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking stdalign.h usability... yes checking stdalign.h presence... yes checking for stdalign.h... yes checking errno.h usability... yes checking errno.h presence... yes checking for errno.h... yes checking for inttypes.h... 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(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... 4 checking size of long long... 8 checking size of double... 8 checking size of size_t... 4 checking size of long double... 8 checking whether we can compute C Make dependencies... yes, using $(CC) -MM checking whether gcc -std=gnu99 supports -c -o FILE.lo... yes checking for gcc -std=gnu99 option to support OpenMP... -fopenmp checking how to get verbose linking output from gfortran... -v checking for Fortran 77 libraries of gfortran... -L/usr/lib/gcc/arm-linux-gnueabihf/7 -L/usr/lib/gcc/arm-linux-gnueabihf/7/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/7/../../../../lib -L/lib/arm-linux-gnueabihf -L/lib/../lib -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/../lib -L/usr/lib/gcc/arm-linux-gnueabihf/7/../../.. -lgfortran -lm checking how to get verbose linking output from gcc -std=gnu99... -v checking for C libraries of gcc -std=gnu99... -L/usr/lib/gcc/arm-linux-gnueabihf/7 -L/usr/lib/gcc/arm-linux-gnueabihf/7/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/7/../../../../lib -L/lib/arm-linux-gnueabihf -L/lib/../lib -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/../lib -L/usr/lib/gcc/arm-linux-gnueabihf/7/../../.. -lgcc_s checking for dummy main to link with Fortran 77 libraries... none checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore checking whether 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 for g++ option to support OpenMP... -fopenmp 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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 rint 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 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 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... no checking complex.h usability... yes checking complex.h presence... yes checking for 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'struct tm' includes tm_gmtoff... yes checking for dgemm_... no checking for ATL_xerbla in -latlas... no checking for dgemm_ in -lblas... yes checking for dgemm_ in -ldgemm... no checking for dgemm_ in -lblas... 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(cached) yes checking whether the gfortran linker (/usr/bin/arm-linux-gnueabihf-ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for Fortran flag to compile .f90 files... none checking for Fortran flag to compile .f95 files... none checking for gfortran option to support OpenMP... -fopenmp checking whether NLS is requested... yes Configuring src/extra/intl directory checking for a thread-safe mkdir -p... /bin/mkdir -p checking whether we are using the GNU C Library 2 or newer... yes checking for ranlib... (cached) ranlib checking for simple visibility declarations... yes checking for stdint.h... yes checking for getpagesize... yes checking for working mmap... yes checking whether integer division by zero raises SIGFPE... yes checking for inttypes.h... yes checking for unsigned long long int... yes checking for inttypes.h... 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(cached) yes checking for strtoul... yes checking for tsearch... yes checking for argz_count... yes checking for argz_stringify... yes checking for argz_next... yes checking for __fsetlocking... yes checking whether feof_unlocked is declared... yes checking whether fgets_unlocked is declared... yes checking for iconv... (cached) yes checking for iconv declaration... (cached) extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft); checking for NL_LOCALE_NAME macro... yes checking for bison... bison checking version of bison... 3.0.4, ok checking for long long int... yes checking for long double... yes checking for wchar_t... yes checking for wint_t... yes checking for intmax_t... yes checking whether printf() supports POSIX/XSI format strings... yes checking whether we are using the GNU C Library 2.1 or newer... yes checking for stdint.h... (cached) yes checking for SIZE_MAX... yes checking for stdint.h... (cached) yes checking for CFPreferencesCopyAppValue... no checking for CFLocaleCopyCurrent... no checking for ptrdiff_t... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for asprintf... yes checking for fwprintf... yes checking for putenv... (cached) yes checking for setenv... yes checking for setlocale... yes checking for snprintf... yes checking for wcslen... yes checking whether _snprintf is declared... no checking whether _snwprintf is declared... no checking whether getc_unlocked is declared... yes checking for nl_langinfo and CODESET... (cached) yes checking for LC_MESSAGES... yes checking for CFPreferencesCopyAppValue... (cached) no checking for CFLocaleCopyCurrent... (cached) no checking whether included gettext is requested... no checking for GNU gettext in libc... yes checking whether to use NLS... yes checking where the gettext function comes from... libc Finished configuring src/extra/intl directory 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/f77_f2c config.status: creating src/scripts/javareconf config.status: creating src/scripts/mkinstalldirs config.status: creating src/scripts/pager config.status: creating src/scripts/rtags config.status: creating src/unix/Makefile config.status: creating tests/Makefile config.status: creating tests/Embedding/Makefile config.status: creating tests/Examples/Makefile config.status: creating tools/Makefile config.status: creating src/include/config.h config.status: executing libtool commands config.status: executing stamp-h commands configure: WARNING: unrecognized options: --with-system-bzlib, --with-system-pcre, --with-system-zlib R is now configured for arm-unknown-linux-gnueabihf 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 77 compiler: gfortran -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong Default C++ compiler: g++ -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++ -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 90/95 compiler: gfortran -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 -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dchdc.f -o dchdc.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dpbfa.f -o dpbfa.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dpbsl.f -o dpbsl.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dpoco.f -o dpoco.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dpodi.f -o dpodi.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dpofa.f -o dpofa.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dposl.f -o dposl.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dqrdc.f -o dqrdc.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dqrdc2.f -o dqrdc2.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dqrls.f -o dqrls.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dqrsl.f -o dqrsl.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dqrutl.f -o dqrutl.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dsvdc.f -o dsvdc.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c dtrco.f -o dtrco.o gfortran -fopenmp -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 expm1.d from expm1.c making lgammacor.d from lgammacor.c making gammalims.d from gammalims.c making stirlerr.d from stirlerr.c making bd0.d from bd0.c making gamma.d from gamma.c making lgamma.d from lgamma.c making gamma_cody.d from gamma_cody.c making beta.d from beta.c making lbeta.d from lbeta.c making polygamma.d from polygamma.c making cospi.d from cospi.c making bessel_i.d from bessel_i.c making bessel_j.d from bessel_j.c making bessel_k.d from bessel_k.c making bessel_y.d from bessel_y.c making choose.d from choose.c making snorm.d from snorm.c making sexp.d from sexp.c making dgamma.d from dgamma.c making pgamma.d from pgamma.c making qgamma.d from qgamma.c making rgamma.d from rgamma.c making dbeta.d from dbeta.c making pbeta.d from pbeta.c making qbeta.d from qbeta.c making rbeta.d from rbeta.c making dunif.d from dunif.c making punif.d from punif.c making qunif.d from qunif.c making runif.d from runif.c making dnorm.d from dnorm.c making pnorm.d from pnorm.c making qnorm.d from qnorm.c making rnorm.d from rnorm.c making dlnorm.d from dlnorm.c making plnorm.d from plnorm.c making qlnorm.d from qlnorm.c making rlnorm.d from rlnorm.c making df.d from df.c making pf.d from pf.c making qf.d from qf.c making rf.d from rf.c making dnf.d from dnf.c making dt.d from dt.c making pt.d from pt.c making qt.d from qt.c making rt.d from rt.c making dnt.d from dnt.c making dchisq.d from dchisq.c making pchisq.d from pchisq.c making qchisq.d from qchisq.c making rchisq.d from rchisq.c making rnchisq.d from rnchisq.c making dbinom.d from dbinom.c making pbinom.d from pbinom.c making qbinom.d from qbinom.c making rbinom.d from rbinom.c making rmultinom.d from rmultinom.c making dcauchy.d from dcauchy.c making pcauchy.d from pcauchy.c making qcauchy.d from qcauchy.c making rcauchy.d from rcauchy.c making dexp.d from dexp.c making pexp.d from pexp.c making qexp.d from qexp.c making rexp.d from rexp.c making dgeom.d from dgeom.c making pgeom.d from pgeom.c making qgeom.d from qgeom.c making rgeom.d from rgeom.c making dhyper.d from dhyper.c making phyper.d from phyper.c making qhyper.d from qhyper.c making rhyper.d from rhyper.c making dnbinom.d from dnbinom.c making pnbinom.d from pnbinom.c making qnbinom.d from qnbinom.c making rnbinom.d from rnbinom.c making dpois.d from dpois.c making ppois.d from ppois.c making qpois.d from qpois.c making rpois.d from rpois.c making dweibull.d from dweibull.c making pweibull.d from pweibull.c making qweibull.d from qweibull.c making rweibull.d from rweibull.c making dlogis.d from dlogis.c making plogis.d from plogis.c making qlogis.d from qlogis.c making rlogis.d from rlogis.c making dnchisq.d from dnchisq.c making pnchisq.d from pnchisq.c making qnchisq.d from qnchisq.c making dnbeta.d from dnbeta.c making pnbeta.d from pnbeta.c making qnbeta.d from qnbeta.c making pnf.d from pnf.c making pnt.d from pnt.c making qnf.d from qnf.c making qnt.d from qnt.c making ptukey.d from ptukey.c making qtukey.d from qtukey.c making toms708.d from toms708.c making wilcox.d from wilcox.c making signrank.d from signrank.c make[4]: Entering directory '/<>/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 expm1.c -o expm1.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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qgeom.c -o qgeom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rgeom.c -o rgeom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dhyper.c -o dhyper.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c phyper.c -o phyper.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -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 expm1.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o ranlib libnmath.a make[4]: Leaving directory '/<>/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 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 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 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 main.c: In function ‘dummy_ii’: main.c:1669:12: warning: function returns address of local variable [-Wreturn-local-addr] return (uintptr_t) ⅈ ^~~~~~~~~~~~~~~ gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -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 -fopenmp -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 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 -lreadline -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 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/arm-linux-gnueabihf -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -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/arm-linux-gnueabihf -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -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/arm-linux-gnueabihf -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -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 -ljpeg -lpng16 -lz -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt -lR -lm gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/arm-linux-gnueabihf -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -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 -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/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -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 -ljpeg -lpng16 -lz -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -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 -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c bsplvd.f -o bsplvd.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c bvalue.f -o bvalue.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c bvalus.f -o bvalus.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c loessf.f -o loessf.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c ppr.f -o ppr.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c qsbart.f -o qsbart.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c sgram.f -o sgram.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c sinerp.f -o sinerp.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c sslvrg.f -o sslvrg.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c stxwx.f -o stxwx.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c hclust.f -o hclust.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c kmns.f -o kmns.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -c eureka.f -o eureka.o gfortran -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 -ffloat-store -c portsrc.f -o portsrc.o gfortran -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 -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/arm-linux-gnueabihf -ltcl8.6 -L/usr/lib/arm-linux-gnueabihf -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 expm1.d from expm1.c making lgammacor.d from lgammacor.c making gammalims.d from gammalims.c making stirlerr.d from stirlerr.c making bd0.d from bd0.c making gamma.d from gamma.c making lgamma.d from lgamma.c making gamma_cody.d from gamma_cody.c making beta.d from beta.c making lbeta.d from lbeta.c making polygamma.d from polygamma.c making cospi.d from cospi.c making bessel_i.d from bessel_i.c making bessel_j.d from bessel_j.c making bessel_k.d from bessel_k.c making bessel_y.d from bessel_y.c making choose.d from choose.c making snorm.d from snorm.c making sexp.d from sexp.c making dgamma.d from dgamma.c making pgamma.d from pgamma.c making qgamma.d from qgamma.c making rgamma.d from rgamma.c making dbeta.d from dbeta.c making pbeta.d from pbeta.c making qbeta.d from qbeta.c making rbeta.d from rbeta.c making dunif.d from dunif.c making punif.d from punif.c making qunif.d from qunif.c making runif.d from runif.c making dnorm.d from dnorm.c making pnorm.d from pnorm.c making qnorm.d from qnorm.c making rnorm.d from rnorm.c making dlnorm.d from dlnorm.c making plnorm.d from plnorm.c making qlnorm.d from qlnorm.c making rlnorm.d from rlnorm.c making df.d from df.c making pf.d from pf.c making qf.d from qf.c making rf.d from rf.c making dnf.d from dnf.c making dt.d from dt.c making pt.d from pt.c making qt.d from qt.c making rt.d from rt.c making dnt.d from dnt.c making dchisq.d from dchisq.c making pchisq.d from pchisq.c making qchisq.d from qchisq.c making rchisq.d from rchisq.c making rnchisq.d from rnchisq.c making dbinom.d from dbinom.c making pbinom.d from pbinom.c making qbinom.d from qbinom.c making rbinom.d from rbinom.c making rmultinom.d from rmultinom.c making dcauchy.d from dcauchy.c making pcauchy.d from pcauchy.c making qcauchy.d from qcauchy.c making rcauchy.d from rcauchy.c making dexp.d from dexp.c making pexp.d from pexp.c making qexp.d from qexp.c making rexp.d from rexp.c making dgeom.d from dgeom.c making pgeom.d from pgeom.c making qgeom.d from qgeom.c making rgeom.d from rgeom.c making dhyper.d from dhyper.c making phyper.d from phyper.c making qhyper.d from qhyper.c making rhyper.d from rhyper.c making dnbinom.d from dnbinom.c making pnbinom.d from pnbinom.c making qnbinom.d from qnbinom.c making rnbinom.d from rnbinom.c making dpois.d from dpois.c making ppois.d from ppois.c making qpois.d from qpois.c making rpois.d from rpois.c making dweibull.d from dweibull.c making pweibull.d from pweibull.c making qweibull.d from qweibull.c making rweibull.d from rweibull.c making dlogis.d from dlogis.c making plogis.d from plogis.c making qlogis.d from qlogis.c making rlogis.d from rlogis.c making dnchisq.d from dnchisq.c making pnchisq.d from pnchisq.c making qnchisq.d from qnchisq.c making dnbeta.d from dnbeta.c making pnbeta.d from pnbeta.c making qnbeta.d from qnbeta.c making pnf.d from pnf.c making pnt.d from pnt.c making qnf.d from qnf.c making qnt.d from qnt.c making ptukey.d from ptukey.c making qtukey.d from qtukey.c making toms708.d from toms708.c making wilcox.d from wilcox.c making signrank.d from signrank.c making std_unif.d from std_unif.c make[2]: Leaving directory '/<>/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 expm1.c -o expm1.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -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 -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c wilcox.c -o wilcox.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c signrank.c -o signrank.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c std_unif.c -o std_unif.lo gcc -std=gnu99 -shared -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -o libRmath.so -Wl,-soname,libRmath.so.1 mlutils.lo d1mach.lo i1mach.lo fmax2.lo fmin2.lo fprec.lo fround.lo ftrunc.lo sign.lo fsign.lo imax2.lo imin2.lo chebyshev.lo log1p.lo expm1.lo lgammacor.lo gammalims.lo stirlerr.lo bd0.lo gamma.lo lgamma.lo gamma_cody.lo beta.lo lbeta.lo polygamma.lo cospi.lo bessel_i.lo bessel_j.lo bessel_k.lo bessel_y.lo choose.lo snorm.lo sexp.lo dgamma.lo pgamma.lo qgamma.lo rgamma.lo dbeta.lo pbeta.lo qbeta.lo rbeta.lo dunif.lo punif.lo qunif.lo runif.lo dnorm.lo pnorm.lo qnorm.lo rnorm.lo dlnorm.lo plnorm.lo qlnorm.lo rlnorm.lo df.lo pf.lo qf.lo rf.lo dnf.lo dt.lo pt.lo qt.lo rt.lo dnt.lo dchisq.lo pchisq.lo qchisq.lo rchisq.lo rnchisq.lo dbinom.lo pbinom.lo qbinom.lo rbinom.lo rmultinom.lo dcauchy.lo pcauchy.lo qcauchy.lo rcauchy.lo dexp.lo pexp.lo qexp.lo rexp.lo dgeom.lo pgeom.lo qgeom.lo rgeom.lo dhyper.lo phyper.lo qhyper.lo rhyper.lo dnbinom.lo pnbinom.lo qnbinom.lo rnbinom.lo dpois.lo ppois.lo qpois.lo rpois.lo dweibull.lo pweibull.lo qweibull.lo rweibull.lo dlogis.lo plogis.lo qlogis.lo rlogis.lo dnchisq.lo pnchisq.lo qnchisq.lo dnbeta.lo pnbeta.lo qnbeta.lo pnf.lo pnt.lo qnf.lo qnt.lo ptukey.lo qtukey.lo toms708.lo wilcox.lo signrank.lo std_unif.lo -lm make[2]: Leaving directory '/<>/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 -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fround.c -o fround.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ftrunc.c -o ftrunc.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c sign.c -o sign.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fsign.c -o fsign.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -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 expm1.c -o expm1.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 -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pexp.c -o pexp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qexp.c -o qexp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rexp.c -o rexp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dgeom.c -o dgeom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pgeom.c -o pgeom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qgeom.c -o qgeom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rgeom.c -o rgeom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dhyper.c -o dhyper.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c phyper.c -o phyper.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qhyper.c -o qhyper.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rhyper.c -o rhyper.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnbinom.c -o dnbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnbinom.c -o pnbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnbinom.c -o qnbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnbinom.c -o rnbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -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 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qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o std_unif.o ranlib libRmath.a make[2]: Leaving directory '/<>/src/nmath/standalone' make[1]: Leaving directory '/<>/src/nmath/standalone' R_GZIPCMD="/bin/gzip -n" \ /usr/bin/make docs R_CMD_BUILD_HELP_OPTS="--txt --example" 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]: 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'/<>/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' 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_HOME is not a valid path, ignoring Java interpreter : /usr/bin/java Java version : 9.0.4 Java home path : /usr/lib/jvm/java-9-openjdk-armhf Java compiler : /usr/bin/javac Java headers gen.: /usr/bin/javah Java archive tool: /usr/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.Bsn9uY' gcc -std=gnu99 -I/<>/include -DNDEBUG -I/usr/lib/jvm/java-9-openjdk-armhf/include -I/usr/lib/jvm/java-9-openjdk-armhf/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 g++ -shared -L/<>/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/java-9-openjdk-armhf/lib/server -ljvm -L/<>/lib -lR make[3]: Leaving directory '/tmp/Rjavareconf.Bsn9uY' JAVA_HOME : /usr/lib/jvm/java-9-openjdk-armhf 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 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'/<>' make[2]: Entering directory '/<>/doc' make[3]: Entering directory '/<>/doc/manual' /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. 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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 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 3 language(s) loaded. 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(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/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 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 296--300 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 385--388 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 533--539 []\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 1144--1147 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1901--1901 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2086--2088 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] Underfull \vbox (badness 10000) has occurred while \output is active [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3607--3609 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] [60] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3848--3848 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] Underfull \hbox (badness 2521) in paragraph at lines 4823--4825 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] Overfull \hbox (5.27168pt too wide) in paragraph at lines 5954--5954 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [94] [95] [96] Underfull \hbox (badness 2096) in paragraph at lines 6137--6150 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [97] [98] [99] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6341--6343 []\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 : [100] [101] Underfull \hbox (badness 10000) in paragraph at lines 6483--6486 []\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 [102] [103] Underfull \hbox (badness 1442) in paragraph at lines 6646--6652 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6646--6652 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6646--6652 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). 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[115] [116] Underfull \hbox (badness 3000) in paragraph at lines 7453--7455 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7478--7481 [][][]\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 , [117] [118] [119] [120] Underfull \hbox (badness 10000) in paragraph at lines 7733--7743 []\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing [121] [122] Underfull \hbox (badness 4479) in paragraph at lines 7804--7814 [][][]\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), [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] Underfull \hbox (badness 1394) in paragraph at lines 9477--9482 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [148] [149] [150] [151] [152] Underfull \hbox (badness 1194) in paragraph at lines 9822--9827 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 9822--9827 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . 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Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 12072--12081 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [187] [188] [189] [190] [191] Underfull \vbox (badness 3803) has occurred while \output is active [192] [193] [194] [195] [196] Underfull \hbox (badness 6236) in paragraph at lines 12731--12734 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [197] [198] [199] [200] [201] [202] Underfull \hbox (badness 2253) in paragraph at lines 13143--13145 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [203] Underfull \hbox (badness 1565) in paragraph at lines 13214--13218 [][][]\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 [204] Underfull \hbox (badness 10000) in paragraph at lines 13258--13260 []\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 [205] [206] Underfull \hbox (badness 1466) in paragraph at lines 13398--13401 []\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 [207] [208] Underfull \hbox (badness 10000) in paragraph at lines 13517--13521 [][][]\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 13528--13531 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [209] [210] [211] [212] Underfull \hbox (badness 3965) in paragraph at lines 13791--13795 []\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, [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] Underfull \hbox (badness 4429) in paragraph at lines 14553--14556 []\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 [225] [226] Underfull \hbox (badness 10000) in paragraph at lines 14653--14655 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14659--14663 []\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 10000) in paragraph at lines 14698--14702 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 14698--14702 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] Underfull \hbox (badness 2452) in paragraph at lines 15287--15291 []\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 15287--15291 \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 [237] [238] [239] Underfull \hbox (badness 1092) in paragraph at lines 15460--15465 [][]\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 [240] [241] [242] Underfull \hbox (badness 6741) in paragraph at lines 15708--15712 \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 , [243] [244] [245] [246] [247] Underfull \hbox (badness 1867) in paragraph at lines 16014--16021 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [248] [249] [250] [251] Underfull \vbox (badness 10000) has occurred while \output is active [252] [253] [254] Underfull \hbox (badness 3679) in paragraph at lines 16424--16426 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [255] [256] [257] [258] [259] [260] [261] [262] Underfull \hbox (badness 1478) in paragraph at lines 16979--16982 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [263] [264] [265] Underfull \hbox (badness 10000) in paragraph at lines 17232--17234 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] Underfull \hbox (badness 1442) in paragraph at lines 17822--17824 []\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 [276] Underfull \hbox (badness 2452) in paragraph at lines 17914--17930 [][][]\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 , [277] [278] [279] [280] [281] [282] [283] Underfull \hbox (badness 1248) in paragraph at lines 18328--18331 []\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 , [284] [285] [286] [287] Underfull \hbox (badness 4739) in paragraph at lines 18586--18588 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] Underfull \hbox (badness 2469) in paragraph at lines 19603--19608 []\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 19617--19624 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [305] Underfull \hbox (badness 10000) in paragraph at lines 19691--19695 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 19691--19695 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$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 ' [306] [307] Underfull \hbox (badness 1509) in paragraph at lines 19826--19833 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 19826--19833 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19842--19847 []\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 [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] Underfull \hbox (badness 1264) in paragraph at lines 20575--20580 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [319] Underfull \hbox (badness 4441) in paragraph at lines 20604--20607 []\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 , [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] Underfull \hbox (badness 10000) in paragraph at lines 21330--21332 []\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 [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] Underfull \hbox (badness 1077) in paragraph at lines 22365--22371 \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 . [347] [348] [349] Underfull \hbox (badness 1484) in paragraph at lines 22526--22534 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [350] [351] [352] [353] Underfull \hbox (badness 2790) in paragraph at lines 22797--22800 []\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 22797--22800 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [354] [355] [356] [357] Underfull \hbox (badness 1194) in paragraph at lines 23079--23082 []\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 [358] [359] [360] [361] Underfull \hbox (badness 10000) in paragraph at lines 23285--23291 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23285--23291 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23295--23298 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23295--23298 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] [373] [374] [375] Underfull \hbox (badness 10000) in paragraph at lines 24245--24247 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [376] [377] [378] [379] Underfull \hbox (badness 1199) in paragraph at lines 24489--24495 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24489--24495 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [380] [381] [382] [383] [384] [385] [386] [387] [388] Underfull \hbox (badness 1038) in paragraph at lines 25068--25076 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 1881) in paragraph at lines 25077--25080 []\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 25096--25098 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [389] Underfull \hbox (badness 10000) in paragraph at lines 25205--25215 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25216--25222 []\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 [390] Underfull \hbox (badness 1968) in paragraph at lines 25252--25257 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 25262--25264 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [391] [392] [393] Underfull \hbox (badness 10000) in paragraph at lines 25521--25527 []\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 25521--25527 \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 25521--25527 \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 25534--25537 []\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 25558--25560 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [394] Underfull \hbox (badness 10000) in paragraph at lines 25590--25595 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 25596--25607 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 25608--25611 []\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 3713) in paragraph at lines 25618--25630 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 25618--25630 \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). Underfull \hbox (badness 2351) in paragraph at lines 25618--25630 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25632--25639 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 25632--25639 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 25632--25639 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1874) in paragraph at lines 25632--25639 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [395] [396] [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 25979--25983 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 25979--25983 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [400] [401] [402] [403] [404] Underfull \hbox (badness 1735) in paragraph at lines 26297--26301 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] Underfull \hbox (badness 2726) in paragraph at lines 26868--26871 []\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 [415] [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] [427] Underfull \hbox (badness 1052) in paragraph at lines 27695--27700 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [428] [429] [430] [431] [432] Underfull \vbox (badness 10000) has occurred while \output is active [433] [434] [435] [436] [437] [438] [439] Underfull \hbox (badness 1533) in paragraph at lines 28504--28507 []\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 [440] [441] [442] Underfull \hbox (badness 1163) in paragraph at lines 28666--28677 []\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 [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] Underfull \hbox (badness 10000) in paragraph at lines 30189--30193 []\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 30189--30193 \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 30211--30213 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [467] [468] [469] [470] [471] [472] [473] [474] [475] Underfull \hbox (badness 1655) in paragraph at lines 30759--30761 []\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 [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] Underfull \hbox (badness 10000) in paragraph at lines 31434--31438 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [487] [488] [489] [490] Underfull \hbox (badness 2302) in paragraph at lines 31674--31681 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 31674--31681 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 3333) in paragraph at lines 31674--31681 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 31674--31681 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [491] [492] Underfull \hbox (badness 2261) in paragraph at lines 31830--31835 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if Underfull \hbox (badness 10000) in paragraph at lines 31857--31863 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [493] Underfull \hbox (badness 10000) in paragraph at lines 31933--31938 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] Underfull \vbox (badness 3803) has occurred while \output is active [533] [534] [535] [536] [537] [538] [539] [540] Underfull \hbox (badness 1072) in paragraph at lines 34971--34975 []\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 34976--34980 []\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 35004--35010 []\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 35004--35010 \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 35004--35010 \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 [541] Underfull \hbox (badness 3343) in paragraph at lines 35016--35023 \T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 35016--35023 \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 35016--35023 \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 [542] [543] [544] [545] Underfull \hbox (badness 10000) in paragraph at lines 35314--35320 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35314--35320 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] Underfull \hbox (badness 3333) in paragraph at lines 37158--37163 []\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 [576] [577] [578] [579] [580] [581] Underfull \vbox (badness 10000) has occurred while \output is active [582] [583] [584] [585] Underfull \hbox (badness 1472) in paragraph at lines 37781--37784 []\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 [586] [587] [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] Underfull \vbox (badness 3803) has occurred while \output is active [599] Underfull \hbox (badness 10000) in paragraph at lines 38646--38650 []\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., [600] [601] [602] [603] Underfull \hbox (badness 10000) in paragraph at lines 38894--38897 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [604] [605] Underfull \hbox (badness 10000) in paragraph at lines 39012--39016 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [606] Underfull \hbox (badness 10000) in paragraph at lines 39074--39078 [][][]\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 \ [][]$\T1/zi4/m/n/10 https : / / developer . [607] [608] [609] [610] [611] [612] [613] [614] Underfull \hbox (badness 4013) in paragraph at lines 39619--39621 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [615] [616] [617] [618] [619] [620] Underfull \vbox (badness 10000) has occurred while \output is active [621] [622] [623] [624] [625] [626] [627] Underfull \hbox (badness 3460) in paragraph at lines 40480--40483 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via [628] Underfull \hbox (badness 1990) in paragraph at lines 40487--40495 []\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 40487--40495 \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 [629] [630] [631] [632] Underfull \hbox (badness 10000) in paragraph at lines 40764--40767 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [633] [634] [635] Underfull \hbox (badness 1917) in paragraph at lines 40992--40999 []\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 [636] [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] Underfull \hbox (badness 3668) in paragraph at lines 41671--41673 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [647] Underfull \hbox (badness 2401) in paragraph at lines 41777--41781 []\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 [648] [649] [650] Underfull \hbox (badness 2111) in paragraph at lines 41953--41958 \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. [651] Underfull \hbox (badness 7362) in paragraph at lines 41969--41974 []\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 [652] [653] [654] [655] [656] [657] [658] [659] [660] Underfull \hbox (badness 5417) in paragraph at lines 42526--42530 []\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 [661] Underfull \hbox (badness 10000) in paragraph at lines 42587--42591 []\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 [662]) (./compiler-pkg.tex Chapter 2. [663] [664] [665] [666]) (./datasets-pkg.tex Chapter 3. [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] Underfull \vbox (badness 1515) has occurred while \output is active [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] Underfull \hbox (badness 6658) in paragraph at lines 3954--3956 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h ttp : / / www . ltrr . arizona . edu / ~hallman / [734] Underfull \vbox (badness 10000) has occurred while \output is active [735] [736] [737] [738] Underfull \vbox (badness 10000) has occurred while \output is active [739] [740] [741] [742] [743] [744] Overfull \vbox (18.9959pt too high) has occurred while \output is active [745] [746] [747]) (./grDevices-pkg.tex [748] Chapter 4. [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] Underfull \hbox (badness 5175) in paragraph at lines 1069--1071 []\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 [766] [767] [768] [769] Underfull \hbox (badness 1852) in paragraph at lines 1266--1269 []\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 [770] [771] [772] Underfull \hbox (badness 1490) in paragraph at lines 1472--1477 \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 [773] [774] Underfull \hbox (badness 10000) in paragraph at lines 1595--1599 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [775] [776] [777] [778] Underfull \hbox (badness 1325) in paragraph at lines 1878--1888 \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 , [779] [780] Underfull \hbox (badness 10000) in paragraph at lines 1983--1985 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [781] [782] [783] Underfull \hbox (badness 6758) in paragraph at lines 2144--2147 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [784] [785] [786] [787] [788] [789] [790] [791] [792] Underfull \hbox (badness 10000) in paragraph at lines 2737--2738 [793] [794] [795] [796] [797] [798] [799] [800] Underfull \hbox (badness 10000) in paragraph at lines 3235--3240 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [801] [802] [803] [804] Underfull \hbox (badness 3302) in paragraph at lines 3494--3497 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3508--3510 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] [816] [817] Underfull \hbox (badness 1067) in paragraph at lines 4331--4338 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [818] [819] Underfull \hbox (badness 3364) in paragraph at lines 4491--4493 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$ \T1/zi4/m/n/10 https : / / partners . adobe . com / public / [820] Underfull \hbox (badness 1789) in paragraph at lines 4568--4570 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [821] Underfull \hbox (badness 1377) in paragraph at lines 4618--4623 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [822] Underfull \hbox (badness 2671) in paragraph at lines 4645--4653 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4694--4701 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4702--4711 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4702--4711 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4712--4714 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [823] [824] Underfull \hbox (badness 1377) in paragraph at lines 4823--4828 []\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 [825] Underfull \hbox (badness 7344) in paragraph at lines 4883--4885 []\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 [826] [827] Underfull \hbox (badness 2035) in paragraph at lines 5007--5016 []\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 5007--5016 \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 5007--5016 \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 , [828] Underfull \hbox (badness 10000) in paragraph at lines 5075--5082 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5075--5082 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [829] [830] [831] Underfull \hbox (badness 1546) in paragraph at lines 5217--5225 []\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 , [832] Underfull \hbox (badness 1648) in paragraph at lines 5294--5298 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [833] [834] [835] [836] [837] [838] [839] Underfull \hbox (badness 10000) in paragraph at lines 5746--5749 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [840] [841] [842] [843] [844] [845] Underfull \hbox (badness 1189) in paragraph at lines 6143--6145 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [846] [847] Underfull \hbox (badness 10000) in paragraph at lines 6241--6243 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [848] [849] [850] [851] Underfull \hbox (badness 3780) in paragraph at lines 6532--6538 []\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 , [852] [853] [854] Underfull \hbox (badness 2680) in paragraph at lines 6733--6735 []\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 [855] [856] [857]) (./graphics-pkg.tex [858] Chapter 5. [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] [869] Underfull \hbox (badness 10000) in paragraph at lines 683--690 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [870] [871] [872] [873] Underfull \vbox (badness 3803) has occurred while \output is active [874] [875] [876] [877] [878] [879] Underfull \hbox (badness 4634) in paragraph at lines 1255--1258 [][][]\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 , [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] [894] [895] [896] Underfull \hbox (badness 1009) in paragraph at lines 2289--2296 \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 [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] Underfull \vbox (badness 10000) has occurred while \output is active [919] [920] [921] [922] Underfull \hbox (badness 1867) in paragraph at lines 3931--3935 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [923] [924] [925] [926] [927] [928] [929] [930] Underfull \hbox (badness 1924) in paragraph at lines 4378--4383 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain Underfull \hbox (badness 2529) in paragraph at lines 4409--4412 []\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 [931] [932] [933] [934] [935] Underfull \hbox (badness 10000) in paragraph at lines 4759--4765 []\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 4759--4765 \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 [936] [937] Underfull \hbox (badness 10000) in paragraph at lines 4890--4893 [938 >/library/graphics/help/figures/mai.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 4951--4953 Underfull \vbox (badness 10000) has occurred while \output is active [939] [940 >/library/graphics/help/figures/oma.pdf>] [941] Underfull \hbox (badness 10000) in paragraph at lines 5141--5143 []\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 [942] Underfull \vbox (badness 3803) has occurred while \output is active [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6612--6613 [][] [965] [966 >/library/graphics/help/figures/pch .pdf>] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] Underfull \hbox (badness 1048) in paragraph at lines 7321--7326 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [977] [978] Underfull \hbox (badness 1102) in paragraph at lines 7437--7440 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] Underfull \hbox (badness 1043) in paragraph at lines 8272--8276 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [993] [994] [995] [996] [997] [998] [999] Underfull \hbox (badness 10000) in paragraph at lines 8675--8677 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8677--8679 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1000]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8757 \HeaderA{units}{Graphical Units}{units} [1001] [1002] [1003] [1004]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1005] [1006] [1007] [1008] [1009] [1010] Underfull \hbox (badness 2680) in paragraph at lines 390--393 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] Underfull \hbox (badness 4279) in paragraph at lines 970--979 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] Underfull \vbox (badness 3803) has occurred while \output is active [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] Underfull \hbox (badness 1067) in paragraph at lines 4340--4343 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1078] [1079] [1080] [1081] Underfull \hbox (badness 7256) in paragraph at lines 4585--4587 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] Underfull \hbox (badness 10000) in paragraph at lines 5862--5868 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] Underfull \hbox (badness 7649) in paragraph at lines 6341--6344 []\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 [1112] [1113] [1114] [1115]) (./methods-pkg.tex [1116] Chapter 7. [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] Underfull \vbox (badness 3803) has occurred while \output is active [1125] Underfull \vbox (badness 10000) has occurred while \output is active [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] Underfull \hbox (badness 2237) in paragraph at lines 1386--1388 []\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 [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] Underfull \hbox (badness 1077) in paragraph at lines 1933--1940 []\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 [1144] Underfull \hbox (badness 10000) in paragraph at lines 1982--1987 []\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 1982--1987 \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 [1145] [1146] [1147] Underfull \hbox (badness 1242) in paragraph at lines 2215--2220 []\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 = [1148] [1149] [1150] [1151] [1152] Underfull \hbox (badness 10000) in paragraph at lines 2575--2578 []\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 [1153] [1154] Underfull \hbox (badness 1132) in paragraph at lines 2715--2719 []\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 [1155] Underfull \hbox (badness 1033) in paragraph at lines 2747--2752 \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 [1156] [1157] [1158] [1159] [1160] [1161] [1162] Underfull \hbox (badness 1102) in paragraph at lines 3304--3306 []\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 [1163] [1164] [1165] [1166] [1167] [1168] Underfull \hbox (badness 10000) in paragraph at lines 3637--3642 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Underfull \hbox (badness 10000) in paragraph at lines 3645--3654 []\T1/ptm/m/n/10 The [1169] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3765--3766 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3765--3766 [1170] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3849--3850 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] Underfull \hbox (badness 1436) in paragraph at lines 4446--4449 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4475--4481 []\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 4475--4481 \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 [1181] Underfull \hbox (badness 1092) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] Underfull \vbox (badness 10000) has occurred while \output is active [1191] [1192] Underfull \hbox (badness 10000) in paragraph at lines 5358--5359 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1193] Underfull \hbox (badness 4036) in paragraph at lines 5440--5443 []\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 [1194] Underfull \hbox (badness 3803) in paragraph at lines 5515--5517 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1195] [1196] [1197] [1198] Underfull \hbox (badness 1087) in paragraph at lines 5747--5752 []\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 [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] Underfull \hbox (badness 1675) in paragraph at lines 6454--6460 \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 [1207] [1208] [1209] [1210] Underfull \vbox (badness 10000) has occurred while \output is active [1211] [1212] [1213] [1214]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6976 \aliasA{S4}{S3Part}{S4} [1215] [1216] [1217]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7232 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7234 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7235 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7237 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7238 \aliasA{Summary}{S4groupGeneric}{Summary} [1218] Underfull \hbox (badness 2050) in paragraph at lines 7299--7303 []\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 [1219] [1220] [1221] Underfull \hbox (badness 1286) in paragraph at lines 7487--7489 []\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 [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] Underfull \vbox (badness 10000) has occurred while \output is active [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] Underfull \hbox (badness 1852) in paragraph at lines 10567--10571 []\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., [1264] [1265] [1266] [1267]) (./parallel-pkg.tex [1268] 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 [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] Underfull \hbox (badness 3386) in paragraph at lines 1268--1271 []\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 [1289] [1290] [1291]) (./splines-pkg.tex [1292] 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 [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] [1306] [1307]) (./stats-pkg.tex [1308] Chapter 10. [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] Underfull \hbox (badness 1412) in paragraph at lines 848--850 []\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 [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] Underfull \hbox (badness 2503) in paragraph at lines 1329--1332 []\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 , [1330] [1331] [1332] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 3965) in paragraph at lines 2168--2170 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1344] [1345] [1346] [1347] [1348] Underfull \hbox (badness 3965) in paragraph at lines 2510--2512 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] Underfull \hbox (badness 2726) in paragraph at lines 3224--3240 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1360] [1361] Underfull \hbox (badness 2503) in paragraph at lines 3354--3357 []\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 , [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] Underfull \hbox (badness 3989) in paragraph at lines 4582--4589 []\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 = [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] Underfull \hbox (badness 2556) in paragraph at lines 5193--5196 []\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 5210--5212 []\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 [1392] [1393] [1394] [1395] Underfull \hbox (badness 1142) in paragraph at lines 5451--5463 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1396] [1397] [1398] Underfull \hbox (badness 2503) in paragraph at lines 5599--5603 []\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 , [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] Underfull \hbox (badness 8132) in paragraph at lines 6102--6107 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1407] [1408] [1409] [1410] [1411] Underfull \hbox (badness 7081) in paragraph at lines 6380--6383 []\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 6384--6386 []\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 [1412] [1413] [1414] [1415] [1416] Underfull \vbox (badness 3803) has occurred while \output is active [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 10000) in paragraph at lines 7225--7228 []\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 [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] Underfull \hbox (badness 2626) in paragraph at lines 8860--8863 []\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 [1452] Underfull \hbox (badness 2503) in paragraph at lines 8960--8964 []\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 , [1453] [1454] [1455] [1456] [1457] [1458] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9309--9311 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] Underfull \hbox (badness 4518) in paragraph at lines 10235--10240 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1473] [1474] [1475] [1476] [1477] Underfull \hbox (badness 2142) in paragraph at lines 10577--10580 []\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 10596--10599 []\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, [1478] Underfull \hbox (badness 1708) in paragraph at lines 10658--10662 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1479] [1480] [1481] [1482] [1483] [1484] Underfull \hbox (badness 1694) in paragraph at lines 11054--11057 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1485] Underfull \hbox (badness 1867) in paragraph at lines 11073--11082 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1486] [1487] [1488] [1489] [1490] Underfull \hbox (badness 10000) in paragraph at lines 11380--11383 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1491] [1492]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.hat}) has been already used, duplicate ignored \relax l.11534 \aliasA{hat}{influence.measures}{hat} [1493] [1494] Underfull \hbox (badness 1484) in paragraph at lines 11665--11667 []\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 [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] Underfull \hbox (badness 4441) in paragraph at lines 12248--12250 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12255--12257 []\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 [1505] [1506] [1507] [1508] [1509] [1510] Underfull \hbox (badness 2894) in paragraph at lines 12589--12593 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] Underfull \hbox (badness 4518) in paragraph at lines 13287--13292 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] Underfull \hbox (badness 4518) in paragraph at lines 13934--13939 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1532] [1533] [1534] Underfull \hbox (badness 10000) in paragraph at lines 14072--14076 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14079--14081 []\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 [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] Underfull \hbox (badness 2503) in paragraph at lines 15141--15145 []\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 , [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] Underfull \hbox (badness 1584) in paragraph at lines 15653--15659 []\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 [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] Underfull \hbox (badness 2359) in paragraph at lines 17290--17292 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1587] Underfull \vbox (badness 3803) has occurred while \output is active [1588] Underfull \vbox (badness 10000) has occurred while \output is active [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] Underfull \hbox (badness 1377) in paragraph at lines 18201--18206 []\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 18206--18209 []\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 [1602] Underfull \hbox (badness 1454) in paragraph at lines 18219--18223 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18227--18231 []\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 [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] Underfull \hbox (badness 1337) in paragraph at lines 18843--18846 []\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 [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] Underfull \hbox (badness 3049) in paragraph at lines 19329--19333 []\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 [1622] [1623] [1624] [1625] Underfull \hbox (badness 5563) in paragraph at lines 19579--19581 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19582--19585 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1626] [1627] [1628] [1629] [1630] [1631] Underfull \hbox (badness 2503) in paragraph at lines 19957--19960 []\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 , [1632] Underfull \hbox (badness 10000) in paragraph at lines 19984--19986 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648] [1649] [1650] Underfull \hbox (badness 10000) in paragraph at lines 21047--21053 []\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 , [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] Underfull \hbox (badness 1337) in paragraph at lines 22385--22391 []\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 [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] Overfull \hbox (27.74408pt too wide) in paragraph at lines 22930--22930 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1681] [1682] [1683] [1684] [1685] Underfull \hbox (badness 10000) in paragraph at lines 23180--23183 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1686] [1687] [1688] [1689] [1690] [1691] [1692] [1693] [1694] Underfull \hbox (badness 10000) in paragraph at lines 23765--23768 []\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 [1695] Underfull \hbox (badness 3690) in paragraph at lines 23816--23820 [][][]\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 [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] Underfull \hbox (badness 3439) in paragraph at lines 24286--24292 [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1 0 , [1705] [1706] [1707] Underfull \hbox (badness 1867) in paragraph at lines 24483--24485 []\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 24496--24500 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 24496--24500 \T1/zi4/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was Underfull \hbox (badness 1132) in paragraph at lines 24496--24500 \T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o f un-de-ter-mined co-ef-fi-cients, e.g., for [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] Underfull \hbox (badness 10000) in paragraph at lines 24968--24973 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732] Underfull \hbox (badness 3514) in paragraph at lines 26010--26015 []\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 [1733] Underfull \hbox (badness 3514) in paragraph at lines 26072--26077 []\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 [1734] Underfull \hbox (badness 3514) in paragraph at lines 26129--26134 []\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 [1735] Underfull \hbox (badness 3514) in paragraph at lines 26190--26196 []\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 [1736] [1737] [1738] [1739] Underfull \hbox (badness 3514) in paragraph at lines 26403--26408 []\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 [1740] Underfull \hbox (badness 3514) in paragraph at lines 26459--26464 []\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 [1741] Underfull \hbox (badness 3514) in paragraph at lines 26517--26522 []\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 [1742] Underfull \hbox (badness 3514) in paragraph at lines 26572--26577 []\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 [1743] Underfull \hbox (badness 6691) in paragraph at lines 26641--26646 []\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 [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751] [1752] Underfull \hbox (badness 10000) in paragraph at lines 27165--27168 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27165--27168 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] Underfull \hbox (badness 5431) in paragraph at lines 27771--27773 []\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 [1763] [1764] [1765] Underfull \hbox (badness 5431) in paragraph at lines 27981--27984 []\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 [1766] [1767] [1768] [1769] [1770] [1771] Underfull \hbox (badness 1337) in paragraph at lines 28295--28299 []\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 [1772] [1773] Underfull \hbox (badness 10000) in paragraph at lines 28412--28415 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1774] [1775] Underfull \hbox (badness 1616) in paragraph at lines 28595--28598 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1776] [1777] [1778] [1779] [1780] [1781] [1782] [1783] [1784] [1785] [1786] [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] Underfull \hbox (badness 10000) in paragraph at lines 29721--29725 []\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 [1795] [1796] [1797] Underfull \vbox (badness 10000) has occurred while \output is active [1798] [1799] [1800] Underfull \hbox (badness 1337) in paragraph at lines 30085--30089 []\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 [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] Underfull \hbox (badness 1337) in paragraph at lines 30569--30573 []\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 [1809] Underfull \hbox (badness 2142) in paragraph at lines 30646--30651 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the [1810] Underfull \hbox (badness 5161) in paragraph at lines 30668--30670 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1811] [1812] [1813] [1814] [1815] [1816] Underfull \hbox (badness 10000) in paragraph at lines 31050--31055 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1817] [1818]) (./stats4-pkg.tex Chapter 11. [1819] [1820] [1821] [1822] [1823] [1824]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} [1825] [1826] [1827] [1828]) (./tcltk-pkg.tex Chapter 12. [1829] [1830] [1831] [1832] [1833] [1834] [1835] Underfull \vbox (badness 10000) has occurred while \output is active [1836] Underfull \vbox (badness 10000) has occurred while \output is active [1837] 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 [1838] [1839] [1840] [1841] [1842] [1843] [1844] [1845] [1846] [1847] [1848] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1849]) (./tools-pkg.tex [1850] Chapter 13. [1851] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1852] 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 [1853] [1854] 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 [1855] [1856] 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 [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] Underfull \hbox (badness 1635) in paragraph at lines 1054--1056 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1868] Underfull \hbox (badness 4441) in paragraph at lines 1132--1142 \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- [1869] Underfull \hbox (badness 1014) in paragraph at lines 1154--1156 []\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 1160--1162 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1197--1200 []\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 1197--1200 \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 , [1870] [1871] [1872] Underfull \hbox (badness 10000) in paragraph at lines 1366--1368 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1873] [1874] [1875] Underfull \hbox (badness 2293) in paragraph at lines 1540--1542 []\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 [1876] [1877] Underfull \hbox (badness 7981) in paragraph at lines 1678--1683 []\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 1685--1687 []\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 [1878] [1879] [1880] [1881]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1882 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1882] [1883] [1884] [1885] [1886] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2184--2184 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1887] [1888] [1889] Underfull \hbox (badness 7981) in paragraph at lines 2353--2359 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1890] [1891] [1892] [1893] [1894] [1895] [1896] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2818. [1897] [1898] [1899] [1900] Underfull \hbox (badness 1424) in paragraph at lines 3100--3102 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1901] [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] [1910] [1911] [1912] Underfull \hbox (badness 10000) in paragraph at lines 3800--3802 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1913] [1914] Underfull \hbox (badness 10000) in paragraph at lines 3939--3942 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1915] [1916] Underfull \hbox (badness 1137) in paragraph at lines 4037--4039 []\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 [1917] [1918] [1919] Underfull \hbox (badness 1838) in paragraph at lines 4246--4252 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4246--4252 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1920] Underfull \hbox (badness 5726) in paragraph at lines 4326--4331 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4326--4331 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1921] [1922] [1923] Underfull \hbox (badness 2197) in paragraph at lines 4475--4485 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4475--4485 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1924] Underfull \hbox (badness 1571) in paragraph at lines 4538--4542 []\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 [1925] [1926] [1927]) (./utils-pkg.tex [1928] Chapter 14. [1929] Underfull \hbox (badness 2556) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1930] [1931] [1932] [1933] [1934] [1935] [1936] Underfull \hbox (badness 10000) in paragraph at lines 546--552 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 546--552 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1937] [1938] Underfull \hbox (badness 5847) in paragraph at lines 660--666 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 660--666 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1939] Underfull \hbox (badness 3861) in paragraph at lines 728--733 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1940] [1941] [1942] Underfull \hbox (badness 1430) in paragraph at lines 893--900 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 893--900 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 893--900 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 893--900 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 904--906 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1943] [1944] [1945] [1946] [1947] [1948] [1949] Underfull \hbox (badness 1371) in paragraph at lines 1375--1377 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 2057) in paragraph at lines 1863--1865 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1958] Underfull \hbox (badness 10000) in paragraph at lines 1958--1960 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1959] [1960] Underfull \hbox (badness 5189) in paragraph at lines 2060--2062 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1961] Underfull \vbox (badness 3803) has occurred while \output is active [1962] [1963] [1964] Underfull \hbox (badness 1661) in paragraph at lines 2278--2285 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2294--2297 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1965] [1966] [1967] [1968] [1969] [1970] Underfull \hbox (badness 10000) in paragraph at lines 2703--2707 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2708--2711 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1971] [1972] [1973] [1974] [1975] [1976] [1977] [1978] [1979] [1980] [1981] Underfull \hbox (badness 1430) in paragraph at lines 3385--3393 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 1231) in paragraph at lines 3434--3440 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1982] [1983] [1984] [1985] [1986] [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4274 ...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.4274 ...mat Unordered and Ordered Lists}{format} [1996] [1997] [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] Underfull \hbox (badness 1371) in paragraph at lines 5271--5273 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [2012] Underfull \hbox (badness 1502) in paragraph at lines 5360--5365 []\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 5360--5365 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2013] [2014] [2015] Underfull \hbox (badness 10000) in paragraph at lines 5533--5542 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2016] Underfull \hbox (badness 2150) in paragraph at lines 5596--5599 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2017] [2018] Underfull \hbox (badness 3118) in paragraph at lines 5733--5735 []\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 Underfull \hbox (badness 2409) in paragraph at lines 5766--5770 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [2019] [2020] Underfull \hbox (badness 1325) in paragraph at lines 5874--5878 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [2021] Underfull \hbox (badness 10000) in paragraph at lines 5957--5960 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 5957--5960 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2022] Underfull \hbox (badness 3219) in paragraph at lines 6030--6037 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6030--6037 \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 6030--6037 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [2023] Underfull \hbox (badness 10000) in paragraph at lines 6110--6115 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] [2047] Underfull \hbox (badness 10000) in paragraph at lines 7527--7529 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7532--7537 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] Underfull \hbox (badness 1789) in paragraph at lines 8087--8089 []\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 [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] Underfull \hbox (badness 1097) in paragraph at lines 8916--8919 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2069] Underfull \hbox (badness 3000) in paragraph at lines 9052--9057 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] Underfull \hbox (badness 2134) in paragraph at lines 9635--9640 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2079] [2080] [2081] [2082] [2083] [2084] [2085] Underfull \hbox (badness 5077) in paragraph at lines 10060--10064 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10060--10064 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 10072--10076 []\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 10072--10076 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2086] [2087] [2088] [2089] [2090] Overfull \hbox (18.77168pt too wide) in paragraph at lines 10366--10366 []\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 '[] [2091] Underfull \hbox (badness 10000) in paragraph at lines 10429--10431 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][] []\T1/ptm/m/n/10 s are nicely viewed via [2092] [2093] [2094] Underfull \hbox (badness 2150) in paragraph at lines 10605--10607 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2095] [2096] [2097] [2098] Underfull \hbox (badness 10000) in paragraph at lines 10824--10828 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 10855--10861 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2099] [2100] Underfull \hbox (badness 2096) in paragraph at lines 10973--10976 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. 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If [2102] [2103] [2104] [2105] [2106] Underfull \hbox (badness 3780) in paragraph at lines 11355--11359 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 11374--11377 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2107] [2108] [2109] [2110] [2111] [2112] Underfull \hbox (badness 2818) in paragraph at lines 11746--11751 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 11755--11758 []\T1/ptm/m/n/10 the page width to be used. 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LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.write.matrix} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.survreg} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.coxph} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.stepAIC} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.rinvGauss} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.gamma.shape} has been referenced but does not e xist, replaced by a fixed one pdfTeX 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Transcript written on refman.log. This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning input file refman.idx.................done (13388 entries accepted, 34 rejected). Sorting entries.............................................................................................................................................done (205988 comparisons). Generating output file refman.ind................done (13230 lines written, 51 warnings). Output written in refman.ind. Transcript written in refman.ilg. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 3 language(s) loaded. 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[1] [2] Underfull \hbox (badness 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 296--300 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 385--388 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 533--539 []\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 1144--1147 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1901--1901 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2086--2088 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] Underfull \vbox (badness 10000) has occurred while \output is active [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3607--3609 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] [60] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3848--3848 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] Underfull \hbox (badness 2521) in paragraph at lines 4823--4825 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] Overfull \hbox (5.27168pt too wide) in paragraph at lines 5954--5954 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [94] [95] [96] Underfull \hbox (badness 2096) in paragraph at lines 6137--6150 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [97] [98] [99] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6341--6343 []\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 : [100] [101] Underfull \hbox (badness 10000) in paragraph at lines 6483--6486 []\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 [102] [103] Underfull \hbox (badness 1442) in paragraph at lines 6646--6652 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6646--6652 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6646--6652 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [104] Underfull \hbox (badness 3568) in paragraph at lines 6708--6715 \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 [105] [106] Underfull \vbox (badness 10000) has occurred while \output is active [107] [108] [109] Underfull \hbox (badness 1077) in paragraph at lines 7019--7025 []\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 7019--7025 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [110] [111] [112] [113] [114] Underfull \hbox (badness 2096) in paragraph at lines 7360--7364 \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 . [115] [116] Underfull \hbox (badness 3000) in paragraph at lines 7453--7455 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7478--7481 [][][]\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 , [117] [118] [119] [120] Underfull \hbox (badness 10000) in paragraph at lines 7733--7743 []\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing [121] [122] Underfull \hbox (badness 4479) in paragraph at lines 7804--7814 [][][]\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), [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] Underfull \hbox (badness 1394) in paragraph at lines 9477--9482 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [148] [149] [150] [151] [152] Underfull \hbox (badness 1194) in paragraph at lines 9822--9827 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 9822--9827 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [153] [154] Underfull \hbox (badness 1735) in paragraph at lines 9960--9964 \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 . [155] [156] [157] [158] [159] [160] [161] Underfull \hbox (badness 2150) in paragraph at lines 10375--10378 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 6396) in paragraph at lines 10389--10397 []\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 2735) in paragraph at lines 10429--10436 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] Underfull \hbox (badness 4569) in paragraph at lines 11495--11499 []\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 11495--11499 \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 [178] [179] [180] [181] [182] [183] [184] [185] [186] Underfull \hbox (badness 2698) in paragraph at lines 12072--12081 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 12072--12081 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [187] [188] [189] [190] [191] Underfull \vbox (badness 3803) has occurred while \output is active [192] [193] [194] [195] [196] Underfull \hbox (badness 6236) in paragraph at lines 12731--12734 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [197] [198] [199] [200] [201] [202] Underfull \hbox (badness 2253) in paragraph at lines 13143--13145 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [203] Underfull \hbox (badness 1565) in paragraph at lines 13214--13218 [][][]\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 [204] Underfull \hbox (badness 10000) in paragraph at lines 13258--13260 []\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 [205] [206] Underfull \hbox (badness 1466) in paragraph at lines 13398--13401 []\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 [207] [208] Underfull \hbox (badness 10000) in paragraph at lines 13517--13521 [][][]\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 13528--13531 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [209] [210] [211] [212] Underfull \hbox (badness 3965) in paragraph at lines 13791--13795 []\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, [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] Underfull \hbox (badness 4429) in paragraph at lines 14553--14556 []\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 [225] [226] Underfull \hbox (badness 10000) in paragraph at lines 14653--14655 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14659--14663 []\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 10000) in paragraph at lines 14698--14702 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 14698--14702 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] Underfull \hbox (badness 2452) in paragraph at lines 15287--15291 []\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 15287--15291 \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 [237] [238] [239] Underfull \hbox (badness 1092) in paragraph at lines 15460--15465 [][]\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 [240] [241] [242] Underfull \hbox (badness 6741) in paragraph at lines 15708--15712 \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 , [243] [244] [245] [246] [247] Underfull \hbox (badness 1867) in paragraph at lines 16014--16021 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [248] [249] [250] [251] Underfull \vbox (badness 10000) has occurred while \output is active [252] [253] [254] Underfull \hbox (badness 3679) in paragraph at lines 16424--16426 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [255] [256] [257] [258] [259] [260] [261] [262] Underfull \hbox (badness 1478) in paragraph at lines 16979--16982 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [263] [264] [265] Underfull \hbox (badness 10000) in paragraph at lines 17232--17234 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] Underfull \hbox (badness 1442) in paragraph at lines 17822--17824 []\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 [276] Underfull \hbox (badness 2452) in paragraph at lines 17914--17930 [][][]\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 , [277] [278] [279] [280] [281] [282] [283] Underfull \hbox (badness 1248) in paragraph at lines 18328--18331 []\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 , [284] [285] [286] [287] Underfull \hbox (badness 4739) in paragraph at lines 18586--18588 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] Underfull \hbox (badness 2469) in paragraph at lines 19603--19608 []\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 19617--19624 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [305] Underfull \hbox (badness 10000) in paragraph at lines 19691--19695 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 19691--19695 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$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 ' [306] [307] Underfull \hbox (badness 1509) in paragraph at lines 19826--19833 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 19826--19833 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19842--19847 []\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 [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] Underfull \hbox (badness 1264) in paragraph at lines 20575--20580 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [319] Underfull \hbox (badness 4441) in paragraph at lines 20604--20607 []\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 , [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] Underfull \hbox (badness 10000) in paragraph at lines 21330--21332 []\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 [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] Underfull \hbox (badness 1077) in paragraph at lines 22365--22371 \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 . [347] [348] [349] Underfull \hbox (badness 1484) in paragraph at lines 22526--22534 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [350] [351] [352] [353] Underfull \hbox (badness 2790) in paragraph at lines 22797--22800 []\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 22797--22800 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [354] [355] [356] [357] Underfull \hbox (badness 1194) in paragraph at lines 23079--23082 []\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 [358] [359] [360] [361] Underfull \hbox (badness 10000) in paragraph at lines 23285--23291 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23285--23291 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23295--23298 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23295--23298 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] [373] [374] [375] Underfull \hbox (badness 10000) in paragraph at lines 24245--24247 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [376] [377] [378] [379] Underfull \hbox (badness 1199) in paragraph at lines 24489--24495 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24489--24495 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [380] [381] [382] [383] [384] [385] [386] [387] [388] Underfull \hbox (badness 1038) in paragraph at lines 25068--25076 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 1881) in paragraph at lines 25077--25080 []\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 25096--25098 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [389] Underfull \hbox (badness 10000) in paragraph at lines 25205--25215 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25216--25222 []\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 [390] Underfull \hbox (badness 1968) in paragraph at lines 25252--25257 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 25262--25264 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [391] [392] [393] Underfull \hbox (badness 10000) in paragraph at lines 25521--25527 []\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 25521--25527 \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 25521--25527 \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 25534--25537 []\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 25558--25560 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [394] Underfull \hbox (badness 10000) in paragraph at lines 25590--25595 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 25596--25607 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 25608--25611 []\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 3713) in paragraph at lines 25618--25630 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 25618--25630 \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). Underfull \hbox (badness 2351) in paragraph at lines 25618--25630 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25632--25639 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 25632--25639 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 25632--25639 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1874) in paragraph at lines 25632--25639 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [395] [396] [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 25979--25983 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 25979--25983 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [400] [401] [402] [403] [404] Underfull \hbox (badness 1735) in paragraph at lines 26297--26301 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] Underfull \hbox (badness 2726) in paragraph at lines 26868--26871 []\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 [415] [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] [427] Underfull \hbox (badness 1052) in paragraph at lines 27695--27700 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [428] [429] [430] [431] [432] Underfull \vbox (badness 10000) has occurred while \output is active [433] [434] [435] [436] [437] [438] [439] Underfull \hbox (badness 1533) in paragraph at lines 28504--28507 []\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 [440] [441] [442] Underfull \hbox (badness 1163) in paragraph at lines 28666--28677 []\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 [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] Underfull \hbox (badness 10000) in paragraph at lines 30189--30193 []\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 30189--30193 \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 30211--30213 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [467] [468] [469] [470] [471] [472] [473] [474] [475] Underfull \hbox (badness 1655) in paragraph at lines 30759--30761 []\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 [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] Underfull \hbox (badness 10000) in paragraph at lines 31434--31438 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [487] [488] [489] [490] Underfull \hbox (badness 2302) in paragraph at lines 31674--31681 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 31674--31681 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 3333) in paragraph at lines 31674--31681 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 31674--31681 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [491] [492] Underfull \hbox (badness 2261) in paragraph at lines 31830--31835 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if Underfull \hbox (badness 10000) in paragraph at lines 31857--31863 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [493] Underfull \hbox (badness 10000) in paragraph at lines 31933--31938 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] Underfull \vbox (badness 3803) has occurred while \output is active [533] [534] [535] [536] [537] [538] [539] [540] Underfull \hbox (badness 1072) in paragraph at lines 34971--34975 []\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 34976--34980 []\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 35004--35010 []\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 35004--35010 \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 35004--35010 \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 [541] Underfull \hbox (badness 3343) in paragraph at lines 35016--35023 \T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 35016--35023 \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 35016--35023 \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 [542] [543] [544] [545] Underfull \hbox (badness 10000) in paragraph at lines 35314--35320 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35314--35320 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] Underfull \hbox (badness 3333) in paragraph at lines 37158--37163 []\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 [576] [577] [578] [579] [580] [581] Underfull \vbox (badness 10000) has occurred while \output is active [582] [583] [584] [585] Underfull \hbox (badness 1472) in paragraph at lines 37781--37784 []\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 [586] [587] [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] Underfull \vbox (badness 3803) has occurred while \output is active [599] Underfull \hbox (badness 10000) in paragraph at lines 38646--38650 []\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., [600] [601] [602] [603] Underfull \hbox (badness 10000) in paragraph at lines 38894--38897 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [604] [605] Underfull \hbox (badness 10000) in paragraph at lines 39012--39016 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [606] Underfull \hbox (badness 10000) in paragraph at lines 39074--39078 [][][]\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 \ [][]$\T1/zi4/m/n/10 https : / / developer . [607] [608] [609] [610] [611] [612] [613] [614] Underfull \hbox (badness 4013) in paragraph at lines 39619--39621 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [615] [616] [617] [618] [619] [620] Underfull \vbox (badness 10000) has occurred while \output is active [621] [622] [623] [624] [625] [626] [627] Underfull \hbox (badness 3460) in paragraph at lines 40480--40483 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via [628] Underfull \hbox (badness 1990) in paragraph at lines 40487--40495 []\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 40487--40495 \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 [629] [630] [631] [632] Underfull \hbox (badness 10000) in paragraph at lines 40764--40767 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [633] [634] [635] Underfull \hbox (badness 1917) in paragraph at lines 40992--40999 []\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 [636] [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] Underfull \hbox (badness 3668) in paragraph at lines 41671--41673 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [647] Underfull \hbox (badness 2401) in paragraph at lines 41777--41781 []\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 [648] [649] [650] Underfull \hbox (badness 2111) in paragraph at lines 41953--41958 \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. [651] Underfull \hbox (badness 7362) in paragraph at lines 41969--41974 []\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 [652] [653] [654] [655] [656] [657] [658] [659] [660] Underfull \hbox (badness 5417) in paragraph at lines 42526--42530 []\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 [661] Underfull \hbox (badness 10000) in paragraph at lines 42587--42591 []\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 [662]) (./compiler-pkg.tex Chapter 2. [663] [664] [665] [666]) (./datasets-pkg.tex Chapter 3. [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] Underfull \vbox (badness 1515) has occurred while \output is active [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] Underfull \hbox (badness 6658) in paragraph at lines 3954--3956 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h ttp : / / www . ltrr . arizona . edu / ~hallman / [734] Underfull \vbox (badness 10000) has occurred while \output is active [735] [736] [737] [738] Underfull \vbox (badness 10000) has occurred while \output is active [739] [740] [741] [742] [743] [744] Overfull \vbox (18.9959pt too high) has occurred while \output is active [745] [746] [747]) (./grDevices-pkg.tex [748] Chapter 4. [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] Underfull \hbox (badness 5175) in paragraph at lines 1069--1071 []\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 [766] [767] [768] [769] Underfull \hbox (badness 1852) in paragraph at lines 1266--1269 []\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 [770] [771] [772] Underfull \hbox (badness 1490) in paragraph at lines 1472--1477 \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 [773] [774] Underfull \hbox (badness 10000) in paragraph at lines 1595--1599 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [775] [776] [777] [778] Underfull \hbox (badness 1325) in paragraph at lines 1878--1888 \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 , [779] [780] Underfull \hbox (badness 10000) in paragraph at lines 1983--1985 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [781] [782] [783] Underfull \hbox (badness 6758) in paragraph at lines 2144--2147 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [784] [785] [786] [787] [788] [789] [790] [791] [792] Underfull \hbox (badness 10000) in paragraph at lines 2737--2738 [793] [794] [795] [796] [797] [798] [799] [800] Underfull \hbox (badness 10000) in paragraph at lines 3235--3240 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [801] [802] [803] [804] Underfull \hbox (badness 3302) in paragraph at lines 3494--3497 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3508--3510 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] [816] [817] Underfull \hbox (badness 1067) in paragraph at lines 4331--4338 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [818] [819] Underfull \hbox (badness 3364) in paragraph at lines 4491--4493 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$ \T1/zi4/m/n/10 https : / / partners . adobe . com / public / [820] Underfull \hbox (badness 1789) in paragraph at lines 4568--4570 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [821] Underfull \hbox (badness 1377) in paragraph at lines 4618--4623 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [822] Underfull \hbox (badness 2671) in paragraph at lines 4645--4653 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4694--4701 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4702--4711 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4702--4711 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4712--4714 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [823] [824] Underfull \hbox (badness 1377) in paragraph at lines 4823--4828 []\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 [825] Underfull \hbox (badness 7344) in paragraph at lines 4883--4885 []\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 [826] [827] Underfull \hbox (badness 2035) in paragraph at lines 5007--5016 []\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 5007--5016 \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 5007--5016 \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 , [828] Underfull \hbox (badness 10000) in paragraph at lines 5075--5082 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5075--5082 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [829] [830] [831] Underfull \hbox (badness 1546) in paragraph at lines 5217--5225 []\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 , [832] Underfull \hbox (badness 1648) in paragraph at lines 5294--5298 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [833] [834] [835] [836] [837] [838] [839] Underfull \hbox (badness 10000) in paragraph at lines 5746--5749 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [840] [841] [842] [843] [844] [845] Underfull \hbox (badness 1189) in paragraph at lines 6143--6145 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [846] [847] Underfull \hbox (badness 10000) in paragraph at lines 6241--6243 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [848] [849] [850] [851] Underfull \hbox (badness 3780) in paragraph at lines 6532--6538 []\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 , [852] [853] [854] Underfull \hbox (badness 2680) in paragraph at lines 6733--6735 []\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 [855] [856] [857]) (./graphics-pkg.tex [858] Chapter 5. [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] [869] Underfull \hbox (badness 10000) in paragraph at lines 683--690 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [870] [871] [872] [873] Underfull \vbox (badness 3803) has occurred while \output is active [874] [875] [876] [877] [878] [879] Underfull \hbox (badness 4634) in paragraph at lines 1255--1258 [][][]\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 , [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] [894] [895] [896] Underfull \hbox (badness 1009) in paragraph at lines 2289--2296 \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 [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] Underfull \vbox (badness 10000) has occurred while \output is active [919] [920] [921] [922] Underfull \hbox (badness 1867) in paragraph at lines 3931--3935 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [923] [924] [925] [926] [927] [928] [929] [930] Underfull \hbox (badness 1924) in paragraph at lines 4378--4383 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain Underfull \hbox (badness 2529) in paragraph at lines 4409--4412 []\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 [931] [932] [933] [934] [935] Underfull \hbox (badness 10000) in paragraph at lines 4759--4765 []\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 4759--4765 \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 [936] [937] Underfull \hbox (badness 10000) in paragraph at lines 4890--4893 [938 >/library/graphics/help/figures/mai.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 4951--4953 Underfull \vbox (badness 10000) has occurred while \output is active [939] [940 >/library/graphics/help/figures/oma.pdf>] [941] Underfull \hbox (badness 10000) in paragraph at lines 5141--5143 []\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 [942] Underfull \vbox (badness 3803) has occurred while \output is active [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6612--6613 [][] [965] [966 >/library/graphics/help/figures/pch .pdf>] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] Underfull \hbox (badness 1048) in paragraph at lines 7321--7326 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [977] [978] Underfull \hbox (badness 1102) in paragraph at lines 7437--7440 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] Underfull \hbox (badness 1043) in paragraph at lines 8272--8276 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [993] [994] [995] [996] [997] [998] [999] Underfull \hbox (badness 10000) in paragraph at lines 8675--8677 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8677--8679 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1000]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8757 \HeaderA{units}{Graphical Units}{units} [1001] [1002] [1003] [1004]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1005] [1006] [1007] [1008] [1009] [1010] Underfull \hbox (badness 2680) in paragraph at lines 390--393 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] Underfull \hbox (badness 4279) in paragraph at lines 970--979 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] Underfull \vbox (badness 3803) has occurred while \output is active [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] Underfull \hbox (badness 1067) in paragraph at lines 4340--4343 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1078] [1079] [1080] [1081] Underfull \hbox (badness 7256) in paragraph at lines 4585--4587 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] Underfull \hbox (badness 10000) in paragraph at lines 5862--5868 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] Underfull \hbox (badness 7649) in paragraph at lines 6341--6344 []\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 [1112] [1113] [1114] [1115]) (./methods-pkg.tex [1116] Chapter 7. [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] Underfull \vbox (badness 3803) has occurred while \output is active [1125] Underfull \vbox (badness 10000) has occurred while \output is active [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] Underfull \hbox (badness 2237) in paragraph at lines 1386--1388 []\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 [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] Underfull \hbox (badness 1077) in paragraph at lines 1933--1940 []\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 [1144] Underfull \hbox (badness 10000) in paragraph at lines 1982--1987 []\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 1982--1987 \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 [1145] [1146] [1147] Underfull \hbox (badness 1242) in paragraph at lines 2215--2220 []\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 = [1148] [1149] [1150] [1151] [1152] Underfull \hbox (badness 10000) in paragraph at lines 2575--2578 []\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 [1153] [1154] Underfull \hbox (badness 1132) in paragraph at lines 2715--2719 []\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 [1155] Underfull \hbox (badness 1033) in paragraph at lines 2747--2752 \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 [1156] [1157] [1158] [1159] [1160] [1161] [1162] Underfull \hbox (badness 1102) in paragraph at lines 3304--3306 []\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 [1163] [1164] [1165] [1166] [1167] [1168] Underfull \hbox (badness 10000) in paragraph at lines 3637--3642 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Underfull \hbox (badness 10000) in paragraph at lines 3645--3654 []\T1/ptm/m/n/10 The [1169] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3765--3766 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3765--3766 [1170] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3849--3850 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] Underfull \hbox (badness 1436) in paragraph at lines 4446--4449 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4475--4481 []\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 4475--4481 \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 [1181] Underfull \hbox (badness 1092) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] Underfull \vbox (badness 10000) has occurred while \output is active [1191] [1192] Underfull \hbox (badness 10000) in paragraph at lines 5358--5359 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1193] Underfull \hbox (badness 4036) in paragraph at lines 5440--5443 []\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 [1194] Underfull \hbox (badness 3803) in paragraph at lines 5515--5517 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1195] [1196] [1197] [1198] Underfull \hbox (badness 1087) in paragraph at lines 5747--5752 []\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 [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] Underfull \hbox (badness 1675) in paragraph at lines 6454--6460 \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 [1207] [1208] [1209] [1210] Underfull \vbox (badness 10000) has occurred while \output is active [1211] [1212] [1213] [1214]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6976 \aliasA{S4}{S3Part}{S4} [1215] [1216] [1217]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7232 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7234 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7235 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7237 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7238 \aliasA{Summary}{S4groupGeneric}{Summary} [1218] Underfull \hbox (badness 2050) in paragraph at lines 7299--7303 []\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 [1219] [1220] [1221] Underfull \hbox (badness 1286) in paragraph at lines 7487--7489 []\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 [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] Underfull \vbox (badness 10000) has occurred while \output is active [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] Underfull \hbox (badness 1852) in paragraph at lines 10567--10571 []\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., [1264] [1265] [1266] [1267]) (./parallel-pkg.tex [1268] 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 [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] Underfull \hbox (badness 3386) in paragraph at lines 1268--1271 []\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 [1289] [1290] [1291]) (./splines-pkg.tex [1292] 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 [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] [1306] [1307]) (./stats-pkg.tex [1308] Chapter 10. [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] Underfull \hbox (badness 1412) in paragraph at lines 848--850 []\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 [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] Underfull \hbox (badness 2503) in paragraph at lines 1329--1332 []\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 , [1330] [1331] [1332] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 3965) in paragraph at lines 2168--2170 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1344] [1345] [1346] [1347] [1348] Underfull \hbox (badness 3965) in paragraph at lines 2510--2512 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] Underfull \hbox (badness 2726) in paragraph at lines 3224--3240 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1360] [1361] Underfull \hbox (badness 2503) in paragraph at lines 3354--3357 []\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 , [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] Underfull \hbox (badness 3989) in paragraph at lines 4582--4589 []\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 = [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] Underfull \hbox (badness 2556) in paragraph at lines 5193--5196 []\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 5210--5212 []\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 [1392] [1393] [1394] [1395] Underfull \hbox (badness 1142) in paragraph at lines 5451--5463 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1396] [1397] [1398] Underfull \hbox (badness 2503) in paragraph at lines 5599--5603 []\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 , [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] Underfull \hbox (badness 8132) in paragraph at lines 6102--6107 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1407] [1408] [1409] [1410] [1411] Underfull \hbox (badness 7081) in paragraph at lines 6380--6383 []\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 6384--6386 []\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 [1412] [1413] [1414] [1415] [1416] Underfull \vbox (badness 3803) has occurred while \output is active [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 10000) in paragraph at lines 7225--7228 []\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 [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] Underfull \hbox (badness 2626) in paragraph at lines 8860--8863 []\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 [1452] Underfull \hbox (badness 2503) in paragraph at lines 8960--8964 []\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 , [1453] [1454] [1455] [1456] [1457] [1458] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9309--9311 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] Underfull \hbox (badness 4518) in paragraph at lines 10235--10240 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1473] [1474] [1475] [1476] [1477] Underfull \hbox (badness 2142) in paragraph at lines 10577--10580 []\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 10596--10599 []\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, [1478] Underfull \hbox (badness 1708) in paragraph at lines 10658--10662 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1479] [1480] [1481] [1482] [1483] [1484] Underfull \hbox (badness 1694) in paragraph at lines 11054--11057 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1485] Underfull \hbox (badness 1867) in paragraph at lines 11073--11082 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1486] [1487] [1488] [1489] [1490] Underfull \hbox (badness 10000) in paragraph at lines 11380--11383 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1491] [1492]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.hat}) has been already used, duplicate ignored \relax l.11534 \aliasA{hat}{influence.measures}{hat} [1493] [1494] Underfull \hbox (badness 1484) in paragraph at lines 11665--11667 []\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 [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] Underfull \hbox (badness 4441) in paragraph at lines 12248--12250 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12255--12257 []\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 [1505] [1506] [1507] [1508] [1509] [1510] Underfull \hbox (badness 2894) in paragraph at lines 12589--12593 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] Underfull \hbox (badness 4518) in paragraph at lines 13287--13292 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] Underfull \hbox (badness 4518) in paragraph at lines 13934--13939 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1532] [1533] [1534] Underfull \hbox (badness 10000) in paragraph at lines 14072--14076 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14079--14081 []\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 [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] Underfull \hbox (badness 2503) in paragraph at lines 15141--15145 []\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 , [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] Underfull \hbox (badness 1584) in paragraph at lines 15653--15659 []\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 [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] Underfull \hbox (badness 2359) in paragraph at lines 17290--17292 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1587] Underfull \vbox (badness 3803) has occurred while \output is active [1588] Underfull \vbox (badness 10000) has occurred while \output is active [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] Underfull \hbox (badness 1377) in paragraph at lines 18201--18206 []\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 18206--18209 []\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 [1602] Underfull \hbox (badness 1454) in paragraph at lines 18219--18223 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18227--18231 []\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 [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] Underfull \hbox (badness 1337) in paragraph at lines 18843--18846 []\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 [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] Underfull \hbox (badness 3049) in paragraph at lines 19329--19333 []\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 [1622] [1623] [1624] [1625] Underfull \hbox (badness 5563) in paragraph at lines 19579--19581 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19582--19585 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1626] [1627] [1628] [1629] [1630] [1631] Underfull \hbox (badness 2503) in paragraph at lines 19957--19960 []\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 , [1632] Underfull \hbox (badness 10000) in paragraph at lines 19984--19986 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648] [1649] [1650] Underfull \hbox (badness 10000) in paragraph at lines 21047--21053 []\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 , [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] Underfull \hbox (badness 1337) in paragraph at lines 22385--22391 []\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 [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] Overfull \hbox (27.74408pt too wide) in paragraph at lines 22930--22930 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1681] [1682] [1683] [1684] [1685] Underfull \hbox (badness 10000) in paragraph at lines 23180--23183 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1686] [1687] [1688] [1689] [1690] [1691] [1692] [1693] [1694] Underfull \hbox (badness 10000) in paragraph at lines 23765--23768 []\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 [1695] Underfull \hbox (badness 3690) in paragraph at lines 23816--23820 [][][]\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 [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] Underfull \hbox (badness 3439) in paragraph at lines 24286--24292 [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1 0 , [1705] [1706] [1707] Underfull \hbox (badness 1867) in paragraph at lines 24483--24485 []\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 24496--24500 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 24496--24500 \T1/zi4/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was Underfull \hbox (badness 1132) in paragraph at lines 24496--24500 \T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o f un-de-ter-mined co-ef-fi-cients, e.g., for [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] Underfull \hbox (badness 10000) in paragraph at lines 24968--24973 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732] Underfull \hbox (badness 3514) in paragraph at lines 26010--26015 []\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 [1733] Underfull \hbox (badness 3514) in paragraph at lines 26072--26077 []\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 [1734] Underfull \hbox (badness 3514) in paragraph at lines 26129--26134 []\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 [1735] Underfull \hbox (badness 3514) in paragraph at lines 26190--26196 []\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 [1736] [1737] [1738] [1739] Underfull \hbox (badness 3514) in paragraph at lines 26403--26408 []\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 [1740] Underfull \hbox (badness 3514) in paragraph at lines 26459--26464 []\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 [1741] Underfull \hbox (badness 3514) in paragraph at lines 26517--26522 []\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 [1742] Underfull \hbox (badness 3514) in paragraph at lines 26572--26577 []\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 [1743] Underfull \hbox (badness 6691) in paragraph at lines 26641--26646 []\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 [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751] [1752] Underfull \hbox (badness 10000) in paragraph at lines 27165--27168 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27165--27168 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] Underfull \hbox (badness 5431) in paragraph at lines 27771--27773 []\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 [1763] [1764] [1765] Underfull \hbox (badness 5431) in paragraph at lines 27981--27984 []\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 [1766] [1767] [1768] [1769] [1770] [1771] Underfull \hbox (badness 1337) in paragraph at lines 28295--28299 []\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 [1772] [1773] Underfull \hbox (badness 10000) in paragraph at lines 28412--28415 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1774] [1775] Underfull \hbox (badness 1616) in paragraph at lines 28595--28598 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1776] [1777] [1778] [1779] [1780] [1781] [1782] [1783] [1784] [1785] [1786] [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] Underfull \hbox (badness 10000) in paragraph at lines 29721--29725 []\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 [1795] [1796] [1797] Underfull \vbox (badness 10000) has occurred while \output is active [1798] [1799] [1800] Underfull \hbox (badness 1337) in paragraph at lines 30085--30089 []\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 [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] Underfull \hbox (badness 1337) in paragraph at lines 30569--30573 []\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 [1809] Underfull \hbox (badness 2142) in paragraph at lines 30646--30651 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the [1810] Underfull \hbox (badness 5161) in paragraph at lines 30668--30670 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1811] [1812] [1813] [1814] [1815] [1816] Underfull \hbox (badness 10000) in paragraph at lines 31050--31055 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1817] [1818]) (./stats4-pkg.tex Chapter 11. [1819] [1820] [1821] [1822] [1823] [1824]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} [1825] [1826] [1827] [1828]) (./tcltk-pkg.tex Chapter 12. [1829] [1830] [1831] [1832] [1833] [1834] [1835] Underfull \vbox (badness 10000) has occurred while \output is active [1836] Underfull \vbox (badness 10000) has occurred while \output is active [1837] 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 [1838] [1839] [1840] [1841] [1842] [1843] [1844] [1845] [1846] [1847] [1848] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1849]) (./tools-pkg.tex [1850] Chapter 13. [1851] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1852] 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 [1853] [1854] 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 [1855] [1856] 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 [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] Underfull \hbox (badness 1635) in paragraph at lines 1054--1056 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1868] Underfull \hbox (badness 4441) in paragraph at lines 1132--1142 \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- [1869] Underfull \hbox (badness 1014) in paragraph at lines 1154--1156 []\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 1160--1162 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1197--1200 []\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 1197--1200 \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 , [1870] [1871] [1872] Underfull \hbox (badness 10000) in paragraph at lines 1366--1368 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1873] [1874] [1875] Underfull \hbox (badness 2293) in paragraph at lines 1540--1542 []\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 [1876] [1877] Underfull \hbox (badness 7981) in paragraph at lines 1678--1683 []\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 1685--1687 []\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 [1878] [1879] [1880] [1881]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1882 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1882] [1883] [1884] [1885] [1886] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2184--2184 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1887] [1888] [1889] Underfull \hbox (badness 7981) in paragraph at lines 2353--2359 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1890] [1891] [1892] [1893] [1894] [1895] [1896] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2818. [1897] [1898] [1899] [1900] Underfull \hbox (badness 1424) in paragraph at lines 3100--3102 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1901] [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] [1910] [1911] [1912] Underfull \hbox (badness 10000) in paragraph at lines 3800--3802 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1913] [1914] Underfull \hbox (badness 10000) in paragraph at lines 3939--3942 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1915] [1916] Underfull \hbox (badness 1137) in paragraph at lines 4037--4039 []\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 [1917] [1918] [1919] Underfull \hbox (badness 1838) in paragraph at lines 4246--4252 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4246--4252 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1920] Underfull \hbox (badness 5726) in paragraph at lines 4326--4331 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4326--4331 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1921] [1922] [1923] Underfull \hbox (badness 2197) in paragraph at lines 4475--4485 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4475--4485 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1924] Underfull \hbox (badness 1571) in paragraph at lines 4538--4542 []\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 [1925] [1926] [1927]) (./utils-pkg.tex [1928] Chapter 14. [1929] Underfull \hbox (badness 2556) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1930] [1931] [1932] [1933] [1934] [1935] [1936] Underfull \hbox (badness 10000) in paragraph at lines 546--552 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 546--552 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1937] [1938] Underfull \hbox (badness 5847) in paragraph at lines 660--666 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 660--666 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1939] Underfull \hbox (badness 3861) in paragraph at lines 728--733 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1940] [1941] [1942] Underfull \hbox (badness 1430) in paragraph at lines 893--900 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 893--900 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 893--900 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 893--900 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 904--906 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1943] [1944] [1945] [1946] [1947] [1948] [1949] Underfull \hbox (badness 1371) in paragraph at lines 1375--1377 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 2057) in paragraph at lines 1863--1865 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1958] Underfull \hbox (badness 10000) in paragraph at lines 1958--1960 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1959] [1960] Underfull \hbox (badness 5189) in paragraph at lines 2060--2062 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1961] Underfull \vbox (badness 3803) has occurred while \output is active [1962] [1963] [1964] Underfull \hbox (badness 1661) in paragraph at lines 2278--2285 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2294--2297 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1965] [1966] [1967] [1968] [1969] [1970] Underfull \hbox (badness 10000) in paragraph at lines 2703--2707 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2708--2711 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1971] [1972] [1973] [1974] [1975] [1976] [1977] [1978] [1979] [1980] [1981] Underfull \hbox (badness 1430) in paragraph at lines 3385--3393 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 1231) in paragraph at lines 3434--3440 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1982] [1983] [1984] [1985] [1986] [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4274 ...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.4274 ...mat Unordered and Ordered Lists}{format} [1996] [1997] [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] Underfull \hbox (badness 1371) in paragraph at lines 5271--5273 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [2012] Underfull \hbox (badness 1502) in paragraph at lines 5360--5365 []\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 5360--5365 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2013] [2014] [2015] Underfull \hbox (badness 10000) in paragraph at lines 5533--5542 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2016] Underfull \hbox (badness 2150) in paragraph at lines 5596--5599 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2017] [2018] Underfull \hbox (badness 3118) in paragraph at lines 5733--5735 []\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 Underfull \hbox (badness 2409) in paragraph at lines 5766--5770 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [2019] [2020] Underfull \hbox (badness 1325) in paragraph at lines 5874--5878 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [2021] Underfull \hbox (badness 10000) in paragraph at lines 5957--5960 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 5957--5960 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2022] Underfull \hbox (badness 3219) in paragraph at lines 6030--6037 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6030--6037 \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 6030--6037 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [2023] Underfull \hbox (badness 10000) in paragraph at lines 6110--6115 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] [2047] Underfull \hbox (badness 10000) in paragraph at lines 7527--7529 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7532--7537 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] Underfull \hbox (badness 1789) in paragraph at lines 8087--8089 []\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 [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] Underfull \hbox (badness 1097) in paragraph at lines 8916--8919 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2069] Underfull \hbox (badness 3000) in paragraph at lines 9052--9057 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] Underfull \hbox (badness 2134) in paragraph at lines 9635--9640 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2079] [2080] [2081] [2082] [2083] [2084] [2085] Underfull \hbox (badness 5077) in paragraph at lines 10060--10064 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10060--10064 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 10072--10076 []\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 10072--10076 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2086] [2087] [2088] [2089] [2090] Overfull \hbox (18.77168pt too wide) in paragraph at lines 10366--10366 []\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 '[] [2091] Underfull \hbox (badness 10000) in paragraph at lines 10429--10431 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. 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Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 385--388 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 533--539 []\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 1144--1147 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1901--1901 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2086--2088 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] Underfull \vbox (badness 10000) has occurred while \output is active [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3607--3609 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] [60] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3848--3848 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] Underfull \hbox (badness 2521) in paragraph at lines 4823--4825 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] Overfull \hbox (5.27168pt too wide) in paragraph at lines 5954--5954 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [94] [95] [96] Underfull \hbox (badness 2096) in paragraph at lines 6137--6150 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [97] [98] [99] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6341--6343 []\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 : [100] [101] Underfull \hbox (badness 10000) in paragraph at lines 6483--6486 []\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 [102] [103] Underfull \hbox (badness 1442) in paragraph at lines 6646--6652 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6646--6652 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6646--6652 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [104] Underfull \hbox (badness 3568) in paragraph at lines 6708--6715 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [105] [106] Underfull \vbox (badness 10000) has occurred while \output is active [107] [108] [109] Underfull \hbox (badness 1077) in paragraph at lines 7019--7025 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7019--7025 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [110] [111] [112] [113] [114] Underfull \hbox (badness 2096) in paragraph at lines 7360--7364 \T1/zi4/m/n/10 status _ codes$[][] \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 . [115] [116] Underfull \hbox (badness 3000) in paragraph at lines 7453--7455 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7478--7481 [][][]\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 , [117] [118] [119] [120] Underfull \hbox (badness 10000) in paragraph at lines 7733--7743 []\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing [121] [122] Underfull \hbox (badness 4479) in paragraph at lines 7804--7814 [][][]\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), [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] Underfull \hbox (badness 1394) in paragraph at lines 9477--9482 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [148] [149] [150] [151] [152] Underfull \hbox (badness 1194) in paragraph at lines 9822--9827 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 9822--9827 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [153] [154] Underfull \hbox (badness 1735) in paragraph at lines 9960--9964 \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 . [155] [156] [157] [158] [159] [160] [161] Underfull \hbox (badness 2150) in paragraph at lines 10375--10378 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 6396) in paragraph at lines 10389--10397 []\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 2735) in paragraph at lines 10429--10436 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] Underfull \hbox (badness 4569) in paragraph at lines 11495--11499 []\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 11495--11499 \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 [178] [179] [180] [181] [182] [183] [184] [185] [186] Underfull \hbox (badness 2698) in paragraph at lines 12072--12081 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 12072--12081 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [187] [188] [189] [190] [191] Underfull \vbox (badness 3803) has occurred while \output is active [192] [193] [194] [195] [196] Underfull \hbox (badness 6236) in paragraph at lines 12731--12734 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [197] [198] [199] [200] [201] [202] Underfull \hbox (badness 2253) in paragraph at lines 13143--13145 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [203] Underfull \hbox (badness 1565) in paragraph at lines 13214--13218 [][][]\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 [204] Underfull \hbox (badness 10000) in paragraph at lines 13258--13260 []\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 [205] [206] Underfull \hbox (badness 1466) in paragraph at lines 13398--13401 []\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 [207] [208] Underfull \hbox (badness 10000) in paragraph at lines 13517--13521 [][][]\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 13528--13531 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [209] [210] [211] [212] Underfull \hbox (badness 3965) in paragraph at lines 13791--13795 []\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, [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] Underfull \hbox (badness 4429) in paragraph at lines 14553--14556 []\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 [225] [226] Underfull \hbox (badness 10000) in paragraph at lines 14653--14655 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14659--14663 []\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 10000) in paragraph at lines 14698--14702 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 14698--14702 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] Underfull \hbox (badness 2452) in paragraph at lines 15287--15291 []\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 15287--15291 \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 [237] [238] [239] Underfull \hbox (badness 1092) in paragraph at lines 15460--15465 [][]\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 [240] [241] [242] Underfull \hbox (badness 6741) in paragraph at lines 15708--15712 \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 , [243] [244] [245] [246] [247] Underfull \hbox (badness 1867) in paragraph at lines 16014--16021 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [248] [249] [250] [251] Underfull \vbox (badness 10000) has occurred while \output is active [252] [253] [254] Underfull \hbox (badness 3679) in paragraph at lines 16424--16426 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [255] [256] [257] [258] [259] [260] [261] [262] Underfull \hbox (badness 1478) in paragraph at lines 16979--16982 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [263] [264] [265] Underfull \hbox (badness 10000) in paragraph at lines 17232--17234 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] Underfull \hbox (badness 1442) in paragraph at lines 17822--17824 []\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 [276] Underfull \hbox (badness 2452) in paragraph at lines 17914--17930 [][][]\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 , [277] [278] [279] [280] [281] [282] [283] Underfull \hbox (badness 1248) in paragraph at lines 18328--18331 []\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 , [284] [285] [286] [287] Underfull \hbox (badness 4739) in paragraph at lines 18586--18588 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] Underfull \hbox (badness 2469) in paragraph at lines 19603--19608 []\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 19617--19624 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [305] Underfull \hbox (badness 10000) in paragraph at lines 19691--19695 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 19691--19695 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$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 ' [306] [307] Underfull \hbox (badness 1509) in paragraph at lines 19826--19833 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 19826--19833 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19842--19847 []\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 [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] Underfull \hbox (badness 1264) in paragraph at lines 20575--20580 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [319] Underfull \hbox (badness 4441) in paragraph at lines 20604--20607 []\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 , [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] Underfull \hbox (badness 10000) in paragraph at lines 21330--21332 []\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 [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] Underfull \hbox (badness 1077) in paragraph at lines 22365--22371 \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 . [347] [348] [349] Underfull \hbox (badness 1484) in paragraph at lines 22526--22534 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [350] [351] [352] [353] Underfull \hbox (badness 2790) in paragraph at lines 22797--22800 []\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 22797--22800 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [354] [355] [356] [357] Underfull \hbox (badness 1194) in paragraph at lines 23079--23082 []\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 [358] [359] [360] [361] Underfull \hbox (badness 10000) in paragraph at lines 23285--23291 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23285--23291 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23295--23298 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23295--23298 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] [373] [374] [375] Underfull \hbox (badness 10000) in paragraph at lines 24245--24247 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [376] [377] [378] [379] Underfull \hbox (badness 1199) in paragraph at lines 24489--24495 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24489--24495 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [380] [381] [382] [383] [384] [385] [386] [387] [388] Underfull \hbox (badness 1038) in paragraph at lines 25068--25076 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 1881) in paragraph at lines 25077--25080 []\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 25096--25098 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [389] Underfull \hbox (badness 10000) in paragraph at lines 25205--25215 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25216--25222 []\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 [390] Underfull \hbox (badness 1968) in paragraph at lines 25252--25257 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 25262--25264 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [391] [392] [393] Underfull \hbox (badness 10000) in paragraph at lines 25521--25527 []\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 25521--25527 \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 25521--25527 \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 25534--25537 []\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 25558--25560 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [394] Underfull \hbox (badness 10000) in paragraph at lines 25590--25595 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 25596--25607 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 25608--25611 []\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 3713) in paragraph at lines 25618--25630 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 25618--25630 \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). Underfull \hbox (badness 2351) in paragraph at lines 25618--25630 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25632--25639 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 25632--25639 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 25632--25639 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1874) in paragraph at lines 25632--25639 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [395] [396] [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 25979--25983 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 25979--25983 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [400] [401] [402] [403] [404] Underfull \hbox (badness 1735) in paragraph at lines 26297--26301 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] Underfull \hbox (badness 2726) in paragraph at lines 26868--26871 []\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 [415] [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] [427] Underfull \hbox (badness 1052) in paragraph at lines 27695--27700 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [428] [429] [430] [431] [432] Underfull \vbox (badness 10000) has occurred while \output is active [433] [434] [435] [436] [437] [438] [439] Underfull \hbox (badness 1533) in paragraph at lines 28504--28507 []\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 [440] [441] [442] Underfull \hbox (badness 1163) in paragraph at lines 28666--28677 []\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 [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] Underfull \hbox (badness 10000) in paragraph at lines 30189--30193 []\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 30189--30193 \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 30211--30213 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [467] [468] [469] [470] [471] [472] [473] [474] [475] Underfull \hbox (badness 1655) in paragraph at lines 30759--30761 []\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 [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] Underfull \hbox (badness 10000) in paragraph at lines 31434--31438 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [487] [488] [489] [490] Underfull \hbox (badness 2302) in paragraph at lines 31674--31681 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 31674--31681 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 3333) in paragraph at lines 31674--31681 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 31674--31681 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [491] [492] Underfull \hbox (badness 2261) in paragraph at lines 31830--31835 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if Underfull \hbox (badness 10000) in paragraph at lines 31857--31863 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [493] Underfull \hbox (badness 10000) in paragraph at lines 31933--31938 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] Underfull \vbox (badness 3803) has occurred while \output is active [533] [534] [535] [536] [537] [538] [539] [540] Underfull \hbox (badness 1072) in paragraph at lines 34971--34975 []\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 34976--34980 []\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 35004--35010 []\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 35004--35010 \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 35004--35010 \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 [541] Underfull \hbox (badness 3343) in paragraph at lines 35016--35023 \T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 35016--35023 \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 35016--35023 \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 [542] [543] [544] [545] Underfull \hbox (badness 10000) in paragraph at lines 35314--35320 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35314--35320 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] Underfull \hbox (badness 3333) in paragraph at lines 37158--37163 []\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 [576] [577] [578] [579] [580] [581] Underfull \vbox (badness 10000) has occurred while \output is active [582] [583] [584] [585] Underfull \hbox (badness 1472) in paragraph at lines 37781--37784 []\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 [586] [587] [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] Underfull \vbox (badness 3803) has occurred while \output is active [599] Underfull \hbox (badness 10000) in paragraph at lines 38646--38650 []\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., [600] [601] [602] [603] Underfull \hbox (badness 10000) in paragraph at lines 38894--38897 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [604] [605] Underfull \hbox (badness 10000) in paragraph at lines 39012--39016 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [606] Underfull \hbox (badness 10000) in paragraph at lines 39074--39078 [][][]\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 \ [][]$\T1/zi4/m/n/10 https : / / developer . [607] [608] [609] [610] [611] [612] [613] [614] Underfull \hbox (badness 4013) in paragraph at lines 39619--39621 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [615] [616] [617] [618] [619] [620] Underfull \vbox (badness 10000) has occurred while \output is active [621] [622] [623] [624] [625] [626] [627] Underfull \hbox (badness 3460) in paragraph at lines 40480--40483 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via [628] Underfull \hbox (badness 1990) in paragraph at lines 40487--40495 []\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 40487--40495 \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 [629] [630] [631] [632] Underfull \hbox (badness 10000) in paragraph at lines 40764--40767 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [633] [634] [635] Underfull \hbox (badness 1917) in paragraph at lines 40992--40999 []\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 [636] [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] Underfull \hbox (badness 3668) in paragraph at lines 41671--41673 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [647] Underfull \hbox (badness 2401) in paragraph at lines 41777--41781 []\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 [648] [649] [650] Underfull \hbox (badness 2111) in paragraph at lines 41953--41958 \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. [651] Underfull \hbox (badness 7362) in paragraph at lines 41969--41974 []\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 [652] [653] [654] [655] [656] [657] [658] [659] [660] Underfull \hbox (badness 5417) in paragraph at lines 42526--42530 []\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 [661] Underfull \hbox (badness 10000) in paragraph at lines 42587--42591 []\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 [662]) (./compiler-pkg.tex Chapter 2. [663] [664] [665] [666]) (./datasets-pkg.tex Chapter 3. [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] Underfull \vbox (badness 1515) has occurred while \output is active [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] Underfull \hbox (badness 6658) in paragraph at lines 3954--3956 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h ttp : / / www . ltrr . arizona . edu / ~hallman / [734] Underfull \vbox (badness 10000) has occurred while \output is active [735] [736] [737] [738] Underfull \vbox (badness 10000) has occurred while \output is active [739] [740] [741] [742] [743] [744] Overfull \vbox (18.9959pt too high) has occurred while \output is active [745] [746] [747]) (./grDevices-pkg.tex [748] Chapter 4. [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] Underfull \hbox (badness 5175) in paragraph at lines 1069--1071 []\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 [766] [767] [768] [769] Underfull \hbox (badness 1852) in paragraph at lines 1266--1269 []\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 [770] [771] [772] Underfull \hbox (badness 1490) in paragraph at lines 1472--1477 \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 [773] [774] Underfull \hbox (badness 10000) in paragraph at lines 1595--1599 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [775] [776] [777] [778] Underfull \hbox (badness 1325) in paragraph at lines 1878--1888 \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 , [779] [780] Underfull \hbox (badness 10000) in paragraph at lines 1983--1985 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [781] [782] [783] Underfull \hbox (badness 6758) in paragraph at lines 2144--2147 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [784] [785] [786] [787] [788] [789] [790] [791] [792] Underfull \hbox (badness 10000) in paragraph at lines 2737--2738 [793] [794] [795] [796] [797] [798] [799] [800] Underfull \hbox (badness 10000) in paragraph at lines 3235--3240 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [801] [802] [803] [804] Underfull \hbox (badness 3302) in paragraph at lines 3494--3497 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3508--3510 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] [816] [817] Underfull \hbox (badness 1067) in paragraph at lines 4331--4338 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [818] [819] Underfull \hbox (badness 3364) in paragraph at lines 4491--4493 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$ \T1/zi4/m/n/10 https : / / partners . adobe . com / public / [820] Underfull \hbox (badness 1789) in paragraph at lines 4568--4570 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [821] Underfull \hbox (badness 1377) in paragraph at lines 4618--4623 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [822] Underfull \hbox (badness 2671) in paragraph at lines 4645--4653 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4694--4701 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4702--4711 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4702--4711 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4712--4714 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [823] [824] Underfull \hbox (badness 1377) in paragraph at lines 4823--4828 []\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 [825] Underfull \hbox (badness 7344) in paragraph at lines 4883--4885 []\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 [826] [827] Underfull \hbox (badness 2035) in paragraph at lines 5007--5016 []\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 5007--5016 \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 5007--5016 \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 , [828] Underfull \hbox (badness 10000) in paragraph at lines 5075--5082 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5075--5082 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [829] [830] [831] Underfull \hbox (badness 1546) in paragraph at lines 5217--5225 []\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 , [832] Underfull \hbox (badness 1648) in paragraph at lines 5294--5298 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [833] [834] [835] [836] [837] [838] [839] Underfull \hbox (badness 10000) in paragraph at lines 5746--5749 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [840] [841] [842] [843] [844] [845] Underfull \hbox (badness 1189) in paragraph at lines 6143--6145 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [846] [847] Underfull \hbox (badness 10000) in paragraph at lines 6241--6243 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [848] [849] [850] [851] Underfull \hbox (badness 3780) in paragraph at lines 6532--6538 []\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 , [852] [853] [854] Underfull \hbox (badness 2680) in paragraph at lines 6733--6735 []\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 [855] [856] [857]) (./graphics-pkg.tex [858] Chapter 5. [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] [869] Underfull \hbox (badness 10000) in paragraph at lines 683--690 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [870] [871] [872] [873] Underfull \vbox (badness 3803) has occurred while \output is active [874] [875] [876] [877] [878] [879] Underfull \hbox (badness 4634) in paragraph at lines 1255--1258 [][][]\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 , [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] [894] [895] [896] Underfull \hbox (badness 1009) in paragraph at lines 2289--2296 \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 [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] Underfull \vbox (badness 10000) has occurred while \output is active [919] [920] [921] [922] Underfull \hbox (badness 1867) in paragraph at lines 3931--3935 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [923] [924] [925] [926] [927] [928] [929] [930] Underfull \hbox (badness 1924) in paragraph at lines 4378--4383 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain Underfull \hbox (badness 2529) in paragraph at lines 4409--4412 []\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 [931] [932] [933] [934] [935] Underfull \hbox (badness 10000) in paragraph at lines 4759--4765 []\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 4759--4765 \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 [936] [937] Underfull \hbox (badness 10000) in paragraph at lines 4890--4893 [938 >/library/graphics/help/figures/mai.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 4951--4953 Underfull \vbox (badness 10000) has occurred while \output is active [939] [940 >/library/graphics/help/figures/oma.pdf>] [941] Underfull \hbox (badness 10000) in paragraph at lines 5141--5143 []\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 [942] Underfull \vbox (badness 3803) has occurred while \output is active [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6612--6613 [][] [965] [966 >/library/graphics/help/figures/pch .pdf>] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] Underfull \hbox (badness 1048) in paragraph at lines 7321--7326 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [977] [978] Underfull \hbox (badness 1102) in paragraph at lines 7437--7440 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] Underfull \hbox (badness 1043) in paragraph at lines 8272--8276 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [993] [994] [995] [996] [997] [998] [999] Underfull \hbox (badness 10000) in paragraph at lines 8675--8677 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8677--8679 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1000]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8757 \HeaderA{units}{Graphical Units}{units} [1001] [1002] [1003] [1004]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1005] [1006] [1007] [1008] [1009] [1010] Underfull \hbox (badness 2680) in paragraph at lines 390--393 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] Underfull \hbox (badness 4279) in paragraph at lines 970--979 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] Underfull \vbox (badness 3803) has occurred while \output is active [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] Underfull \hbox (badness 1067) in paragraph at lines 4340--4343 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1078] [1079] [1080] [1081] Underfull \hbox (badness 7256) in paragraph at lines 4585--4587 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] Underfull \hbox (badness 10000) in paragraph at lines 5862--5868 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] Underfull \hbox (badness 7649) in paragraph at lines 6341--6344 []\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 [1112] [1113] [1114] [1115]) (./methods-pkg.tex [1116] Chapter 7. [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] Underfull \vbox (badness 3803) has occurred while \output is active [1125] Underfull \vbox (badness 10000) has occurred while \output is active [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] Underfull \hbox (badness 2237) in paragraph at lines 1386--1388 []\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 [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] Underfull \hbox (badness 1077) in paragraph at lines 1933--1940 []\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 [1144] Underfull \hbox (badness 10000) in paragraph at lines 1982--1987 []\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 1982--1987 \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 [1145] [1146] [1147] Underfull \hbox (badness 1242) in paragraph at lines 2215--2220 []\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 = [1148] [1149] [1150] [1151] [1152] Underfull \hbox (badness 10000) in paragraph at lines 2575--2578 []\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 [1153] [1154] Underfull \hbox (badness 1132) in paragraph at lines 2715--2719 []\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 [1155] Underfull \hbox (badness 1033) in paragraph at lines 2747--2752 \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 [1156] [1157] [1158] [1159] [1160] [1161] [1162] Underfull \hbox (badness 1102) in paragraph at lines 3304--3306 []\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 [1163] [1164] [1165] [1166] [1167] [1168] Underfull \hbox (badness 10000) in paragraph at lines 3637--3642 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Underfull \hbox (badness 10000) in paragraph at lines 3645--3654 []\T1/ptm/m/n/10 The [1169] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3765--3766 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3765--3766 [1170] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3849--3850 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] Underfull \hbox (badness 1436) in paragraph at lines 4446--4449 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4475--4481 []\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 4475--4481 \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 [1181] Underfull \hbox (badness 1092) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] Underfull \vbox (badness 10000) has occurred while \output is active [1191] [1192] Underfull \hbox (badness 10000) in paragraph at lines 5358--5359 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1193] Underfull \hbox (badness 4036) in paragraph at lines 5440--5443 []\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 [1194] Underfull \hbox (badness 3803) in paragraph at lines 5515--5517 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1195] [1196] [1197] [1198] Underfull \hbox (badness 1087) in paragraph at lines 5747--5752 []\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 [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] Underfull \hbox (badness 1675) in paragraph at lines 6454--6460 \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 [1207] [1208] [1209] [1210] Underfull \vbox (badness 10000) has occurred while \output is active [1211] [1212] [1213] [1214]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6976 \aliasA{S4}{S3Part}{S4} [1215] [1216] [1217]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7232 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7234 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7235 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7237 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7238 \aliasA{Summary}{S4groupGeneric}{Summary} [1218] Underfull \hbox (badness 2050) in paragraph at lines 7299--7303 []\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 [1219] [1220] [1221] Underfull \hbox (badness 1286) in paragraph at lines 7487--7489 []\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 [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] Underfull \vbox (badness 10000) has occurred while \output is active [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] Underfull \hbox (badness 1852) in paragraph at lines 10567--10571 []\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., [1264] [1265] [1266] [1267]) (./parallel-pkg.tex [1268] 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 [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] Underfull \hbox (badness 3386) in paragraph at lines 1268--1271 []\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 [1289] [1290] [1291]) (./splines-pkg.tex [1292] 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 [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] [1306] [1307]) (./stats-pkg.tex [1308] Chapter 10. [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] Underfull \hbox (badness 1412) in paragraph at lines 848--850 []\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 [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] Underfull \hbox (badness 2503) in paragraph at lines 1329--1332 []\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 , [1330] [1331] [1332] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 3965) in paragraph at lines 2168--2170 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1344] [1345] [1346] [1347] [1348] Underfull \hbox (badness 3965) in paragraph at lines 2510--2512 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] Underfull \hbox (badness 2726) in paragraph at lines 3224--3240 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1360] [1361] Underfull \hbox (badness 2503) in paragraph at lines 3354--3357 []\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 , [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] Underfull \hbox (badness 3989) in paragraph at lines 4582--4589 []\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 = [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] Underfull \hbox (badness 2556) in paragraph at lines 5193--5196 []\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 5210--5212 []\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 [1392] [1393] [1394] [1395] Underfull \hbox (badness 1142) in paragraph at lines 5451--5463 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1396] [1397] [1398] Underfull \hbox (badness 2503) in paragraph at lines 5599--5603 []\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 , [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] Underfull \hbox (badness 8132) in paragraph at lines 6102--6107 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1407] [1408] [1409] [1410] [1411] Underfull \hbox (badness 7081) in paragraph at lines 6380--6383 []\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 6384--6386 []\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 [1412] [1413] [1414] [1415] [1416] Underfull \vbox (badness 3803) has occurred while \output is active [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 10000) in paragraph at lines 7225--7228 []\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 [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] Underfull \hbox (badness 2626) in paragraph at lines 8860--8863 []\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 [1452] Underfull \hbox (badness 2503) in paragraph at lines 8960--8964 []\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 , [1453] [1454] [1455] [1456] [1457] [1458] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9309--9311 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] Underfull \hbox (badness 4518) in paragraph at lines 10235--10240 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1473] [1474] [1475] [1476] [1477] Underfull \hbox (badness 2142) in paragraph at lines 10577--10580 []\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 10596--10599 []\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, [1478] Underfull \hbox (badness 1708) in paragraph at lines 10658--10662 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1479] [1480] [1481] [1482] [1483] [1484] Underfull \hbox (badness 1694) in paragraph at lines 11054--11057 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1485] Underfull \hbox (badness 1867) in paragraph at lines 11073--11082 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1486] [1487] [1488] [1489] [1490] Underfull \hbox (badness 10000) in paragraph at lines 11380--11383 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1491] [1492]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.hat}) has been already used, duplicate ignored \relax l.11534 \aliasA{hat}{influence.measures}{hat} [1493] [1494] Underfull \hbox (badness 1484) in paragraph at lines 11665--11667 []\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 [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] Underfull \hbox (badness 4441) in paragraph at lines 12248--12250 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12255--12257 []\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 [1505] [1506] [1507] [1508] [1509] [1510] Underfull \hbox (badness 2894) in paragraph at lines 12589--12593 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] Underfull \hbox (badness 4518) in paragraph at lines 13287--13292 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] Underfull \hbox (badness 4518) in paragraph at lines 13934--13939 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1532] [1533] [1534] Underfull \hbox (badness 10000) in paragraph at lines 14072--14076 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14079--14081 []\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 [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] Underfull \hbox (badness 2503) in paragraph at lines 15141--15145 []\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 , [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] Underfull \hbox (badness 1584) in paragraph at lines 15653--15659 []\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 [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] Underfull \hbox (badness 2359) in paragraph at lines 17290--17292 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1587] Underfull \vbox (badness 3803) has occurred while \output is active [1588] Underfull \vbox (badness 10000) has occurred while \output is active [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] Underfull \hbox (badness 1377) in paragraph at lines 18201--18206 []\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 18206--18209 []\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 [1602] Underfull \hbox (badness 1454) in paragraph at lines 18219--18223 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18227--18231 []\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 [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] Underfull \hbox (badness 1337) in paragraph at lines 18843--18846 []\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 [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] Underfull \hbox (badness 3049) in paragraph at lines 19329--19333 []\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 [1622] [1623] [1624] [1625] Underfull \hbox (badness 5563) in paragraph at lines 19579--19581 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19582--19585 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1626] [1627] [1628] [1629] [1630] [1631] Underfull \hbox (badness 2503) in paragraph at lines 19957--19960 []\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 , [1632] Underfull \hbox (badness 10000) in paragraph at lines 19984--19986 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648] [1649] [1650] Underfull \hbox (badness 10000) in paragraph at lines 21047--21053 []\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 , [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] Underfull \hbox (badness 1337) in paragraph at lines 22385--22391 []\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 [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] Overfull \hbox (27.74408pt too wide) in paragraph at lines 22930--22930 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1681] [1682] [1683] [1684] [1685] Underfull \hbox (badness 10000) in paragraph at lines 23180--23183 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1686] [1687] [1688] [1689] [1690] [1691] [1692] [1693] [1694] Underfull \hbox (badness 10000) in paragraph at lines 23765--23768 []\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 [1695] Underfull \hbox (badness 3690) in paragraph at lines 23816--23820 [][][]\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 [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] Underfull \hbox (badness 3439) in paragraph at lines 24286--24292 [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1 0 , [1705] [1706] [1707] Underfull \hbox (badness 1867) in paragraph at lines 24483--24485 []\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 24496--24500 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 24496--24500 \T1/zi4/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was Underfull \hbox (badness 1132) in paragraph at lines 24496--24500 \T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o f un-de-ter-mined co-ef-fi-cients, e.g., for [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] Underfull \hbox (badness 10000) in paragraph at lines 24968--24973 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732] Underfull \hbox (badness 3514) in paragraph at lines 26010--26015 []\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 [1733] Underfull \hbox (badness 3514) in paragraph at lines 26072--26077 []\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 [1734] Underfull \hbox (badness 3514) in paragraph at lines 26129--26134 []\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 [1735] Underfull \hbox (badness 3514) in paragraph at lines 26190--26196 []\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 [1736] [1737] [1738] [1739] Underfull \hbox (badness 3514) in paragraph at lines 26403--26408 []\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 [1740] Underfull \hbox (badness 3514) in paragraph at lines 26459--26464 []\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 [1741] Underfull \hbox (badness 3514) in paragraph at lines 26517--26522 []\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 [1742] Underfull \hbox (badness 3514) in paragraph at lines 26572--26577 []\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 [1743] Underfull \hbox (badness 6691) in paragraph at lines 26641--26646 []\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 [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751] [1752] Underfull \hbox (badness 10000) in paragraph at lines 27165--27168 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27165--27168 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] Underfull \hbox (badness 5431) in paragraph at lines 27771--27773 []\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 [1763] [1764] [1765] Underfull \hbox (badness 5431) in paragraph at lines 27981--27984 []\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 [1766] [1767] [1768] [1769] [1770] [1771] Underfull \hbox (badness 1337) in paragraph at lines 28295--28299 []\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 [1772] [1773] Underfull \hbox (badness 10000) in paragraph at lines 28412--28415 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1774] [1775] Underfull \hbox (badness 1616) in paragraph at lines 28595--28598 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1776] [1777] [1778] [1779] [1780] [1781] [1782] [1783] [1784] [1785] [1786] [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] Underfull \hbox (badness 10000) in paragraph at lines 29721--29725 []\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 [1795] [1796] [1797] Underfull \vbox (badness 10000) has occurred while \output is active [1798] [1799] [1800] Underfull \hbox (badness 1337) in paragraph at lines 30085--30089 []\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 [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] Underfull \hbox (badness 1337) in paragraph at lines 30569--30573 []\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 [1809] Underfull \hbox (badness 2142) in paragraph at lines 30646--30651 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the [1810] Underfull \hbox (badness 5161) in paragraph at lines 30668--30670 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1811] [1812] [1813] [1814] [1815] [1816] Underfull \hbox (badness 10000) in paragraph at lines 31050--31055 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1817] [1818]) (./stats4-pkg.tex Chapter 11. [1819] [1820] [1821] [1822] [1823] [1824]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} [1825] [1826] [1827] [1828]) (./tcltk-pkg.tex Chapter 12. [1829] [1830] [1831] [1832] [1833] [1834] [1835] Underfull \vbox (badness 10000) has occurred while \output is active [1836] Underfull \vbox (badness 10000) has occurred while \output is active [1837] 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 [1838] [1839] [1840] [1841] [1842] [1843] [1844] [1845] [1846] [1847] [1848] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1849]) (./tools-pkg.tex [1850] Chapter 13. [1851] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1852] 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 [1853] [1854] 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 [1855] [1856] 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 [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] Underfull \hbox (badness 1635) in paragraph at lines 1054--1056 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1868] Underfull \hbox (badness 4441) in paragraph at lines 1132--1142 \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- [1869] Underfull \hbox (badness 1014) in paragraph at lines 1154--1156 []\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 1160--1162 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1197--1200 []\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 1197--1200 \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 , [1870] [1871] [1872] Underfull \hbox (badness 10000) in paragraph at lines 1366--1368 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1873] [1874] [1875] Underfull \hbox (badness 2293) in paragraph at lines 1540--1542 []\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 [1876] [1877] Underfull \hbox (badness 7981) in paragraph at lines 1678--1683 []\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 1685--1687 []\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 [1878] [1879] [1880] [1881]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1882 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1882] [1883] [1884] [1885] [1886] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2184--2184 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1887] [1888] [1889] Underfull \hbox (badness 7981) in paragraph at lines 2353--2359 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1890] [1891] [1892] [1893] [1894] [1895] [1896] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2818. [1897] [1898] [1899] [1900] Underfull \hbox (badness 1424) in paragraph at lines 3100--3102 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1901] [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] [1910] [1911] [1912] Underfull \hbox (badness 10000) in paragraph at lines 3800--3802 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1913] [1914] Underfull \hbox (badness 10000) in paragraph at lines 3939--3942 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1915] [1916] Underfull \hbox (badness 1137) in paragraph at lines 4037--4039 []\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 [1917] [1918] [1919] Underfull \hbox (badness 1838) in paragraph at lines 4246--4252 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4246--4252 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1920] Underfull \hbox (badness 5726) in paragraph at lines 4326--4331 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4326--4331 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1921] [1922] [1923] Underfull \hbox (badness 2197) in paragraph at lines 4475--4485 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4475--4485 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1924] Underfull \hbox (badness 1571) in paragraph at lines 4538--4542 []\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 [1925] [1926] [1927]) (./utils-pkg.tex [1928] Chapter 14. [1929] Underfull \hbox (badness 2556) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1930] [1931] [1932] [1933] [1934] [1935] [1936] Underfull \hbox (badness 10000) in paragraph at lines 546--552 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 546--552 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1937] [1938] Underfull \hbox (badness 5847) in paragraph at lines 660--666 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 660--666 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1939] Underfull \hbox (badness 3861) in paragraph at lines 728--733 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1940] [1941] [1942] Underfull \hbox (badness 1430) in paragraph at lines 893--900 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 893--900 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 893--900 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 893--900 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 904--906 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1943] [1944] [1945] [1946] [1947] [1948] [1949] Underfull \hbox (badness 1371) in paragraph at lines 1375--1377 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 2057) in paragraph at lines 1863--1865 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1958] Underfull \hbox (badness 10000) in paragraph at lines 1958--1960 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1959] [1960] Underfull \hbox (badness 5189) in paragraph at lines 2060--2062 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1961] Underfull \vbox (badness 3803) has occurred while \output is active [1962] [1963] [1964] Underfull \hbox (badness 1661) in paragraph at lines 2278--2285 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2294--2297 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1965] [1966] [1967] [1968] [1969] [1970] Underfull \hbox (badness 10000) in paragraph at lines 2703--2707 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2708--2711 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1971] [1972] [1973] [1974] [1975] [1976] [1977] [1978] [1979] [1980] [1981] Underfull \hbox (badness 1430) in paragraph at lines 3385--3393 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 1231) in paragraph at lines 3434--3440 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1982] [1983] [1984] [1985] [1986] [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4274 ...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.4274 ...mat Unordered and Ordered Lists}{format} [1996] [1997] [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] Underfull \hbox (badness 1371) in paragraph at lines 5271--5273 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [2012] Underfull \hbox (badness 1502) in paragraph at lines 5360--5365 []\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 5360--5365 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2013] [2014] [2015] Underfull \hbox (badness 10000) in paragraph at lines 5533--5542 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2016] Underfull \hbox (badness 2150) in paragraph at lines 5596--5599 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2017] [2018] Underfull \hbox (badness 3118) in paragraph at lines 5733--5735 []\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 Underfull \hbox (badness 2409) in paragraph at lines 5766--5770 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [2019] [2020] Underfull \hbox (badness 1325) in paragraph at lines 5874--5878 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [2021] Underfull \hbox (badness 10000) in paragraph at lines 5957--5960 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 5957--5960 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2022] Underfull \hbox (badness 3219) in paragraph at lines 6030--6037 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6030--6037 \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 6030--6037 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [2023] Underfull \hbox (badness 10000) in paragraph at lines 6110--6115 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] [2047] Underfull \hbox (badness 10000) in paragraph at lines 7527--7529 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7532--7537 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] Underfull \hbox (badness 1789) in paragraph at lines 8087--8089 []\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 [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] Underfull \hbox (badness 1097) in paragraph at lines 8916--8919 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2069] Underfull \hbox (badness 3000) in paragraph at lines 9052--9057 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] Underfull \hbox (badness 2134) in paragraph at lines 9635--9640 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2079] [2080] [2081] [2082] [2083] [2084] [2085] Underfull \hbox (badness 5077) in paragraph at lines 10060--10064 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10060--10064 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 10072--10076 []\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 10072--10076 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2086] [2087] [2088] [2089] [2090] Overfull \hbox (18.77168pt too wide) in paragraph at lines 10366--10366 []\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 '[] [2091] Underfull \hbox (badness 10000) in paragraph at lines 10429--10431 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][] []\T1/ptm/m/n/10 s are nicely viewed via [2092] [2093] [2094] Underfull \hbox (badness 2150) in paragraph at lines 10605--10607 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2095] [2096] [2097] [2098] Underfull \hbox (badness 10000) in paragraph at lines 10824--10828 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 10855--10861 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2099] [2100] Underfull \hbox (badness 2096) in paragraph at lines 10973--10976 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 10977--10980 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether JPEG fig-ures should be gen-er-ated. Ig-nored if [2101] Underfull \hbox (badness 1009) in paragraph at lines 11049--11060 []\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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See [2132] Underfull \hbox (badness 10000) in paragraph at lines 13016--13021 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined see Underfull \hbox (badness 10000) in paragraph at lines 13016--13021 [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 av ailable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 1297) in paragraph at lines 13016--13021 \T1/zi4/m/sl/10 available.packages(contriburl = contriburl, method = method) \T 1/ptm/m/n/10 and hence by Underfull \hbox (badness 10000) in paragraph at lines 13045--13048 [][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n /10 , [2133] [2134] [2135] [2136] Overfull \hbox (23.85939pt too wide) in paragraph at lines 13287--13290 [][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi -gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](, package = "") [2137] [2138] Underfull \hbox (badness 1454) in paragraph at lines 13364--13368 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, [2139] Underfull \hbox (badness 10000) in paragraph at lines 13434--13436 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion [2140] [2141] [2142]) (./refman.ind [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187] [2188] [2189] [2190] [2191] Overfull \hbox (33.3567pt too wide) in paragraph at lines 8523--8525 []\T1/zi4/m/it/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] Overfull \hbox (5.8567pt too wide) in paragraph at lines 11513--11515 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_depends Overfull \hbox (5.8567pt too wide) in paragraph at lines 11515--11517 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_results Overfull \hbox (5.8567pt too wide) in paragraph at lines 11517--11519 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_timings [2205] [2206] [2207] [2208] [2209] [2210] [2211] [2212] [2213]) (./refman.aux) LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.write.matrix} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.survreg} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.coxph} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.stepAIC} has been referenced but does 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Transcript written on refman.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-admin.texi This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: 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/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-admin.cp Writing index file R-admin.en [1] Chapter 2 [2] Cross reference values unknown; you must run TeX again. [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] Chapter 3 [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 1887--1899 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [23] Chapter 5 [24] Chapter 6 [25] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2033--2033 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [26] [27] Underfull \hbox (badness 6842) in paragraph at lines 2225--2236 []@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age s. No ad-di- [28] [29] [30] [31] [32] [33] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2698--2698 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text tt --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] [34] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2718--2718 []@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 2719--2719 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [35] [36] [37] Chapter 8 [38] Chapter 9 [39] [40] [41] [42] Appendix A [43] [44] Overfull \hbox (49.43388pt too wide) in paragraph at lines 3351--3351 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] Appendix B [55] [56] [57] [58] [59] [60] Appendix C [61] [62] [63] [64] [65] [66] [67] [68] Overfull \hbox (78.17732pt too wide) in paragraph at lines 5075--5075 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] [69] Overfull \hbox (106.92076pt too wide) in paragraph at lines 5113--5113 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [70] Underfull \hbox (badness 10000) in paragraph at lines 5256--5261 []@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled , run [71] Overfull \hbox (20.69044pt too wide) in paragraph at lines 5271--5271 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Content s/Home[] [72] [73] Overfull \hbox (32.18782pt too wide) in paragraph at lines 5449--5449 []@texttt R_LD_LIBRARY_PATH="/opt/developerstudio12.5/lib:/usr/local/lib:/opt/ csw/lib"[] [74] Underfull \hbox (badness 10000) in paragraph at lines 5536--5542 @texttt LDFLAGS=-L/usr/local/lib/amd64[] @textrm or @texttt LDFLAGS=-L/usr/loca l/lib/sparcv9[] @textrm as Overfull \hbox (26.43913pt too wide) in paragraph at lines 5551--5551 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s olaris"[] [75] Underfull \hbox (badness 10000) in paragraph at lines 5603--5607 []@textrm Note that paths such as @texttt /opt/csw/lib[]@textrm , @texttt /usr/ local/lib/amd64[] @textrm and [76] [77] [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, 491046 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: 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/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-admin.toc [-1] [-2]) [-3] (/<>/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] Chapter 3 [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 1887--1899 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [23] Chapter 5 [24] Chapter 6 [25] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2033--2033 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [26] [27] Underfull \hbox (badness 6842) in paragraph at lines 2225--2236 []@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age s. No ad-di- [28] [29] [30] [31] [32] [33] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2698--2698 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text tt --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] [34] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2718--2718 []@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 2719--2719 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [35] [36] [37] Chapter 8 [38] Chapter 9 [39] [40] [41] [42] Appendix A [43] [44] Overfull \hbox (49.43388pt too wide) in paragraph at lines 3351--3351 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [45] [46] [47] [48] [49] [50] [51] [52] [53] Appendix B [54] [55] [56] [57] [58] [59] Appendix C [60] [61] [62] [63] [64] [65] [66] [67] Overfull \hbox (78.17732pt too wide) in paragraph at lines 5075--5075 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] [68] Overfull \hbox (106.92076pt too wide) in paragraph at lines 5113--5113 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [69] Underfull \hbox (badness 10000) in paragraph at lines 5256--5261 []@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled , run [70] Overfull \hbox (20.69044pt too wide) in paragraph at lines 5271--5271 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Content s/Home[] [71] [72] Overfull \hbox (32.18782pt too wide) in paragraph at lines 5449--5449 []@texttt R_LD_LIBRARY_PATH="/opt/developerstudio12.5/lib:/usr/local/lib:/opt/ csw/lib"[] [73] Underfull \hbox (badness 10000) in paragraph at lines 5536--5542 @texttt LDFLAGS=-L/usr/local/lib/amd64[] @textrm or @texttt LDFLAGS=-L/usr/loca l/lib/sparcv9[] @textrm as Overfull \hbox (26.43913pt too wide) in paragraph at lines 5551--5551 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s olaris"[] [74] Underfull \hbox (badness 10000) in paragraph at lines 5603--5607 []@textrm Note that paths such as @texttt /opt/csw/lib[]@textrm , @texttt /usr/ local/lib/amd64[] @textrm and [75] [76] [77] Appendix D [78] [79] [80] (Function and variable index) [81] (Concept index) [82] (Environment variable index) [83] [84] ) (see the transcript file for additional information)pdfTeX warning (dest): name {85} has been referenced but does not exist, replaced by a fixed one Output written on R-admin.pdf (89 pages, 536497 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: 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/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] (/<>/doc/manual/R-admin.toc [-1] [-2]) [-3] (/<>/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] Chapter 3 [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 1887--1899 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [23] Chapter 5 [24] Chapter 6 [25] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2033--2033 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [26] [27] Underfull \hbox (badness 6842) in paragraph at lines 2225--2236 []@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age s. No ad-di- [28] [29] [30] [31] [32] [33] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2698--2698 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text tt --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] [34] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2718--2718 []@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 2719--2719 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [35] [36] [37] Chapter 8 [38] Chapter 9 [39] [40] [41] [42] Appendix A [43] [44] Overfull \hbox (49.43388pt too wide) in paragraph at lines 3351--3351 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [45] [46] [47] [48] [49] [50] [51] [52] [53] Appendix B [54] [55] [56] [57] [58] [59] Appendix C [60] [61] [62] [63] [64] [65] [66] [67] Overfull \hbox (78.17732pt too wide) in paragraph at lines 5075--5075 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] [68] Overfull \hbox (106.92076pt too wide) in paragraph at lines 5113--5113 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [69] Underfull \hbox (badness 10000) in paragraph at lines 5256--5261 []@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled , run [70] Overfull \hbox (20.69044pt too wide) in paragraph at lines 5271--5271 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Content s/Home[] [71] [72] Overfull \hbox (32.18782pt too wide) in paragraph at lines 5449--5449 []@texttt R_LD_LIBRARY_PATH="/opt/developerstudio12.5/lib:/usr/local/lib:/opt/ csw/lib"[] [73] Underfull \hbox (badness 10000) in paragraph at lines 5536--5542 @texttt LDFLAGS=-L/usr/local/lib/amd64[] @textrm or @texttt LDFLAGS=-L/usr/loca l/lib/sparcv9[] @textrm as Overfull \hbox (26.43913pt too wide) in paragraph at lines 5551--5551 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s olaris"[] [74] Underfull \hbox (badness 10000) in paragraph at lines 5603--5607 []@textrm Note that paths such as @texttt /opt/csw/lib[]@textrm , @texttt /usr/ local/lib/amd64[] @textrm and [75] [76] [77] Appendix D [78] [79] [80] (Function and variable index) [81] (Concept index) [82] (Environment variable index) [83] [84] ) (see the transcript file for additional information) Output written on R-admin.pdf (89 pages, 536439 bytes). Transcript written on R-admin.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-data.texi This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: 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/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Underfull \hbox (badness 10000) in paragraph at lines 87--87 [][]@textbf DBI Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87 @texttt package=DBI[]@textrm )[][]| Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt org / Overfull \hbox (67.73643pt too wide) in paragraph at lines 88--88 @texttt package=dataframes2xls[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 89--89 [][]@textbf foreign Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 89--89 @texttt package=foreign[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 90--90 [][]@textbf gdata Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90 @texttt package=gdata[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 91--91 [][]@textbf ncdf4 Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91 @texttt package=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf rJava Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92 @texttt package=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf RJDBC Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RMySQL Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt org / Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RNetCDF Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RODBC Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf ROracle Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt org / Overfull \hbox (50.49037pt too wide) in paragraph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 103--103 [][]@textbf WriteXLS Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt org / Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf XLConnect Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt org / Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] Writing index file R-data.cp Cross reference values unknown; you must run TeX again. [4] [5] [6] [7] Chapter 2 [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15] [16] Chapter 4 [17] [18] [19] [20] [21] [22] [23] Chapter 5 [24] Chapter 6 [25] Chapter 7 [26] [27] [28] [29] [30] Chapter 8 [31] Chapter 9 [32] Appendix A [33] (Function and variable index) [34] 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, 272955 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: 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/lib/texmf/f onts/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 Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87 @texttt package=DBI[]@textrm )[][]| Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt org / Overfull \hbox (67.73643pt too wide) in paragraph at lines 88--88 @texttt package=dataframes2xls[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 89--89 [][]@textbf foreign Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 89--89 @texttt package=foreign[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 90--90 [][]@textbf gdata Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90 @texttt package=gdata[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 91--91 [][]@textbf ncdf4 Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91 @texttt package=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf rJava Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92 @texttt package=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf RJDBC Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RMySQL Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt org / Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RNetCDF Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RODBC Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf ROracle Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt org / Overfull \hbox (50.49037pt too wide) in paragraph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 103--103 [][]@textbf WriteXLS Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt org / Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf XLConnect Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt org / Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] Writing index file R-data.cp [4] [5] [6] [7] Chapter 2 [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15] [16] Chapter 4 [17] [18] [19] [20] [21] [22] [23] Chapter 5 [24] Chapter 6 [25] Chapter 7 [26] [27] [28] [29] [30] Chapter 8 [31] Chapter 9 [32] Appendix A [33] (Function and variable index) [34] [35] (Concept index) [36] [37] Overfull \vbox (1.73251pt too high) has occurred while \output is active [38] ) (see the transcript file for additional information) Output written on R-data.pdf (42 pages, 312993 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: 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/lib/texmf/f onts/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 Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87 @texttt package=DBI[]@textrm )[][]| Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt org / Overfull \hbox (67.73643pt too wide) in paragraph at lines 88--88 @texttt package=dataframes2xls[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 89--89 [][]@textbf foreign Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 89--89 @texttt package=foreign[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 90--90 [][]@textbf gdata Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90 @texttt package=gdata[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 91--91 [][]@textbf ncdf4 Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91 @texttt package=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf rJava Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt CRAN . 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Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] Writing index file R-data.cp [4] [5] [6] [7] Chapter 2 [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15] [16] Chapter 4 [17] [18] [19] [20] [21] [22] [23] Chapter 5 [24] Chapter 6 [25] Chapter 7 [26] [27] [28] [29] [30] Chapter 8 [31] Chapter 9 [32] Appendix A [33] (Function and variable index) [34] [35] (Concept index) [36] [37] Overfull \vbox (1.73251pt too high) has occurred while \output is active [38] ) (see the transcript file for additional information) Output written on R-data.pdf (42 pages, 312995 bytes). Transcript written on R-data.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-exts.texi This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: 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/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Chapter 1 [1] Writing index file R-exts.cp Cross reference values unknown; you must run TeX again. [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 494--497 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1915--1915 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [25] [26] [27] [28] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2248--2248 []@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 2250--2250 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [29] [30] [31] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2392--2392 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [32] Underfull \hbox (badness 10000) in paragraph at lines 2499--2501 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [33] [34] Overfull \hbox (60.93126pt too wide) in paragraph at lines 2623--2623 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [35] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2750--2752 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] Overfull \hbox (53.86903pt too wide) in paragraph at lines 4589--4589 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 4591--4591 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 4592--4592 [] @texttt if(jvn < 1.8) stop("Java 8 is needed for this package but not avai lable")[] Overfull \hbox (76.86378pt too wide) in paragraph at lines 4602--4602 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [60] [61] [62] [63] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4887--4887 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [64] [65] Overfull \hbox (30.87428pt too wide) in paragraph at lines 5093--5093 []@texttt abs acos atan calloc ceil div exp fabs floor fmod free log malloc me mcpy[] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5094--5094 []@texttt memset pow printf qsort round sin sprintf sqrt strcmp strcpy strerro r[] [66] [67] Overfull \hbox (25.1256pt too wide) in paragraph at lines 5188--5188 []@texttt erf expm1 fmin fmax lgamma lround loglp round snprintf strcasecmp tr unc[] Overfull \hbox (53.86903pt too wide) in paragraph at lines 5220--5220 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [68] [69] [70] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5457--5457 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [71] [72] [73] Chapter 2 [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] Underfull \hbox (badness 10000) in paragraph at lines 6717--6724 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [88] [89] [90] [91] Underfull \hbox (badness 10000) in paragraph at lines 7036--7040 []@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file [92] [93] Chapter 3 [94] [95] [96] [97] [98] [99] [100] Overfull \hbox (20.69044pt too wide) in paragraph at lines 7637--7637 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [101] [102] [103] Chapter 4 [104] [105] [106] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8014--8014 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [107] Overfull \hbox (25.25755pt too wide) in paragraph at lines 8055--8055 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [108] Overfull \hbox (20.53261pt too wide) in paragraph at lines 8159--8159 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] [109] Overfull \hbox (38.96663pt too wide) in paragraph at lines 8189--8198 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [110] [111] [112] Overfull \hbox (44.18301pt too wide) in paragraph at lines 8466--8467 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [113] [114] Overfull \hbox (78.17732pt too wide) in paragraph at lines 8599--8599 []@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 8627--8629 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8640--8640 []@texttt null,object-size,pointer-overflow,return,returns-nonnull-attribute,s hift,[] Overfull \hbox (32.18782pt too wide) in paragraph at lines 8641--8641 []@texttt signed-integer-overflow,unreachable,unsigned-integer-overflow,vla-bo und,vptr[] [115] [116] Overfull \hbox (72.42863pt too wide) in paragraph at lines 8758--8758 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [117] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8807--8807 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8810--8810 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [118] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8889--8889 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [119] [120] Chapter 5 [121] [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] Overfull \hbox (30.87428pt too wide) in paragraph at lines 9854--9854 [] @texttt double *w, int *iper, double *span, double *al pha,[] Overfull \hbox (51.66371pt too wide) in paragraph at lines 9903--9903 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [132] [133] [134] [135] [136] [137] [138] [139] Overfull \hbox (37.93651pt too wide) in paragraph at lines 10481--10481 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11253--11253 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [150] Underfull \hbox (badness 10000) in paragraph at lines 11314--11316 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [151] [152] [153] [154] [155] [156] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11823--11823 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [157] [158] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11946--11946 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [159] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11951--11951 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12006--12006 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12018--12018 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [160] Overfull \hbox (26.43913pt too wide) in paragraph at lines 12117--12117 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [161] [162] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12253--12253 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [163] Overfull \hbox (43.6852pt too wide) in paragraph at lines 12334--12334 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [164] [165] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12421--12421 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] Underfull \hbox (badness 10000) in paragraph at lines 13580--13584 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [179] [180] Warning: unbalanced parentheses in @def... [181] [182] [183] [184] [185] Chapter 7 [186] [187] Chapter 8 [188] [189] [190] Overfull \hbox (43.6852pt too wide) in paragraph at lines 14458--14458 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [191] Overfull \hbox (20.69044pt too wide) in paragraph at lines 14501--14501 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 14517--14517 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [192] [193] [194] [195] Underfull \hbox (badness 10000) in paragraph at lines 14760--14767 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [196] [197] [198] [199] [200] Underfull \hbox (badness 10000) in paragraph at lines 15143--15147 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [201] No file R-exts.vrs. (Concept index) [202] No file R-exts.cps. [203] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl Output written on R-exts.pdf (206 pages, 894825 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: 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/lib/texmf/f onts/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 494--497 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1915--1915 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [25] [26] [27] [28] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2248--2248 []@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 2250--2250 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [29] [30] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2392--2392 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [31] Underfull \hbox (badness 10000) in paragraph at lines 2499--2501 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [32] [33] Overfull \hbox (60.93126pt too wide) in paragraph at lines 2623--2623 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [34] [35] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2750--2752 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] Overfull \hbox (53.86903pt too wide) in paragraph at lines 4589--4589 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 4591--4591 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 4592--4592 [] @texttt if(jvn < 1.8) stop("Java 8 is needed for this package but not avai lable")[] Overfull \hbox (76.86378pt too wide) in paragraph at lines 4602--4602 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [59] [60] [61] [62] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4887--4887 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [63] [64] [65] Overfull \hbox (30.87428pt too wide) in paragraph at lines 5093--5093 []@texttt abs acos atan calloc ceil div exp fabs floor fmod free log malloc me mcpy[] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5094--5094 []@texttt memset pow printf qsort round sin sprintf sqrt strcmp strcpy strerro r[] [66] Overfull \hbox (25.1256pt too wide) in paragraph at lines 5188--5188 []@texttt erf expm1 fmin fmax lgamma lround loglp round snprintf strcasecmp tr unc[] [67] Overfull \hbox (53.86903pt too wide) in paragraph at lines 5220--5220 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [68] [69] [70] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5457--5457 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [71] [72] Chapter 2 [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] Underfull \hbox (badness 10000) in paragraph at lines 6717--6724 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [87] [88] [89] [90] Underfull \hbox (badness 10000) in paragraph at lines 7036--7040 []@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file [91] [92] Chapter 3 [93] [94] [95] [96] [97] [98] [99] Overfull \hbox (20.69044pt too wide) in paragraph at lines 7637--7637 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [100] [101] [102] Chapter 4 [103] [104] [105] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8014--8014 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [106] Overfull \hbox (25.25755pt too wide) in paragraph at lines 8055--8055 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [107] Overfull \hbox (20.53261pt too wide) in paragraph at lines 8159--8159 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] [108] Overfull \hbox (38.96663pt too wide) in paragraph at lines 8189--8198 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [109] [110] [111] Overfull \hbox (44.18301pt too wide) in paragraph at lines 8466--8467 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [112] [113] Overfull \hbox (78.17732pt too wide) in paragraph at lines 8599--8599 []@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 8627--8629 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8640--8640 []@texttt null,object-size,pointer-overflow,return,returns-nonnull-attribute,s hift,[] Overfull \hbox (32.18782pt too wide) in paragraph at lines 8641--8641 []@texttt signed-integer-overflow,unreachable,unsigned-integer-overflow,vla-bo und,vptr[] [114] [115] Overfull \hbox (72.42863pt too wide) in paragraph at lines 8758--8758 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [116] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8807--8807 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8810--8810 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [117] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8889--8889 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [118] [119] Chapter 5 [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] [130] Overfull \hbox (30.87428pt too wide) in paragraph at lines 9854--9854 [] @texttt double *w, int *iper, double *span, double *al pha,[] Overfull \hbox (51.66371pt too wide) in paragraph at lines 9903--9903 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [131] [132] [133] [134] [135] [136] [137] [138] Overfull \hbox (37.93651pt too wide) in paragraph at lines 10481--10481 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11253--11253 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [149] Underfull \hbox (badness 10000) in paragraph at lines 11314--11316 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [150] [151] [152] [153] [154] [155] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11823--11823 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [156] [157] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11946--11946 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [158] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11951--11951 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12006--12006 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12018--12018 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [159] Overfull \hbox (26.43913pt too wide) in paragraph at lines 12117--12117 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [160] [161] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12253--12253 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [162] Overfull \hbox (43.6852pt too wide) in paragraph at lines 12334--12334 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [163] [164] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12421--12421 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] Underfull \hbox (badness 10000) in paragraph at lines 13580--13584 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [178] Warning: unbalanced parentheses in @def... [179] [180] [181] [182] [183] [184] Chapter 7 [185] [186] Chapter 8 [187] [188] [189] Overfull \hbox (43.6852pt too wide) in paragraph at lines 14458--14458 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [190] Overfull \hbox (20.69044pt too wide) in paragraph at lines 14501--14501 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 14517--14517 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [191] [192] [193] [194] Underfull \hbox (badness 10000) in paragraph at lines 14760--14767 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [195] [196] [197] [198] [199] Underfull \hbox (badness 10000) in paragraph at lines 15143--15147 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [200] [201] [202] [203] (Concept index) [204] [205] [206] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmss10.pfb> Output written on R-exts.pdf (213 pages, 957514 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: 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/lib/texmf/f onts/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 494--497 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1915--1915 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [25] [26] [27] [28] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2248--2248 []@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 2250--2250 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [29] [30] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2392--2392 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [31] Underfull \hbox (badness 10000) in paragraph at lines 2499--2501 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [32] [33] Overfull \hbox (60.93126pt too wide) in paragraph at lines 2623--2623 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [34] [35] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2750--2752 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] Overfull \hbox (53.86903pt too wide) in paragraph at lines 4589--4589 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 4591--4591 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 4592--4592 [] @texttt if(jvn < 1.8) stop("Java 8 is needed for this package but not avai lable")[] Overfull \hbox (76.86378pt too wide) in paragraph at lines 4602--4602 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [59] [60] [61] [62] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4887--4887 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [63] [64] [65] Overfull \hbox (30.87428pt too wide) in paragraph at lines 5093--5093 []@texttt abs acos atan calloc ceil div exp fabs floor fmod free log malloc me mcpy[] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5094--5094 []@texttt memset pow printf qsort round sin sprintf sqrt strcmp strcpy strerro r[] [66] Overfull \hbox (25.1256pt too wide) in paragraph at lines 5188--5188 []@texttt erf expm1 fmin fmax lgamma lround loglp round snprintf strcasecmp tr unc[] [67] Overfull \hbox (53.86903pt too wide) in paragraph at lines 5220--5220 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [68] [69] [70] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5457--5457 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [71] [72] Chapter 2 [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] Underfull \hbox (badness 10000) in paragraph at lines 6717--6724 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [87] [88] [89] [90] Underfull \hbox (badness 10000) in paragraph at lines 7036--7040 []@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file [91] [92] Chapter 3 [93] [94] [95] [96] [97] [98] [99] Overfull \hbox (20.69044pt too wide) in paragraph at lines 7637--7637 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [100] [101] [102] Chapter 4 [103] [104] [105] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8014--8014 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [106] Overfull \hbox (25.25755pt too wide) in paragraph at lines 8055--8055 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [107] Overfull \hbox (20.53261pt too wide) in paragraph at lines 8159--8159 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] [108] Overfull \hbox (38.96663pt too wide) in paragraph at lines 8189--8198 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [109] [110] [111] Overfull \hbox (44.18301pt too wide) in paragraph at lines 8466--8467 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [112] [113] Overfull \hbox (78.17732pt too wide) in paragraph at lines 8599--8599 []@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 8627--8629 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8640--8640 []@texttt null,object-size,pointer-overflow,return,returns-nonnull-attribute,s hift,[] Overfull \hbox (32.18782pt too wide) in paragraph at lines 8641--8641 []@texttt signed-integer-overflow,unreachable,unsigned-integer-overflow,vla-bo und,vptr[] [114] [115] Overfull \hbox (72.42863pt too wide) in paragraph at lines 8758--8758 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [116] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8807--8807 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8810--8810 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [117] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8889--8889 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [118] [119] Chapter 5 [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] [130] Overfull \hbox (30.87428pt too wide) in paragraph at lines 9854--9854 [] @texttt double *w, int *iper, double *span, double *al pha,[] Overfull \hbox (51.66371pt too wide) in paragraph at lines 9903--9903 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [131] [132] [133] [134] [135] [136] [137] [138] Overfull \hbox (37.93651pt too wide) in paragraph at lines 10481--10481 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11253--11253 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [149] Underfull \hbox (badness 10000) in paragraph at lines 11314--11316 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [150] [151] [152] [153] [154] [155] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11823--11823 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [156] [157] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11946--11946 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [158] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11951--11951 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12006--12006 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12018--12018 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [159] Overfull \hbox (26.43913pt too wide) in paragraph at lines 12117--12117 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [160] [161] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12253--12253 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [162] Overfull \hbox (43.6852pt too wide) in paragraph at lines 12334--12334 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [163] [164] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12421--12421 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] Underfull \hbox (badness 10000) in paragraph at lines 13580--13584 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [178] Warning: unbalanced parentheses in @def... [179] [180] [181] [182] [183] [184] Chapter 7 [185] [186] Chapter 8 [187] [188] [189] Overfull \hbox (43.6852pt too wide) in paragraph at lines 14458--14458 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [190] Overfull \hbox (20.69044pt too wide) in paragraph at lines 14501--14501 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 14517--14517 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [191] [192] [193] [194] Underfull \hbox (badness 10000) in paragraph at lines 14760--14767 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [195] [196] [197] [198] [199] Underfull \hbox (badness 10000) in paragraph at lines 15143--15147 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [200] [201] [202] [203] (Concept index) [204] [205] [206] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmss10.pfb> Output written on R-exts.pdf (213 pages, 957506 bytes). Transcript written on R-exts.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-FAQ.texi This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/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 2018-01-09.11]: 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] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6 [26] [27] Chapter 7 [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] Writing index file R-FAQ.fn [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3385--3393 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [43] Chapter 8 [44] Chapter 9 [45] [46] Chapter 10 [47] [48] [49] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (51 pages, 367708 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/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 2018-01-09.11]: 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] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6 [26] [27] Chapter 7 [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] Writing index file R-FAQ.fn [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3385--3393 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [43] Chapter 8 [44] Chapter 9 [45] [46] Chapter 10 [47] [48] [49] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (53 pages, 384325 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/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 2018-01-09.11]: 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] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6 [26] [27] Chapter 7 [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] Writing index file R-FAQ.fn [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3385--3393 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [43] Chapter 8 [44] Chapter 9 [45] [46] Chapter 10 [47] [48] [49] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (53 pages, 384323 bytes). Transcript written on R-FAQ.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: 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/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Preface) Cross reference values unknown; you must run TeX again. Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] [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/h ist.pdf> >/doc/manual/images/ecdf.pdf> [38] >/doc/manual/images/QQ.pdf> [39] [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/f ig11.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, 577005 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: 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/lib/texmf/f onts/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/h ist.pdf> >/doc/manual/images/ecdf.pdf> [38] >/doc/manual/images/QQ.pdf> [39] [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/f ig11.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] [102] [103] Appendix E [104] [105] Appendix F [106] [107] ) (see the transcript file for additional information) Output written on R-intro.pdf (113 pages, 626514 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: 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/lib/texmf/f onts/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/h ist.pdf> >/doc/manual/images/ecdf.pdf> [38] >/doc/manual/images/QQ.pdf> [39] [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/f ig11.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] [102] [103] Appendix E [104] [105] Appendix F [106] [107] ) (see the transcript file for additional information) Output written on R-intro.pdf (113 pages, 626581 bytes). Transcript written on R-intro.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-ints.texi This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: 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/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] Overfull \hbox (49.43388pt too wide) in paragraph at lines 1443--1443 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (78.17732pt too wide) in paragraph at lines 1444--1444 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 1445--1445 [] @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 1446--1446 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [18] [19] [20] [21] [22] [23] Chapter 2 [24] Overfull \hbox (26.43913pt too wide) in paragraph at lines 1971--1971 [] @texttt if (!is.character(x)) x <- structure(as.character(x), names = na mes(x))[] [25] [26] [27] [28] Chapter 3 [29] [30] Chapter 4 [31] [32] Chapter 5 [33] Chapter 6 [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] Chapter 7 [47] Underfull \hbox (badness 10000) in paragraph at lines 3619--3628 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3619--3628 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [48] Chapter 8 [49] [50] [51] [52] [53] Underfull \hbox (badness 10000) in paragraph at lines 3994--4002 @texttt CRAN . R-project . org / package=codetools[]@textrm )[][] func-tions u sed for Underfull \hbox (badness 7869) in paragraph at lines 3994--4002 @textrm an-a-lyz-ing pack-age code. E.g., use @texttt _R_CHECK_CODETOOLS_PROFI LE_ Underfull \hbox (badness 10000) in paragraph at lines 3994--4002 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [54] [55] [56] Chapter 9 [57] [58] Chapter 10 [59] Chapter 11 [60] Chapter 12 [61] [62] (Function and variable index) [63] [64] No file R-ints.vrs. (Concept index) [65] No file R-ints.cps. [66] ) (see the transcript file for additional information) Output written on R-ints.pdf (69 pages, 392275 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: 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/lib/texmf/f onts/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] Overfull \hbox (49.43388pt too wide) in paragraph at lines 1443--1443 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (78.17732pt too wide) in paragraph at lines 1444--1444 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 1445--1445 [] @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 1446--1446 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [18] [19] [20] [21] [22] [23] Chapter 2 [24] Overfull \hbox (26.43913pt too wide) in paragraph at lines 1971--1971 [] @texttt if (!is.character(x)) x <- structure(as.character(x), names = na mes(x))[] [25] [26] [27] [28] Chapter 3 [29] [30] Chapter 4 [31] [32] Chapter 5 [33] Chapter 6 [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] Chapter 7 [47] Underfull \hbox (badness 10000) in paragraph at lines 3619--3628 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3619--3628 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [48] Chapter 8 [49] [50] [51] [52] [53] Underfull \hbox (badness 10000) in paragraph at lines 3994--4002 @texttt CRAN . R-project . org / package=codetools[]@textrm )[][] func-tions u sed for Underfull \hbox (badness 7869) in paragraph at lines 3994--4002 @textrm an-a-lyz-ing pack-age code. E.g., use @texttt _R_CHECK_CODETOOLS_PROFI LE_ Underfull \hbox (badness 10000) in paragraph at lines 3994--4002 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [54] [55] [56] Chapter 9 [57] [58] Chapter 10 [59] Chapter 11 [60] Chapter 12 [61] [62] (Function and variable index) [63] [64] [65] (Concept index) [66] [67] ) (see the transcript file for additional information) Output written on R-ints.pdf (72 pages, 440580 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: 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/lib/texmf/f onts/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] Overfull \hbox (49.43388pt too wide) in paragraph at lines 1443--1443 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (78.17732pt too wide) in paragraph at lines 1444--1444 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 1445--1445 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (158.65895pt too wide) in paragraph at lines 1446--1446 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [18] [19] [20] [21] [22] [23] Chapter 2 [24] Overfull \hbox (26.43913pt too wide) in paragraph at lines 1971--1971 [] @texttt if (!is.character(x)) x <- structure(as.character(x), names = na mes(x))[] [25] [26] [27] [28] Chapter 3 [29] [30] Chapter 4 [31] [32] Chapter 5 [33] Chapter 6 [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] Chapter 7 [47] Underfull \hbox (badness 10000) in paragraph at lines 3619--3628 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3619--3628 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [48] Chapter 8 [49] [50] [51] [52] [53] Underfull \hbox (badness 10000) in paragraph at lines 3994--4002 @texttt CRAN . R-project . org / package=codetools[]@textrm )[][] func-tions u sed for Underfull \hbox (badness 7869) in paragraph at lines 3994--4002 @textrm an-a-lyz-ing pack-age code. E.g., use @texttt _R_CHECK_CODETOOLS_PROFI LE_ Underfull \hbox (badness 10000) in paragraph at lines 3994--4002 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [54] [55] [56] Chapter 9 [57] [58] Chapter 10 [59] Chapter 11 [60] Chapter 12 [61] [62] (Function and variable index) [63] [64] [65] (Concept index) [66] [67] ) (see the transcript file for additional information) Output written on R-ints.pdf (72 pages, 440580 bytes). Transcript written on R-ints.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-lang.texi This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: 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/lib/texmf/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-lang.cp Chapter 2 [1] [2] Cross reference values unknown; you must run TeX again. Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [4] [5] [6] [7] [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, 330526 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: 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/lib/texmf/f onts/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] [60] (Concept Index) [61] [62] Overfull \vbox (1.73251pt too high) has occurred while \output is active Overfull \vbox (1.73251pt too high) has occurred while \output is active Appendix A [63] [64] ) (see the transcript file for additional information) Output written on R-lang.pdf (69 pages, 379630 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/<>/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2018-01-09.11]: 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/lib/texmf/f onts/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] [60] (Concept Index) [61] [62] Overfull \vbox (1.73251pt too high) has occurred while \output is active Overfull \vbox (1.73251pt too high) has occurred while \output is active Appendix A [63] [64] ) (see the transcript file for additional information) Output written on R-lang.pdf (69 pages, 379624 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 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./fullrefman.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h 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/ts1enc.def)) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.112, 2017/01/04 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/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 366. 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(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/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 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 296--300 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 385--388 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 533--539 []\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 1144--1147 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1901--1901 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2086--2088 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] Underfull \vbox (badness 10000) has occurred while \output is active [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3607--3609 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] [60] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3848--3848 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] Underfull \hbox (badness 2521) in paragraph at lines 4823--4825 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] Overfull \hbox (5.27168pt too wide) in paragraph at lines 5954--5954 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [94] [95] [96] Underfull \hbox (badness 2096) in paragraph at lines 6137--6150 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [97] [98] [99] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6341--6343 []\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 : [100] [101] Underfull \hbox (badness 10000) in paragraph at lines 6483--6486 []\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 [102] [103] Underfull \hbox (badness 1442) in paragraph at lines 6646--6652 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6646--6652 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6646--6652 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [104] Underfull \hbox (badness 3568) in paragraph at lines 6708--6715 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [105] [106] Underfull \vbox (badness 10000) has occurred while \output is active [107] [108] [109] Underfull \hbox (badness 1077) in paragraph at lines 7019--7025 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7019--7025 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [110] [111] [112] [113] [114] Underfull \hbox (badness 2096) in paragraph at lines 7360--7364 \T1/zi4/m/n/10 status _ codes$[][] \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 . [115] [116] Underfull \hbox (badness 3000) in paragraph at lines 7453--7455 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7478--7481 [][][]\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 , [117] [118] [119] [120] Underfull \hbox (badness 10000) in paragraph at lines 7733--7743 []\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing [121] [122] Underfull \hbox (badness 4479) in paragraph at lines 7804--7814 [][][]\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), [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] Underfull \hbox (badness 1394) in paragraph at lines 9477--9482 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [148] [149] [150] [151] [152] Underfull \hbox (badness 1194) in paragraph at lines 9822--9827 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 9822--9827 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [153] [154] Underfull \hbox (badness 1735) in paragraph at lines 9960--9964 \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 . [155] [156] [157] [158] [159] [160] [161] Underfull \hbox (badness 2150) in paragraph at lines 10375--10378 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 6396) in paragraph at lines 10389--10397 []\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 2735) in paragraph at lines 10429--10436 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] Underfull \hbox (badness 4569) in paragraph at lines 11495--11499 []\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 11495--11499 \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 [178] [179] [180] [181] [182] [183] [184] [185] [186] Underfull \hbox (badness 2698) in paragraph at lines 12072--12081 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 12072--12081 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [187] [188] [189] [190] [191] Underfull \vbox (badness 3803) has occurred while \output is active [192] [193] [194] [195] [196] Underfull \hbox (badness 6236) in paragraph at lines 12731--12734 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [197] [198] [199] [200] [201] [202] Underfull \hbox (badness 2253) in paragraph at lines 13143--13145 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [203] Underfull \hbox (badness 1565) in paragraph at lines 13214--13218 [][][]\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 [204] Underfull \hbox (badness 10000) in paragraph at lines 13258--13260 []\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 [205] [206] Underfull \hbox (badness 1466) in paragraph at lines 13398--13401 []\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 [207] [208] Underfull \hbox (badness 10000) in paragraph at lines 13517--13521 [][][]\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 13528--13531 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [209] [210] [211] [212] Underfull \hbox (badness 3965) in paragraph at lines 13791--13795 []\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, [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] Underfull \hbox (badness 4429) in paragraph at lines 14553--14556 []\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 [225] [226] Underfull \hbox (badness 10000) in paragraph at lines 14653--14655 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14659--14663 []\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 10000) in paragraph at lines 14698--14702 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 14698--14702 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] Underfull \hbox (badness 2452) in paragraph at lines 15287--15291 []\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 15287--15291 \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 [237] [238] [239] Underfull \hbox (badness 1092) in paragraph at lines 15460--15465 [][]\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 [240] [241] [242] Underfull \hbox (badness 6741) in paragraph at lines 15708--15712 \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 , [243] [244] [245] [246] [247] Underfull \hbox (badness 1867) in paragraph at lines 16014--16021 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [248] [249] [250] [251] Underfull \vbox (badness 10000) has occurred while \output is active [252] [253] [254] Underfull \hbox (badness 3679) in paragraph at lines 16424--16426 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [255] [256] [257] [258] [259] [260] [261] [262] Underfull \hbox (badness 1478) in paragraph at lines 16979--16982 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [263] [264] [265] Underfull \hbox (badness 10000) in paragraph at lines 17232--17234 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] Underfull \hbox (badness 1442) in paragraph at lines 17822--17824 []\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 [276] Underfull \hbox (badness 2452) in paragraph at lines 17914--17930 [][][]\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 , [277] [278] [279] [280] [281] [282] [283] Underfull \hbox (badness 1248) in paragraph at lines 18328--18331 []\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 , [284] [285] [286] [287] Underfull \hbox (badness 4739) in paragraph at lines 18586--18588 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] Underfull \hbox (badness 2469) in paragraph at lines 19603--19608 []\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 19617--19624 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [305] Underfull \hbox (badness 10000) in paragraph at lines 19691--19695 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 19691--19695 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$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 ' [306] [307] Underfull \hbox (badness 1509) in paragraph at lines 19826--19833 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 19826--19833 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19842--19847 []\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 [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] Underfull \hbox (badness 1264) in paragraph at lines 20575--20580 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [319] Underfull \hbox (badness 4441) in paragraph at lines 20604--20607 []\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 , [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] Underfull \hbox (badness 10000) in paragraph at lines 21330--21332 []\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 [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] Underfull \hbox (badness 1077) in paragraph at lines 22365--22371 \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 . [347] [348] [349] Underfull \hbox (badness 1484) in paragraph at lines 22526--22534 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [350] [351] [352] [353] Underfull \hbox (badness 2790) in paragraph at lines 22797--22800 []\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 22797--22800 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [354] [355] [356] [357] Underfull \hbox (badness 1194) in paragraph at lines 23079--23082 []\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 [358] [359] [360] [361] Underfull \hbox (badness 10000) in paragraph at lines 23285--23291 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23285--23291 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23295--23298 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23295--23298 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] [373] [374] [375] Underfull \hbox (badness 10000) in paragraph at lines 24245--24247 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [376] [377] [378] [379] Underfull \hbox (badness 1199) in paragraph at lines 24489--24495 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24489--24495 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [380] [381] [382] [383] [384] [385] [386] [387] [388] Underfull \hbox (badness 1038) in paragraph at lines 25068--25076 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 1881) in paragraph at lines 25077--25080 []\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 25096--25098 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [389] Underfull \hbox (badness 10000) in paragraph at lines 25205--25215 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25216--25222 []\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 [390] Underfull \hbox (badness 1968) in paragraph at lines 25252--25257 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 25262--25264 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [391] [392] [393] Underfull \hbox (badness 10000) in paragraph at lines 25521--25527 []\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 25521--25527 \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 25521--25527 \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 25534--25537 []\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 25558--25560 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [394] Underfull \hbox (badness 10000) in paragraph at lines 25590--25595 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 25596--25607 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 25608--25611 []\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 3713) in paragraph at lines 25618--25630 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 25618--25630 \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). Underfull \hbox (badness 2351) in paragraph at lines 25618--25630 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25632--25639 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 25632--25639 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 25632--25639 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1874) in paragraph at lines 25632--25639 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [395] [396] [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 25979--25983 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 25979--25983 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [400] [401] [402] [403] [404] Underfull \hbox (badness 1735) in paragraph at lines 26297--26301 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] Underfull \hbox (badness 2726) in paragraph at lines 26868--26871 []\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 [415] [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] [427] Underfull \hbox (badness 1052) in paragraph at lines 27695--27700 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [428] [429] [430] [431] [432] Underfull \vbox (badness 10000) has occurred while \output is active [433] [434] [435] [436] [437] [438] [439] Underfull \hbox (badness 1533) in paragraph at lines 28504--28507 []\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 [440] [441] [442] Underfull \hbox (badness 1163) in paragraph at lines 28666--28677 []\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 [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] Underfull \hbox (badness 10000) in paragraph at lines 30189--30193 []\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 30189--30193 \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 30211--30213 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [467] [468] [469] [470] [471] [472] [473] [474] [475] Underfull \hbox (badness 1655) in paragraph at lines 30759--30761 []\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 [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] Underfull \hbox (badness 10000) in paragraph at lines 31434--31438 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [487] [488] [489] [490] Underfull \hbox (badness 2302) in paragraph at lines 31674--31681 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 31674--31681 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 3333) in paragraph at lines 31674--31681 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 31674--31681 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [491] [492] Underfull \hbox (badness 2261) in paragraph at lines 31830--31835 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if Underfull \hbox (badness 10000) in paragraph at lines 31857--31863 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [493] Underfull \hbox (badness 10000) in paragraph at lines 31933--31938 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] Underfull \vbox (badness 3803) has occurred while \output is active [533] [534] [535] [536] [537] [538] [539] [540] Underfull \hbox (badness 1072) in paragraph at lines 34971--34975 []\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 34976--34980 []\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 35004--35010 []\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 35004--35010 \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 35004--35010 \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 [541] Underfull \hbox (badness 3343) in paragraph at lines 35016--35023 \T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 35016--35023 \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 35016--35023 \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 [542] [543] [544] [545] Underfull \hbox (badness 10000) in paragraph at lines 35314--35320 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35314--35320 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] Underfull \hbox (badness 3333) in paragraph at lines 37158--37163 []\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 [576] [577] [578] [579] [580] [581] Underfull \vbox (badness 10000) has occurred while \output is active [582] [583] [584] [585] Underfull \hbox (badness 1472) in paragraph at lines 37781--37784 []\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 [586] [587] [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] Underfull \vbox (badness 3803) has occurred while \output is active [599] Underfull \hbox (badness 10000) in paragraph at lines 38646--38650 []\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., [600] [601] [602] [603] Underfull \hbox (badness 10000) in paragraph at lines 38894--38897 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [604] [605] Underfull \hbox (badness 10000) in paragraph at lines 39012--39016 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [606] Underfull \hbox (badness 10000) in paragraph at lines 39074--39078 [][][]\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 \ [][]$\T1/zi4/m/n/10 https : / / developer . [607] [608] [609] [610] [611] [612] [613] [614] Underfull \hbox (badness 4013) in paragraph at lines 39619--39621 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [615] [616] [617] [618] [619] [620] Underfull \vbox (badness 10000) has occurred while \output is active [621] [622] [623] [624] [625] [626] [627] Underfull \hbox (badness 3460) in paragraph at lines 40480--40483 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via [628] Underfull \hbox (badness 1990) in paragraph at lines 40487--40495 []\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 40487--40495 \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 [629] [630] [631] [632] Underfull \hbox (badness 10000) in paragraph at lines 40764--40767 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [633] [634] [635] Underfull \hbox (badness 1917) in paragraph at lines 40992--40999 []\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 [636] [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] Underfull \hbox (badness 3668) in paragraph at lines 41671--41673 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [647] Underfull \hbox (badness 2401) in paragraph at lines 41777--41781 []\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 [648] [649] [650] Underfull \hbox (badness 2111) in paragraph at lines 41953--41958 \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. [651] Underfull \hbox (badness 7362) in paragraph at lines 41969--41974 []\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 [652] [653] [654] [655] [656] [657] [658] [659] [660] Underfull \hbox (badness 5417) in paragraph at lines 42526--42530 []\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 [661] Underfull \hbox (badness 10000) in paragraph at lines 42587--42591 []\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 [662]) (./compiler-pkg.tex Chapter 2. [663] [664] [665] [666]) (./datasets-pkg.tex Chapter 3. [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] Underfull \vbox (badness 1515) has occurred while \output is active [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] Underfull \hbox (badness 6658) in paragraph at lines 3954--3956 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h ttp : / / www . ltrr . arizona . edu / ~hallman / [734] Underfull \vbox (badness 10000) has occurred while \output is active [735] [736] [737] [738] Underfull \vbox (badness 10000) has occurred while \output is active [739] [740] [741] [742] [743] [744] Overfull \vbox (18.9959pt too high) has occurred while \output is active [745] [746] [747]) (./grDevices-pkg.tex [748] Chapter 4. [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] Underfull \hbox (badness 5175) in paragraph at lines 1069--1071 []\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 [766] [767] [768] [769] Underfull \hbox (badness 1852) in paragraph at lines 1266--1269 []\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 [770] [771] [772] Underfull \hbox (badness 1490) in paragraph at lines 1472--1477 \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 [773] [774] Underfull \hbox (badness 10000) in paragraph at lines 1595--1599 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [775] [776] [777] [778] Underfull \hbox (badness 1325) in paragraph at lines 1878--1888 \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 , [779] [780] Underfull \hbox (badness 10000) in paragraph at lines 1983--1985 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [781] [782] [783] Underfull \hbox (badness 6758) in paragraph at lines 2144--2147 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [784] [785] [786] [787] [788] [789] [790] [791] [792] Underfull \hbox (badness 10000) in paragraph at lines 2737--2738 [793] [794] [795] [796] [797] [798] [799] [800] Underfull \hbox (badness 10000) in paragraph at lines 3235--3240 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [801] [802] [803] [804] Underfull \hbox (badness 3302) in paragraph at lines 3494--3497 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3508--3510 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] [816] [817] Underfull \hbox (badness 1067) in paragraph at lines 4331--4338 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [818] [819] Underfull \hbox (badness 3364) in paragraph at lines 4491--4493 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$ \T1/zi4/m/n/10 https : / / partners . adobe . com / public / [820] Underfull \hbox (badness 1789) in paragraph at lines 4568--4570 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [821] Underfull \hbox (badness 1377) in paragraph at lines 4618--4623 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [822] Underfull \hbox (badness 2671) in paragraph at lines 4645--4653 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4694--4701 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4702--4711 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4702--4711 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4712--4714 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [823] [824] Underfull \hbox (badness 1377) in paragraph at lines 4823--4828 []\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 [825] Underfull \hbox (badness 7344) in paragraph at lines 4883--4885 []\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 [826] [827] Underfull \hbox (badness 2035) in paragraph at lines 5007--5016 []\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 5007--5016 \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 5007--5016 \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 , [828] Underfull \hbox (badness 10000) in paragraph at lines 5075--5082 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5075--5082 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [829] [830] [831] Underfull \hbox (badness 1546) in paragraph at lines 5217--5225 []\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 , [832] Underfull \hbox (badness 1648) in paragraph at lines 5294--5298 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [833] [834] [835] [836] [837] [838] [839] Underfull \hbox (badness 10000) in paragraph at lines 5746--5749 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [840] [841] [842] [843] [844] [845] Underfull \hbox (badness 1189) in paragraph at lines 6143--6145 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [846] [847] Underfull \hbox (badness 10000) in paragraph at lines 6241--6243 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [848] [849] [850] [851] Underfull \hbox (badness 3780) in paragraph at lines 6532--6538 []\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 , [852] [853] [854] Underfull \hbox (badness 2680) in paragraph at lines 6733--6735 []\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 [855] [856] [857]) (./graphics-pkg.tex [858] Chapter 5. [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] [869] Underfull \hbox (badness 10000) in paragraph at lines 683--690 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [870] [871] [872] [873] Underfull \vbox (badness 3803) has occurred while \output is active [874] [875] [876] [877] [878] [879] Underfull \hbox (badness 4634) in paragraph at lines 1255--1258 [][][]\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 , [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] [894] [895] [896] Underfull \hbox (badness 1009) in paragraph at lines 2289--2296 \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 [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] Underfull \vbox (badness 10000) has occurred while \output is active [919] [920] [921] [922] Underfull \hbox (badness 1867) in paragraph at lines 3931--3935 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [923] [924] [925] [926] [927] [928] [929] [930] Underfull \hbox (badness 1924) in paragraph at lines 4378--4383 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain Underfull \hbox (badness 2529) in paragraph at lines 4409--4412 []\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 [931] [932] [933] [934] [935] Underfull \hbox (badness 10000) in paragraph at lines 4759--4765 []\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 4759--4765 \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 [936] [937] Underfull \hbox (badness 10000) in paragraph at lines 4890--4893 [938 >/library/graphics/help/figures/mai.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 4951--4953 Underfull \vbox (badness 10000) has occurred while \output is active [939] [940 >/library/graphics/help/figures/oma.pdf>] [941] Underfull \hbox (badness 10000) in paragraph at lines 5141--5143 []\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 [942] Underfull \vbox (badness 3803) has occurred while \output is active [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6612--6613 [][] [965] [966 >/library/graphics/help/figures/pch .pdf>] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] Underfull \hbox (badness 1048) in paragraph at lines 7321--7326 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [977] [978] Underfull \hbox (badness 1102) in paragraph at lines 7437--7440 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] Underfull \hbox (badness 1043) in paragraph at lines 8272--8276 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [993] [994] [995] [996] [997] [998] [999] Underfull \hbox (badness 10000) in paragraph at lines 8675--8677 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8677--8679 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1000]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8757 \HeaderA{units}{Graphical Units}{units} [1001] [1002] [1003] [1004]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1005] [1006] [1007] [1008] [1009] [1010] Underfull \hbox (badness 2680) in paragraph at lines 390--393 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] Underfull \hbox (badness 4279) in paragraph at lines 970--979 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] Underfull \vbox (badness 3803) has occurred while \output is active [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] Underfull \hbox (badness 1067) in paragraph at lines 4340--4343 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1078] [1079] [1080] [1081] Underfull \hbox (badness 7256) in paragraph at lines 4585--4587 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] Underfull \hbox (badness 10000) in paragraph at lines 5862--5868 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] Underfull \hbox (badness 7649) in paragraph at lines 6341--6344 []\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 [1112] [1113] [1114] [1115]) (./methods-pkg.tex [1116] Chapter 7. [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] Underfull \vbox (badness 3803) has occurred while \output is active [1125] Underfull \vbox (badness 10000) has occurred while \output is active [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] Underfull \hbox (badness 2237) in paragraph at lines 1386--1388 []\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 [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] Underfull \hbox (badness 1077) in paragraph at lines 1933--1940 []\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 [1144] Underfull \hbox (badness 10000) in paragraph at lines 1982--1987 []\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 1982--1987 \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 [1145] [1146] [1147] Underfull \hbox (badness 1242) in paragraph at lines 2215--2220 []\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 = [1148] [1149] [1150] [1151] [1152] Underfull \hbox (badness 10000) in paragraph at lines 2575--2578 []\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 [1153] [1154] Underfull \hbox (badness 1132) in paragraph at lines 2715--2719 []\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 [1155] Underfull \hbox (badness 1033) in paragraph at lines 2747--2752 \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 [1156] [1157] [1158] [1159] [1160] [1161] [1162] Underfull \hbox (badness 1102) in paragraph at lines 3304--3306 []\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 [1163] [1164] [1165] [1166] [1167] [1168] Underfull \hbox (badness 10000) in paragraph at lines 3637--3642 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Underfull \hbox (badness 10000) in paragraph at lines 3645--3654 []\T1/ptm/m/n/10 The [1169] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3765--3766 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3765--3766 [1170] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3849--3850 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] Underfull \hbox (badness 1436) in paragraph at lines 4446--4449 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4475--4481 []\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 4475--4481 \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 [1181] Underfull \hbox (badness 1092) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] Underfull \vbox (badness 10000) has occurred while \output is active [1191] [1192] Underfull \hbox (badness 10000) in paragraph at lines 5358--5359 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1193] Underfull \hbox (badness 4036) in paragraph at lines 5440--5443 []\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 [1194] Underfull \hbox (badness 3803) in paragraph at lines 5515--5517 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1195] [1196] [1197] [1198] Underfull \hbox (badness 1087) in paragraph at lines 5747--5752 []\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 [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] Underfull \hbox (badness 1675) in paragraph at lines 6454--6460 \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 [1207] [1208] [1209] [1210] Underfull \vbox (badness 10000) has occurred while \output is active [1211] [1212] [1213] [1214]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6976 \aliasA{S4}{S3Part}{S4} [1215] [1216] [1217]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7232 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7234 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7235 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7237 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7238 \aliasA{Summary}{S4groupGeneric}{Summary} [1218] Underfull \hbox (badness 2050) in paragraph at lines 7299--7303 []\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 [1219] [1220] [1221] Underfull \hbox (badness 1286) in paragraph at lines 7487--7489 []\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 [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] Underfull \vbox (badness 10000) has occurred while \output is active [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] Underfull \hbox (badness 1852) in paragraph at lines 10567--10571 []\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., [1264] [1265] [1266] [1267]) (./parallel-pkg.tex [1268] 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 [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] Underfull \hbox (badness 3386) in paragraph at lines 1268--1271 []\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 [1289] [1290] [1291]) (./splines-pkg.tex [1292] 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 [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] [1306] [1307]) (./stats-pkg.tex [1308] Chapter 10. [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] Underfull \hbox (badness 1412) in paragraph at lines 848--850 []\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 [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] Underfull \hbox (badness 2503) in paragraph at lines 1329--1332 []\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 , [1330] [1331] [1332] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 3965) in paragraph at lines 2168--2170 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1344] [1345] [1346] [1347] [1348] Underfull \hbox (badness 3965) in paragraph at lines 2510--2512 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] Underfull \hbox (badness 2726) in paragraph at lines 3224--3240 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1360] [1361] Underfull \hbox (badness 2503) in paragraph at lines 3354--3357 []\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 , [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] Underfull \hbox (badness 3989) in paragraph at lines 4582--4589 []\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 = [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] Underfull \hbox (badness 2556) in paragraph at lines 5193--5196 []\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 5210--5212 []\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 [1392] [1393] [1394] [1395] Underfull \hbox (badness 1142) in paragraph at lines 5451--5463 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1396] [1397] [1398] Underfull \hbox (badness 2503) in paragraph at lines 5599--5603 []\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 , [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] Underfull \hbox (badness 8132) in paragraph at lines 6102--6107 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1407] [1408] [1409] [1410] [1411] Underfull \hbox (badness 7081) in paragraph at lines 6380--6383 []\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 6384--6386 []\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 [1412] [1413] [1414] [1415] [1416] Underfull \vbox (badness 3803) has occurred while \output is active [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 10000) in paragraph at lines 7225--7228 []\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 [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] Underfull \hbox (badness 2626) in paragraph at lines 8860--8863 []\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 [1452] Underfull \hbox (badness 2503) in paragraph at lines 8960--8964 []\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 , [1453] [1454] [1455] [1456] [1457] [1458] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9309--9311 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] Underfull \hbox (badness 4518) in paragraph at lines 10235--10240 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1473] [1474] [1475] [1476] [1477] Underfull \hbox (badness 2142) in paragraph at lines 10577--10580 []\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 10596--10599 []\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, [1478] Underfull \hbox (badness 1708) in paragraph at lines 10658--10662 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1479] [1480] [1481] [1482] [1483] [1484] Underfull \hbox (badness 1694) in paragraph at lines 11054--11057 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1485] Underfull \hbox (badness 1867) in paragraph at lines 11073--11082 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1486] [1487] [1488] [1489] [1490] Underfull \hbox (badness 10000) in paragraph at lines 11380--11383 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1491] [1492]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.hat}) has been already used, duplicate ignored \relax l.11534 \aliasA{hat}{influence.measures}{hat} [1493] [1494] Underfull \hbox (badness 1484) in paragraph at lines 11665--11667 []\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 [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] Underfull \hbox (badness 4441) in paragraph at lines 12248--12250 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12255--12257 []\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 [1505] [1506] [1507] [1508] [1509] [1510] Underfull \hbox (badness 2894) in paragraph at lines 12589--12593 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] Underfull \hbox (badness 4518) in paragraph at lines 13287--13292 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] Underfull \hbox (badness 4518) in paragraph at lines 13934--13939 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1532] [1533] [1534] Underfull \hbox (badness 10000) in paragraph at lines 14072--14076 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14079--14081 []\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 [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] Underfull \hbox (badness 2503) in paragraph at lines 15141--15145 []\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 , [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] Underfull \hbox (badness 1584) in paragraph at lines 15653--15659 []\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 [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] Underfull \hbox (badness 2359) in paragraph at lines 17290--17292 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1587] Underfull \vbox (badness 3803) has occurred while \output is active [1588] Underfull \vbox (badness 10000) has occurred while \output is active [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] Underfull \hbox (badness 1377) in paragraph at lines 18201--18206 []\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 18206--18209 []\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 [1602] Underfull \hbox (badness 1454) in paragraph at lines 18219--18223 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18227--18231 []\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 [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] Underfull \hbox (badness 1337) in paragraph at lines 18843--18846 []\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 [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] Underfull \hbox (badness 3049) in paragraph at lines 19329--19333 []\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 [1622] [1623] [1624] [1625] Underfull \hbox (badness 5563) in paragraph at lines 19579--19581 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19582--19585 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1626] [1627] [1628] [1629] [1630] [1631] Underfull \hbox (badness 2503) in paragraph at lines 19957--19960 []\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 , [1632] Underfull \hbox (badness 10000) in paragraph at lines 19984--19986 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648] [1649] [1650] Underfull \hbox (badness 10000) in paragraph at lines 21047--21053 []\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 , [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] Underfull \hbox (badness 1337) in paragraph at lines 22385--22391 []\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 [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] Overfull \hbox (27.74408pt too wide) in paragraph at lines 22930--22930 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1681] [1682] [1683] [1684] [1685] Underfull \hbox (badness 10000) in paragraph at lines 23180--23183 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1686] [1687] [1688] [1689] [1690] [1691] [1692] [1693] [1694] Underfull \hbox (badness 10000) in paragraph at lines 23765--23768 []\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 [1695] Underfull \hbox (badness 3690) in paragraph at lines 23816--23820 [][][]\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 [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] Underfull \hbox (badness 3439) in paragraph at lines 24286--24292 [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1 0 , [1705] [1706] [1707] Underfull \hbox (badness 1867) in paragraph at lines 24483--24485 []\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 24496--24500 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 24496--24500 \T1/zi4/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was Underfull \hbox (badness 1132) in paragraph at lines 24496--24500 \T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o f un-de-ter-mined co-ef-fi-cients, e.g., for [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] Underfull \hbox (badness 10000) in paragraph at lines 24968--24973 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732] Underfull \hbox (badness 3514) in paragraph at lines 26010--26015 []\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 [1733] Underfull \hbox (badness 3514) in paragraph at lines 26072--26077 []\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 [1734] Underfull \hbox (badness 3514) in paragraph at lines 26129--26134 []\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 [1735] Underfull \hbox (badness 3514) in paragraph at lines 26190--26196 []\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 [1736] [1737] [1738] [1739] Underfull \hbox (badness 3514) in paragraph at lines 26403--26408 []\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 [1740] Underfull \hbox (badness 3514) in paragraph at lines 26459--26464 []\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 [1741] Underfull \hbox (badness 3514) in paragraph at lines 26517--26522 []\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 [1742] Underfull \hbox (badness 3514) in paragraph at lines 26572--26577 []\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 [1743] Underfull \hbox (badness 6691) in paragraph at lines 26641--26646 []\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 [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751] [1752] Underfull \hbox (badness 10000) in paragraph at lines 27165--27168 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27165--27168 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] Underfull \hbox (badness 5431) in paragraph at lines 27771--27773 []\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 [1763] [1764] [1765] Underfull \hbox (badness 5431) in paragraph at lines 27981--27984 []\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 [1766] [1767] [1768] [1769] [1770] [1771] Underfull \hbox (badness 1337) in paragraph at lines 28295--28299 []\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 [1772] [1773] Underfull \hbox (badness 10000) in paragraph at lines 28412--28415 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1774] [1775] Underfull \hbox (badness 1616) in paragraph at lines 28595--28598 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1776] [1777] [1778] [1779] [1780] [1781] [1782] [1783] [1784] [1785] [1786] [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] Underfull \hbox (badness 10000) in paragraph at lines 29721--29725 []\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 [1795] [1796] [1797] Underfull \vbox (badness 10000) has occurred while \output is active [1798] [1799] [1800] Underfull \hbox (badness 1337) in paragraph at lines 30085--30089 []\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 [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] Underfull \hbox (badness 1337) in paragraph at lines 30569--30573 []\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 [1809] Underfull \hbox (badness 2142) in paragraph at lines 30646--30651 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the [1810] Underfull \hbox (badness 5161) in paragraph at lines 30668--30670 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1811] [1812] [1813] [1814] [1815] [1816] Underfull \hbox (badness 10000) in paragraph at lines 31050--31055 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1817] [1818]) (./stats4-pkg.tex Chapter 11. [1819] [1820] [1821] [1822] [1823] [1824]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} [1825] [1826] [1827] [1828]) (./tcltk-pkg.tex Chapter 12. [1829] [1830] [1831] [1832] [1833] [1834] [1835] Underfull \vbox (badness 10000) has occurred while \output is active [1836] Underfull \vbox (badness 10000) has occurred while \output is active [1837] 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 [1838] [1839] [1840] [1841] [1842] [1843] [1844] [1845] [1846] [1847] [1848] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1849]) (./tools-pkg.tex [1850] Chapter 13. [1851] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1852] 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 [1853] [1854] 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 [1855] [1856] 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 [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] Underfull \hbox (badness 1635) in paragraph at lines 1054--1056 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1868] Underfull \hbox (badness 4441) in paragraph at lines 1132--1142 \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- [1869] Underfull \hbox (badness 1014) in paragraph at lines 1154--1156 []\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 1160--1162 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1197--1200 []\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 1197--1200 \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 , [1870] [1871] [1872] Underfull \hbox (badness 10000) in paragraph at lines 1366--1368 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1873] [1874] [1875] Underfull \hbox (badness 2293) in paragraph at lines 1540--1542 []\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 [1876] [1877] Underfull \hbox (badness 7981) in paragraph at lines 1678--1683 []\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 1685--1687 []\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 [1878] [1879] [1880] [1881]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1882 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1882] [1883] [1884] [1885] [1886] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2184--2184 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1887] [1888] [1889] Underfull \hbox (badness 7981) in paragraph at lines 2353--2359 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1890] [1891] [1892] [1893] [1894] [1895] [1896] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2818. [1897] [1898] [1899] [1900] Underfull \hbox (badness 1424) in paragraph at lines 3100--3102 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1901] [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] [1910] [1911] [1912] Underfull \hbox (badness 10000) in paragraph at lines 3800--3802 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1913] [1914] Underfull \hbox (badness 10000) in paragraph at lines 3939--3942 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1915] [1916] Underfull \hbox (badness 1137) in paragraph at lines 4037--4039 []\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 [1917] [1918] [1919] Underfull \hbox (badness 1838) in paragraph at lines 4246--4252 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4246--4252 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1920] Underfull \hbox (badness 5726) in paragraph at lines 4326--4331 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4326--4331 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1921] [1922] [1923] Underfull \hbox (badness 2197) in paragraph at lines 4475--4485 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4475--4485 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1924] Underfull \hbox (badness 1571) in paragraph at lines 4538--4542 []\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 [1925] [1926] [1927]) (./utils-pkg.tex [1928] Chapter 14. [1929] Underfull \hbox (badness 2556) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1930] [1931] [1932] [1933] [1934] [1935] [1936] Underfull \hbox (badness 10000) in paragraph at lines 546--552 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 546--552 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1937] [1938] Underfull \hbox (badness 5847) in paragraph at lines 660--666 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 660--666 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1939] Underfull \hbox (badness 3861) in paragraph at lines 728--733 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1940] [1941] [1942] Underfull \hbox (badness 1430) in paragraph at lines 893--900 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 893--900 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 893--900 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 893--900 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 904--906 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1943] [1944] [1945] [1946] [1947] [1948] [1949] Underfull \hbox (badness 1371) in paragraph at lines 1375--1377 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 2057) in paragraph at lines 1863--1865 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1958] Underfull \hbox (badness 10000) in paragraph at lines 1958--1960 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1959] [1960] Underfull \hbox (badness 5189) in paragraph at lines 2060--2062 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1961] Underfull \vbox (badness 3803) has occurred while \output is active [1962] [1963] [1964] Underfull \hbox (badness 1661) in paragraph at lines 2278--2285 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2294--2297 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1965] [1966] [1967] [1968] [1969] [1970] Underfull \hbox (badness 10000) in paragraph at lines 2703--2707 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2708--2711 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1971] [1972] [1973] [1974] [1975] [1976] [1977] [1978] [1979] [1980] [1981] Underfull \hbox (badness 1430) in paragraph at lines 3385--3393 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 1231) in paragraph at lines 3434--3440 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1982] [1983] [1984] [1985] [1986] [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4274 ...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.4274 ...mat Unordered and Ordered Lists}{format} [1996] [1997] [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] Underfull \hbox (badness 1371) in paragraph at lines 5271--5273 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [2012] Underfull \hbox (badness 1502) in paragraph at lines 5360--5365 []\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 5360--5365 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2013] [2014] [2015] Underfull \hbox (badness 10000) in paragraph at lines 5533--5542 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2016] Underfull \hbox (badness 2150) in paragraph at lines 5596--5599 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2017] [2018] Underfull \hbox (badness 3118) in paragraph at lines 5733--5735 []\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 Underfull \hbox (badness 2409) in paragraph at lines 5766--5770 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [2019] [2020] Underfull \hbox (badness 1325) in paragraph at lines 5874--5878 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [2021] Underfull \hbox (badness 10000) in paragraph at lines 5957--5960 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 5957--5960 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2022] Underfull \hbox (badness 3219) in paragraph at lines 6030--6037 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6030--6037 \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 6030--6037 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [2023] Underfull \hbox (badness 10000) in paragraph at lines 6110--6115 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] [2047] Underfull \hbox (badness 10000) in paragraph at lines 7527--7529 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7532--7537 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] Underfull \hbox (badness 1789) in paragraph at lines 8087--8089 []\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 [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] Underfull \hbox (badness 1097) in paragraph at lines 8916--8919 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2069] Underfull \hbox (badness 3000) in paragraph at lines 9052--9057 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] Underfull \hbox (badness 2134) in paragraph at lines 9635--9640 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2079] [2080] [2081] [2082] [2083] [2084] [2085] Underfull \hbox (badness 5077) in paragraph at lines 10060--10064 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10060--10064 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 10072--10076 []\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 10072--10076 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2086] [2087] [2088] [2089] [2090] Overfull \hbox (18.77168pt too wide) in paragraph at lines 10366--10366 []\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 '[] [2091] Underfull \hbox (badness 10000) in paragraph at lines 10429--10431 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][] []\T1/ptm/m/n/10 s are nicely viewed via [2092] [2093] [2094] Underfull \hbox (badness 2150) in paragraph at lines 10605--10607 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2095] [2096] [2097] [2098] Underfull \hbox (badness 10000) in paragraph at lines 10824--10828 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 10855--10861 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2099] [2100] Underfull \hbox (badness 2096) in paragraph at lines 10973--10976 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. 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If [2102] [2103] [2104] [2105] [2106] Underfull \hbox (badness 3780) in paragraph at lines 11355--11359 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 11374--11377 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2107] [2108] [2109] [2110] [2111] [2112] Underfull \hbox (badness 2818) in paragraph at lines 11746--11751 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 11755--11758 []\T1/ptm/m/n/10 the page width to be used. 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LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.write.matrix} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.survreg} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.coxph} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.stepAIC} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.rinvGauss} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.gamma.shape} has been referenced but does not e xist, replaced by a fixed one pdfTeX 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Transcript written on fullrefman.log. This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning input file fullrefman.idx.................done (13388 entries accepted, 34 rejected). Sorting entries.............................................................................................................................................done (205988 comparisons). Generating output file fullrefman.ind................done (13230 lines written, 51 warnings). Output written in fullrefman.ind. Transcript written in fullrefman.ilg. This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./fullrefman.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 3 language(s) loaded. 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[1] [2] Underfull \hbox (badness 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 296--300 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 385--388 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 533--539 []\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 1144--1147 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1901--1901 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2086--2088 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] Underfull \vbox (badness 10000) has occurred while \output is active [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3607--3609 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] [60] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3848--3848 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] Underfull \hbox (badness 2521) in paragraph at lines 4823--4825 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] Overfull \hbox (5.27168pt too wide) in paragraph at lines 5954--5954 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [94] [95] [96] Underfull \hbox (badness 2096) in paragraph at lines 6137--6150 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [97] [98] [99] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6341--6343 []\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 : [100] [101] Underfull \hbox (badness 10000) in paragraph at lines 6483--6486 []\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 [102] [103] Underfull \hbox (badness 1442) in paragraph at lines 6646--6652 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6646--6652 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6646--6652 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [104] Underfull \hbox (badness 3568) in paragraph at lines 6708--6715 \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 [105] [106] Underfull \vbox (badness 10000) has occurred while \output is active [107] [108] [109] Underfull \hbox (badness 1077) in paragraph at lines 7019--7025 []\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 7019--7025 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [110] [111] [112] [113] [114] Underfull \hbox (badness 2096) in paragraph at lines 7360--7364 \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 . [115] [116] Underfull \hbox (badness 3000) in paragraph at lines 7453--7455 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7478--7481 [][][]\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 , [117] [118] [119] [120] Underfull \hbox (badness 10000) in paragraph at lines 7733--7743 []\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing [121] [122] Underfull \hbox (badness 4479) in paragraph at lines 7804--7814 [][][]\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), [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] Underfull \hbox (badness 1394) in paragraph at lines 9477--9482 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [148] [149] [150] [151] [152] Underfull \hbox (badness 1194) in paragraph at lines 9822--9827 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 9822--9827 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [153] [154] Underfull \hbox (badness 1735) in paragraph at lines 9960--9964 \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 . [155] [156] [157] [158] [159] [160] [161] Underfull \hbox (badness 2150) in paragraph at lines 10375--10378 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 6396) in paragraph at lines 10389--10397 []\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 2735) in paragraph at lines 10429--10436 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] Underfull \hbox (badness 4569) in paragraph at lines 11495--11499 []\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 11495--11499 \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 [178] [179] [180] [181] [182] [183] [184] [185] [186] Underfull \hbox (badness 2698) in paragraph at lines 12072--12081 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 12072--12081 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [187] [188] [189] [190] [191] Underfull \vbox (badness 3803) has occurred while \output is active [192] [193] [194] [195] [196] Underfull \hbox (badness 6236) in paragraph at lines 12731--12734 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [197] [198] [199] [200] [201] [202] Underfull \hbox (badness 2253) in paragraph at lines 13143--13145 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [203] Underfull \hbox (badness 1565) in paragraph at lines 13214--13218 [][][]\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 [204] Underfull \hbox (badness 10000) in paragraph at lines 13258--13260 []\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 [205] [206] Underfull \hbox (badness 1466) in paragraph at lines 13398--13401 []\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 [207] [208] Underfull \hbox (badness 10000) in paragraph at lines 13517--13521 [][][]\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 13528--13531 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [209] [210] [211] [212] Underfull \hbox (badness 3965) in paragraph at lines 13791--13795 []\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, [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] Underfull \hbox (badness 4429) in paragraph at lines 14553--14556 []\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 [225] [226] Underfull \hbox (badness 10000) in paragraph at lines 14653--14655 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14659--14663 []\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 10000) in paragraph at lines 14698--14702 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 14698--14702 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] Underfull \hbox (badness 2452) in paragraph at lines 15287--15291 []\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 15287--15291 \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 [237] [238] [239] Underfull \hbox (badness 1092) in paragraph at lines 15460--15465 [][]\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 [240] [241] [242] Underfull \hbox (badness 6741) in paragraph at lines 15708--15712 \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 , [243] [244] [245] [246] [247] Underfull \hbox (badness 1867) in paragraph at lines 16014--16021 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [248] [249] [250] [251] Underfull \vbox (badness 10000) has occurred while \output is active [252] [253] [254] Underfull \hbox (badness 3679) in paragraph at lines 16424--16426 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [255] [256] [257] [258] [259] [260] [261] [262] Underfull \hbox (badness 1478) in paragraph at lines 16979--16982 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [263] [264] [265] Underfull \hbox (badness 10000) in paragraph at lines 17232--17234 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] Underfull \hbox (badness 1442) in paragraph at lines 17822--17824 []\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 [276] Underfull \hbox (badness 2452) in paragraph at lines 17914--17930 [][][]\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 , [277] [278] [279] [280] [281] [282] [283] Underfull \hbox (badness 1248) in paragraph at lines 18328--18331 []\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 , [284] [285] [286] [287] Underfull \hbox (badness 4739) in paragraph at lines 18586--18588 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] Underfull \hbox (badness 2469) in paragraph at lines 19603--19608 []\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 19617--19624 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [305] Underfull \hbox (badness 10000) in paragraph at lines 19691--19695 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 19691--19695 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$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 ' [306] [307] Underfull \hbox (badness 1509) in paragraph at lines 19826--19833 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 19826--19833 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19842--19847 []\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 [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] Underfull \hbox (badness 1264) in paragraph at lines 20575--20580 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [319] Underfull \hbox (badness 4441) in paragraph at lines 20604--20607 []\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 , [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] Underfull \hbox (badness 10000) in paragraph at lines 21330--21332 []\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 [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] Underfull \hbox (badness 1077) in paragraph at lines 22365--22371 \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 . [347] [348] [349] Underfull \hbox (badness 1484) in paragraph at lines 22526--22534 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [350] [351] [352] [353] Underfull \hbox (badness 2790) in paragraph at lines 22797--22800 []\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 22797--22800 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [354] [355] [356] [357] Underfull \hbox (badness 1194) in paragraph at lines 23079--23082 []\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 [358] [359] [360] [361] Underfull \hbox (badness 10000) in paragraph at lines 23285--23291 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23285--23291 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23295--23298 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23295--23298 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] [373] [374] [375] Underfull \hbox (badness 10000) in paragraph at lines 24245--24247 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [376] [377] [378] [379] Underfull \hbox (badness 1199) in paragraph at lines 24489--24495 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24489--24495 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [380] [381] [382] [383] [384] [385] [386] [387] [388] Underfull \hbox (badness 1038) in paragraph at lines 25068--25076 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 1881) in paragraph at lines 25077--25080 []\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 25096--25098 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [389] Underfull \hbox (badness 10000) in paragraph at lines 25205--25215 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25216--25222 []\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 [390] Underfull \hbox (badness 1968) in paragraph at lines 25252--25257 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 25262--25264 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [391] [392] [393] Underfull \hbox (badness 10000) in paragraph at lines 25521--25527 []\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 25521--25527 \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 25521--25527 \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 25534--25537 []\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 25558--25560 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [394] Underfull \hbox (badness 10000) in paragraph at lines 25590--25595 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 25596--25607 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 25608--25611 []\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 3713) in paragraph at lines 25618--25630 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 25618--25630 \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). Underfull \hbox (badness 2351) in paragraph at lines 25618--25630 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25632--25639 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 25632--25639 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 25632--25639 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1874) in paragraph at lines 25632--25639 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [395] [396] [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 25979--25983 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 25979--25983 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [400] [401] [402] [403] [404] Underfull \hbox (badness 1735) in paragraph at lines 26297--26301 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] Underfull \hbox (badness 2726) in paragraph at lines 26868--26871 []\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 [415] [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] [427] Underfull \hbox (badness 1052) in paragraph at lines 27695--27700 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [428] [429] [430] [431] [432] Underfull \vbox (badness 10000) has occurred while \output is active [433] [434] [435] [436] [437] [438] [439] Underfull \hbox (badness 1533) in paragraph at lines 28504--28507 []\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 [440] [441] [442] Underfull \hbox (badness 1163) in paragraph at lines 28666--28677 []\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 [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] Underfull \hbox (badness 10000) in paragraph at lines 30189--30193 []\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 30189--30193 \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 30211--30213 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [467] [468] [469] [470] [471] [472] [473] [474] [475] Underfull \hbox (badness 1655) in paragraph at lines 30759--30761 []\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 [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] Underfull \hbox (badness 10000) in paragraph at lines 31434--31438 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [487] [488] [489] [490] Underfull \hbox (badness 2302) in paragraph at lines 31674--31681 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 31674--31681 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 3333) in paragraph at lines 31674--31681 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 31674--31681 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [491] [492] Underfull \hbox (badness 2261) in paragraph at lines 31830--31835 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if Underfull \hbox (badness 10000) in paragraph at lines 31857--31863 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [493] Underfull \hbox (badness 10000) in paragraph at lines 31933--31938 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] Underfull \vbox (badness 3803) has occurred while \output is active [533] [534] [535] [536] [537] [538] [539] [540] Underfull \hbox (badness 1072) in paragraph at lines 34971--34975 []\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 34976--34980 []\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 35004--35010 []\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 35004--35010 \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 35004--35010 \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 [541] Underfull \hbox (badness 3343) in paragraph at lines 35016--35023 \T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 35016--35023 \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 35016--35023 \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 [542] [543] [544] [545] Underfull \hbox (badness 10000) in paragraph at lines 35314--35320 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35314--35320 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] Underfull \hbox (badness 3333) in paragraph at lines 37158--37163 []\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 [576] [577] [578] [579] [580] [581] Underfull \vbox (badness 10000) has occurred while \output is active [582] [583] [584] [585] Underfull \hbox (badness 1472) in paragraph at lines 37781--37784 []\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 [586] [587] [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] Underfull \vbox (badness 3803) has occurred while \output is active [599] Underfull \hbox (badness 10000) in paragraph at lines 38646--38650 []\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., [600] [601] [602] [603] Underfull \hbox (badness 10000) in paragraph at lines 38894--38897 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [604] [605] Underfull \hbox (badness 10000) in paragraph at lines 39012--39016 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [606] Underfull \hbox (badness 10000) in paragraph at lines 39074--39078 [][][]\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 \ [][]$\T1/zi4/m/n/10 https : / / developer . [607] [608] [609] [610] [611] [612] [613] [614] Underfull \hbox (badness 4013) in paragraph at lines 39619--39621 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [615] [616] [617] [618] [619] [620] Underfull \vbox (badness 10000) has occurred while \output is active [621] [622] [623] [624] [625] [626] [627] Underfull \hbox (badness 3460) in paragraph at lines 40480--40483 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via [628] Underfull \hbox (badness 1990) in paragraph at lines 40487--40495 []\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 40487--40495 \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 [629] [630] [631] [632] Underfull \hbox (badness 10000) in paragraph at lines 40764--40767 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [633] [634] [635] Underfull \hbox (badness 1917) in paragraph at lines 40992--40999 []\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 [636] [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] Underfull \hbox (badness 3668) in paragraph at lines 41671--41673 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [647] Underfull \hbox (badness 2401) in paragraph at lines 41777--41781 []\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 [648] [649] [650] Underfull \hbox (badness 2111) in paragraph at lines 41953--41958 \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. [651] Underfull \hbox (badness 7362) in paragraph at lines 41969--41974 []\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 [652] [653] [654] [655] [656] [657] [658] [659] [660] Underfull \hbox (badness 5417) in paragraph at lines 42526--42530 []\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 [661] Underfull \hbox (badness 10000) in paragraph at lines 42587--42591 []\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 [662]) (./compiler-pkg.tex Chapter 2. [663] [664] [665] [666]) (./datasets-pkg.tex Chapter 3. [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] Underfull \vbox (badness 1515) has occurred while \output is active [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] Underfull \hbox (badness 6658) in paragraph at lines 3954--3956 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h ttp : / / www . ltrr . arizona . edu / ~hallman / [734] Underfull \vbox (badness 10000) has occurred while \output is active [735] [736] [737] [738] Underfull \vbox (badness 10000) has occurred while \output is active [739] [740] [741] [742] [743] [744] Overfull \vbox (18.9959pt too high) has occurred while \output is active [745] [746] [747]) (./grDevices-pkg.tex [748] Chapter 4. [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] Underfull \hbox (badness 5175) in paragraph at lines 1069--1071 []\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 [766] [767] [768] [769] Underfull \hbox (badness 1852) in paragraph at lines 1266--1269 []\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 [770] [771] [772] Underfull \hbox (badness 1490) in paragraph at lines 1472--1477 \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 [773] [774] Underfull \hbox (badness 10000) in paragraph at lines 1595--1599 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [775] [776] [777] [778] Underfull \hbox (badness 1325) in paragraph at lines 1878--1888 \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 , [779] [780] Underfull \hbox (badness 10000) in paragraph at lines 1983--1985 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [781] [782] [783] Underfull \hbox (badness 6758) in paragraph at lines 2144--2147 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [784] [785] [786] [787] [788] [789] [790] [791] [792] Underfull \hbox (badness 10000) in paragraph at lines 2737--2738 [793] [794] [795] [796] [797] [798] [799] [800] Underfull \hbox (badness 10000) in paragraph at lines 3235--3240 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [801] [802] [803] [804] Underfull \hbox (badness 3302) in paragraph at lines 3494--3497 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3508--3510 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] [816] [817] Underfull \hbox (badness 1067) in paragraph at lines 4331--4338 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [818] [819] Underfull \hbox (badness 3364) in paragraph at lines 4491--4493 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$ \T1/zi4/m/n/10 https : / / partners . adobe . com / public / [820] Underfull \hbox (badness 1789) in paragraph at lines 4568--4570 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [821] Underfull \hbox (badness 1377) in paragraph at lines 4618--4623 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [822] Underfull \hbox (badness 2671) in paragraph at lines 4645--4653 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4694--4701 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4702--4711 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4702--4711 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4712--4714 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [823] [824] Underfull \hbox (badness 1377) in paragraph at lines 4823--4828 []\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 [825] Underfull \hbox (badness 7344) in paragraph at lines 4883--4885 []\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 [826] [827] Underfull \hbox (badness 2035) in paragraph at lines 5007--5016 []\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 5007--5016 \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 5007--5016 \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 , [828] Underfull \hbox (badness 10000) in paragraph at lines 5075--5082 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5075--5082 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [829] [830] [831] Underfull \hbox (badness 1546) in paragraph at lines 5217--5225 []\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 , [832] Underfull \hbox (badness 1648) in paragraph at lines 5294--5298 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [833] [834] [835] [836] [837] [838] [839] Underfull \hbox (badness 10000) in paragraph at lines 5746--5749 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [840] [841] [842] [843] [844] [845] Underfull \hbox (badness 1189) in paragraph at lines 6143--6145 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [846] [847] Underfull \hbox (badness 10000) in paragraph at lines 6241--6243 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [848] [849] [850] [851] Underfull \hbox (badness 3780) in paragraph at lines 6532--6538 []\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 , [852] [853] [854] Underfull \hbox (badness 2680) in paragraph at lines 6733--6735 []\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 [855] [856] [857]) (./graphics-pkg.tex [858] Chapter 5. [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] [869] Underfull \hbox (badness 10000) in paragraph at lines 683--690 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [870] [871] [872] [873] Underfull \vbox (badness 3803) has occurred while \output is active [874] [875] [876] [877] [878] [879] Underfull \hbox (badness 4634) in paragraph at lines 1255--1258 [][][]\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 , [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] [894] [895] [896] Underfull \hbox (badness 1009) in paragraph at lines 2289--2296 \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 [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] Underfull \vbox (badness 10000) has occurred while \output is active [919] [920] [921] [922] Underfull \hbox (badness 1867) in paragraph at lines 3931--3935 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [923] [924] [925] [926] [927] [928] [929] [930] Underfull \hbox (badness 1924) in paragraph at lines 4378--4383 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain Underfull \hbox (badness 2529) in paragraph at lines 4409--4412 []\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 [931] [932] [933] [934] [935] Underfull \hbox (badness 10000) in paragraph at lines 4759--4765 []\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 4759--4765 \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 [936] [937] Underfull \hbox (badness 10000) in paragraph at lines 4890--4893 [938 >/library/graphics/help/figures/mai.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 4951--4953 Underfull \vbox (badness 10000) has occurred while \output is active [939] [940 >/library/graphics/help/figures/oma.pdf>] [941] Underfull \hbox (badness 10000) in paragraph at lines 5141--5143 []\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 [942] Underfull \vbox (badness 3803) has occurred while \output is active [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6612--6613 [][] [965] [966 >/library/graphics/help/figures/pch .pdf>] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] Underfull \hbox (badness 1048) in paragraph at lines 7321--7326 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [977] [978] Underfull \hbox (badness 1102) in paragraph at lines 7437--7440 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] Underfull \hbox (badness 1043) in paragraph at lines 8272--8276 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [993] [994] [995] [996] [997] [998] [999] Underfull \hbox (badness 10000) in paragraph at lines 8675--8677 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8677--8679 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1000]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8757 \HeaderA{units}{Graphical Units}{units} [1001] [1002] [1003] [1004]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1005] [1006] [1007] [1008] [1009] [1010] Underfull \hbox (badness 2680) in paragraph at lines 390--393 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] Underfull \hbox (badness 4279) in paragraph at lines 970--979 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] Underfull \vbox (badness 3803) has occurred while \output is active [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] Underfull \hbox (badness 1067) in paragraph at lines 4340--4343 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1078] [1079] [1080] [1081] Underfull \hbox (badness 7256) in paragraph at lines 4585--4587 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] Underfull \hbox (badness 10000) in paragraph at lines 5862--5868 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] Underfull \hbox (badness 7649) in paragraph at lines 6341--6344 []\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 [1112] [1113] [1114] [1115]) (./methods-pkg.tex [1116] Chapter 7. [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] Underfull \vbox (badness 3803) has occurred while \output is active [1125] Underfull \vbox (badness 10000) has occurred while \output is active [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] Underfull \hbox (badness 2237) in paragraph at lines 1386--1388 []\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 [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] Underfull \hbox (badness 1077) in paragraph at lines 1933--1940 []\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 [1144] Underfull \hbox (badness 10000) in paragraph at lines 1982--1987 []\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 1982--1987 \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 [1145] [1146] [1147] Underfull \hbox (badness 1242) in paragraph at lines 2215--2220 []\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 = [1148] [1149] [1150] [1151] [1152] Underfull \hbox (badness 10000) in paragraph at lines 2575--2578 []\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 [1153] [1154] Underfull \hbox (badness 1132) in paragraph at lines 2715--2719 []\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 [1155] Underfull \hbox (badness 1033) in paragraph at lines 2747--2752 \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 [1156] [1157] [1158] [1159] [1160] [1161] [1162] Underfull \hbox (badness 1102) in paragraph at lines 3304--3306 []\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 [1163] [1164] [1165] [1166] [1167] [1168] Underfull \hbox (badness 10000) in paragraph at lines 3637--3642 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Underfull \hbox (badness 10000) in paragraph at lines 3645--3654 []\T1/ptm/m/n/10 The [1169] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3765--3766 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3765--3766 [1170] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3849--3850 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] Underfull \hbox (badness 1436) in paragraph at lines 4446--4449 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4475--4481 []\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 4475--4481 \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 [1181] Underfull \hbox (badness 1092) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] Underfull \vbox (badness 10000) has occurred while \output is active [1191] [1192] Underfull \hbox (badness 10000) in paragraph at lines 5358--5359 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1193] Underfull \hbox (badness 4036) in paragraph at lines 5440--5443 []\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 [1194] Underfull \hbox (badness 3803) in paragraph at lines 5515--5517 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1195] [1196] [1197] [1198] Underfull \hbox (badness 1087) in paragraph at lines 5747--5752 []\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 [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] Underfull \hbox (badness 1675) in paragraph at lines 6454--6460 \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 [1207] [1208] [1209] [1210] Underfull \vbox (badness 10000) has occurred while \output is active [1211] [1212] [1213] [1214]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6976 \aliasA{S4}{S3Part}{S4} [1215] [1216] [1217]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7232 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7234 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7235 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7237 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7238 \aliasA{Summary}{S4groupGeneric}{Summary} [1218] Underfull \hbox (badness 2050) in paragraph at lines 7299--7303 []\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 [1219] [1220] [1221] Underfull \hbox (badness 1286) in paragraph at lines 7487--7489 []\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 [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] Underfull \vbox (badness 10000) has occurred while \output is active [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] Underfull \hbox (badness 1852) in paragraph at lines 10567--10571 []\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., [1264] [1265] [1266] [1267]) (./parallel-pkg.tex [1268] 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 [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] Underfull \hbox (badness 3386) in paragraph at lines 1268--1271 []\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 [1289] [1290] [1291]) (./splines-pkg.tex [1292] 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 [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] [1306] [1307]) (./stats-pkg.tex [1308] Chapter 10. [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] Underfull \hbox (badness 1412) in paragraph at lines 848--850 []\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 [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] Underfull \hbox (badness 2503) in paragraph at lines 1329--1332 []\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 , [1330] [1331] [1332] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 3965) in paragraph at lines 2168--2170 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1344] [1345] [1346] [1347] [1348] Underfull \hbox (badness 3965) in paragraph at lines 2510--2512 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] Underfull \hbox (badness 2726) in paragraph at lines 3224--3240 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1360] [1361] Underfull \hbox (badness 2503) in paragraph at lines 3354--3357 []\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 , [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] Underfull \hbox (badness 3989) in paragraph at lines 4582--4589 []\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 = [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] Underfull \hbox (badness 2556) in paragraph at lines 5193--5196 []\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 5210--5212 []\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 [1392] [1393] [1394] [1395] Underfull \hbox (badness 1142) in paragraph at lines 5451--5463 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1396] [1397] [1398] Underfull \hbox (badness 2503) in paragraph at lines 5599--5603 []\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 , [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] Underfull \hbox (badness 8132) in paragraph at lines 6102--6107 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1407] [1408] [1409] [1410] [1411] Underfull \hbox (badness 7081) in paragraph at lines 6380--6383 []\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 6384--6386 []\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 [1412] [1413] [1414] [1415] [1416] Underfull \vbox (badness 3803) has occurred while \output is active [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 10000) in paragraph at lines 7225--7228 []\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 [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] Underfull \hbox (badness 2626) in paragraph at lines 8860--8863 []\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 [1452] Underfull \hbox (badness 2503) in paragraph at lines 8960--8964 []\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 , [1453] [1454] [1455] [1456] [1457] [1458] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9309--9311 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] Underfull \hbox (badness 4518) in paragraph at lines 10235--10240 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1473] [1474] [1475] [1476] [1477] Underfull \hbox (badness 2142) in paragraph at lines 10577--10580 []\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 10596--10599 []\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, [1478] Underfull \hbox (badness 1708) in paragraph at lines 10658--10662 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1479] [1480] [1481] [1482] [1483] [1484] Underfull \hbox (badness 1694) in paragraph at lines 11054--11057 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1485] Underfull \hbox (badness 1867) in paragraph at lines 11073--11082 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1486] [1487] [1488] [1489] [1490] Underfull \hbox (badness 10000) in paragraph at lines 11380--11383 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1491] [1492]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.hat}) has been already used, duplicate ignored \relax l.11534 \aliasA{hat}{influence.measures}{hat} [1493] [1494] Underfull \hbox (badness 1484) in paragraph at lines 11665--11667 []\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 [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] Underfull \hbox (badness 4441) in paragraph at lines 12248--12250 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12255--12257 []\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 [1505] [1506] [1507] [1508] [1509] [1510] Underfull \hbox (badness 2894) in paragraph at lines 12589--12593 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] Underfull \hbox (badness 4518) in paragraph at lines 13287--13292 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] Underfull \hbox (badness 4518) in paragraph at lines 13934--13939 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1532] [1533] [1534] Underfull \hbox (badness 10000) in paragraph at lines 14072--14076 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14079--14081 []\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 [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] Underfull \hbox (badness 2503) in paragraph at lines 15141--15145 []\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 , [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] Underfull \hbox (badness 1584) in paragraph at lines 15653--15659 []\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 [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] Underfull \hbox (badness 2359) in paragraph at lines 17290--17292 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1587] Underfull \vbox (badness 3803) has occurred while \output is active [1588] Underfull \vbox (badness 10000) has occurred while \output is active [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] Underfull \hbox (badness 1377) in paragraph at lines 18201--18206 []\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 18206--18209 []\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 [1602] Underfull \hbox (badness 1454) in paragraph at lines 18219--18223 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18227--18231 []\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 [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] Underfull \hbox (badness 1337) in paragraph at lines 18843--18846 []\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 [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] Underfull \hbox (badness 3049) in paragraph at lines 19329--19333 []\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 [1622] [1623] [1624] [1625] Underfull \hbox (badness 5563) in paragraph at lines 19579--19581 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19582--19585 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1626] [1627] [1628] [1629] [1630] [1631] Underfull \hbox (badness 2503) in paragraph at lines 19957--19960 []\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 , [1632] Underfull \hbox (badness 10000) in paragraph at lines 19984--19986 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648] [1649] [1650] Underfull \hbox (badness 10000) in paragraph at lines 21047--21053 []\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 , [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] Underfull \hbox (badness 1337) in paragraph at lines 22385--22391 []\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 [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] Overfull \hbox (27.74408pt too wide) in paragraph at lines 22930--22930 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1681] [1682] [1683] [1684] [1685] Underfull \hbox (badness 10000) in paragraph at lines 23180--23183 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1686] [1687] [1688] [1689] [1690] [1691] [1692] [1693] [1694] Underfull \hbox (badness 10000) in paragraph at lines 23765--23768 []\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 [1695] Underfull \hbox (badness 3690) in paragraph at lines 23816--23820 [][][]\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 [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] Underfull \hbox (badness 3439) in paragraph at lines 24286--24292 [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1 0 , [1705] [1706] [1707] Underfull \hbox (badness 1867) in paragraph at lines 24483--24485 []\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 24496--24500 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 24496--24500 \T1/zi4/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was Underfull \hbox (badness 1132) in paragraph at lines 24496--24500 \T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o f un-de-ter-mined co-ef-fi-cients, e.g., for [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] Underfull \hbox (badness 10000) in paragraph at lines 24968--24973 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732] Underfull \hbox (badness 3514) in paragraph at lines 26010--26015 []\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 [1733] Underfull \hbox (badness 3514) in paragraph at lines 26072--26077 []\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 [1734] Underfull \hbox (badness 3514) in paragraph at lines 26129--26134 []\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 [1735] Underfull \hbox (badness 3514) in paragraph at lines 26190--26196 []\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 [1736] [1737] [1738] [1739] Underfull \hbox (badness 3514) in paragraph at lines 26403--26408 []\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 [1740] Underfull \hbox (badness 3514) in paragraph at lines 26459--26464 []\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 [1741] Underfull \hbox (badness 3514) in paragraph at lines 26517--26522 []\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 [1742] Underfull \hbox (badness 3514) in paragraph at lines 26572--26577 []\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 [1743] Underfull \hbox (badness 6691) in paragraph at lines 26641--26646 []\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 [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751] [1752] Underfull \hbox (badness 10000) in paragraph at lines 27165--27168 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27165--27168 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] Underfull \hbox (badness 5431) in paragraph at lines 27771--27773 []\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 [1763] [1764] [1765] Underfull \hbox (badness 5431) in paragraph at lines 27981--27984 []\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 [1766] [1767] [1768] [1769] [1770] [1771] Underfull \hbox (badness 1337) in paragraph at lines 28295--28299 []\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 [1772] [1773] Underfull \hbox (badness 10000) in paragraph at lines 28412--28415 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1774] [1775] Underfull \hbox (badness 1616) in paragraph at lines 28595--28598 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1776] [1777] [1778] [1779] [1780] [1781] [1782] [1783] [1784] [1785] [1786] [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] Underfull \hbox (badness 10000) in paragraph at lines 29721--29725 []\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 [1795] [1796] [1797] Underfull \vbox (badness 10000) has occurred while \output is active [1798] [1799] [1800] Underfull \hbox (badness 1337) in paragraph at lines 30085--30089 []\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 [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] Underfull \hbox (badness 1337) in paragraph at lines 30569--30573 []\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 [1809] Underfull \hbox (badness 2142) in paragraph at lines 30646--30651 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the [1810] Underfull \hbox (badness 5161) in paragraph at lines 30668--30670 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1811] [1812] [1813] [1814] [1815] [1816] Underfull \hbox (badness 10000) in paragraph at lines 31050--31055 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1817] [1818]) (./stats4-pkg.tex Chapter 11. [1819] [1820] [1821] [1822] [1823] [1824]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} [1825] [1826] [1827] [1828]) (./tcltk-pkg.tex Chapter 12. [1829] [1830] [1831] [1832] [1833] [1834] [1835] Underfull \vbox (badness 10000) has occurred while \output is active [1836] Underfull \vbox (badness 10000) has occurred while \output is active [1837] 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 [1838] [1839] [1840] [1841] [1842] [1843] [1844] [1845] [1846] [1847] [1848] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1849]) (./tools-pkg.tex [1850] Chapter 13. [1851] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1852] 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 [1853] [1854] 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 [1855] [1856] 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 [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] Underfull \hbox (badness 1635) in paragraph at lines 1054--1056 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1868] Underfull \hbox (badness 4441) in paragraph at lines 1132--1142 \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- [1869] Underfull \hbox (badness 1014) in paragraph at lines 1154--1156 []\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 1160--1162 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1197--1200 []\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 1197--1200 \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 , [1870] [1871] [1872] Underfull \hbox (badness 10000) in paragraph at lines 1366--1368 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1873] [1874] [1875] Underfull \hbox (badness 2293) in paragraph at lines 1540--1542 []\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 [1876] [1877] Underfull \hbox (badness 7981) in paragraph at lines 1678--1683 []\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 1685--1687 []\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 [1878] [1879] [1880] [1881]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1882 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1882] [1883] [1884] [1885] [1886] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2184--2184 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1887] [1888] [1889] Underfull \hbox (badness 7981) in paragraph at lines 2353--2359 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1890] [1891] [1892] [1893] [1894] [1895] [1896] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2818. [1897] [1898] [1899] [1900] Underfull \hbox (badness 1424) in paragraph at lines 3100--3102 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1901] [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] [1910] [1911] [1912] Underfull \hbox (badness 10000) in paragraph at lines 3800--3802 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1913] [1914] Underfull \hbox (badness 10000) in paragraph at lines 3939--3942 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1915] [1916] Underfull \hbox (badness 1137) in paragraph at lines 4037--4039 []\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 [1917] [1918] [1919] Underfull \hbox (badness 1838) in paragraph at lines 4246--4252 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4246--4252 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1920] Underfull \hbox (badness 5726) in paragraph at lines 4326--4331 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4326--4331 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1921] [1922] [1923] Underfull \hbox (badness 2197) in paragraph at lines 4475--4485 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4475--4485 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1924] Underfull \hbox (badness 1571) in paragraph at lines 4538--4542 []\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 [1925] [1926] [1927]) (./utils-pkg.tex [1928] Chapter 14. [1929] Underfull \hbox (badness 2556) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1930] [1931] [1932] [1933] [1934] [1935] [1936] Underfull \hbox (badness 10000) in paragraph at lines 546--552 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 546--552 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1937] [1938] Underfull \hbox (badness 5847) in paragraph at lines 660--666 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 660--666 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1939] Underfull \hbox (badness 3861) in paragraph at lines 728--733 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1940] [1941] [1942] Underfull \hbox (badness 1430) in paragraph at lines 893--900 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 893--900 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 893--900 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 893--900 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 904--906 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1943] [1944] [1945] [1946] [1947] [1948] [1949] Underfull \hbox (badness 1371) in paragraph at lines 1375--1377 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 2057) in paragraph at lines 1863--1865 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1958] Underfull \hbox (badness 10000) in paragraph at lines 1958--1960 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1959] [1960] Underfull \hbox (badness 5189) in paragraph at lines 2060--2062 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1961] Underfull \vbox (badness 3803) has occurred while \output is active [1962] [1963] [1964] Underfull \hbox (badness 1661) in paragraph at lines 2278--2285 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2294--2297 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1965] [1966] [1967] [1968] [1969] [1970] Underfull \hbox (badness 10000) in paragraph at lines 2703--2707 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2708--2711 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1971] [1972] [1973] [1974] [1975] [1976] [1977] [1978] [1979] [1980] [1981] Underfull \hbox (badness 1430) in paragraph at lines 3385--3393 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 1231) in paragraph at lines 3434--3440 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1982] [1983] [1984] [1985] [1986] [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4274 ...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.4274 ...mat Unordered and Ordered Lists}{format} [1996] [1997] [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] Underfull \hbox (badness 1371) in paragraph at lines 5271--5273 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [2012] Underfull \hbox (badness 1502) in paragraph at lines 5360--5365 []\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 5360--5365 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2013] [2014] [2015] Underfull \hbox (badness 10000) in paragraph at lines 5533--5542 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2016] Underfull \hbox (badness 2150) in paragraph at lines 5596--5599 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2017] [2018] Underfull \hbox (badness 3118) in paragraph at lines 5733--5735 []\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 Underfull \hbox (badness 2409) in paragraph at lines 5766--5770 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [2019] [2020] Underfull \hbox (badness 1325) in paragraph at lines 5874--5878 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [2021] Underfull \hbox (badness 10000) in paragraph at lines 5957--5960 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 5957--5960 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2022] Underfull \hbox (badness 3219) in paragraph at lines 6030--6037 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6030--6037 \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 6030--6037 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [2023] Underfull \hbox (badness 10000) in paragraph at lines 6110--6115 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] [2047] Underfull \hbox (badness 10000) in paragraph at lines 7527--7529 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7532--7537 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] Underfull \hbox (badness 1789) in paragraph at lines 8087--8089 []\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 [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] Underfull \hbox (badness 1097) in paragraph at lines 8916--8919 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2069] Underfull \hbox (badness 3000) in paragraph at lines 9052--9057 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] Underfull \hbox (badness 2134) in paragraph at lines 9635--9640 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2079] [2080] [2081] [2082] [2083] [2084] [2085] Underfull \hbox (badness 5077) in paragraph at lines 10060--10064 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10060--10064 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 10072--10076 []\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 10072--10076 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2086] [2087] [2088] [2089] [2090] Overfull \hbox (18.77168pt too wide) in paragraph at lines 10366--10366 []\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 '[] [2091] Underfull \hbox (badness 10000) in paragraph at lines 10429--10431 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. 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[1] [2] Underfull \hbox (badness 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 296--300 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 385--388 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) in paragraph at lines 533--539 []\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 1144--1147 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1901--1901 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2086--2088 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] Underfull \vbox (badness 10000) has occurred while \output is active [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3607--3609 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] [60] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3848--3848 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] Underfull \hbox (badness 2521) in paragraph at lines 4823--4825 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] Overfull \hbox (5.27168pt too wide) in paragraph at lines 5954--5954 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [94] [95] [96] Underfull \hbox (badness 2096) in paragraph at lines 6137--6150 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [97] [98] [99] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6341--6343 []\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 : [100] [101] Underfull \hbox (badness 10000) in paragraph at lines 6483--6486 []\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 [102] [103] Underfull \hbox (badness 1442) in paragraph at lines 6646--6652 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a Underfull \hbox (badness 1248) in paragraph at lines 6646--6652 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6646--6652 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it [104] Underfull \hbox (badness 3568) in paragraph at lines 6708--6715 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [105] [106] Underfull \vbox (badness 10000) has occurred while \output is active [107] [108] [109] Underfull \hbox (badness 1077) in paragraph at lines 7019--7025 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7019--7025 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [110] [111] [112] [113] [114] Underfull \hbox (badness 2096) in paragraph at lines 7360--7364 \T1/zi4/m/n/10 status _ codes$[][] \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 . [115] [116] Underfull \hbox (badness 3000) in paragraph at lines 7453--7455 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7478--7481 [][][]\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 , [117] [118] [119] [120] Underfull \hbox (badness 10000) in paragraph at lines 7733--7743 []\T1/zi4/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing [121] [122] Underfull \hbox (badness 4479) in paragraph at lines 7804--7814 [][][]\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), [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] Underfull \hbox (badness 1394) in paragraph at lines 9477--9482 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [148] [149] [150] [151] [152] Underfull \hbox (badness 1194) in paragraph at lines 9822--9827 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) in paragraph at lines 9822--9827 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [153] [154] Underfull \hbox (badness 1735) in paragraph at lines 9960--9964 \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 . [155] [156] [157] [158] [159] [160] [161] Underfull \hbox (badness 2150) in paragraph at lines 10375--10378 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 6396) in paragraph at lines 10389--10397 []\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 2735) in paragraph at lines 10429--10436 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] Underfull \hbox (badness 4569) in paragraph at lines 11495--11499 []\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 11495--11499 \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 [178] [179] [180] [181] [182] [183] [184] [185] [186] Underfull \hbox (badness 2698) in paragraph at lines 12072--12081 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l-lowed Underfull \hbox (badness 4341) in paragraph at lines 12072--12081 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [187] [188] [189] [190] [191] Underfull \vbox (badness 3803) has occurred while \output is active [192] [193] [194] [195] [196] Underfull \hbox (badness 6236) in paragraph at lines 12731--12734 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [197] [198] [199] [200] [201] [202] Underfull \hbox (badness 2253) in paragraph at lines 13143--13145 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [203] Underfull \hbox (badness 1565) in paragraph at lines 13214--13218 [][][]\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 [204] Underfull \hbox (badness 10000) in paragraph at lines 13258--13260 []\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 [205] [206] Underfull \hbox (badness 1466) in paragraph at lines 13398--13401 []\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 [207] [208] Underfull \hbox (badness 10000) in paragraph at lines 13517--13521 [][][]\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 13528--13531 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [209] [210] [211] [212] Underfull \hbox (badness 3965) in paragraph at lines 13791--13795 []\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, [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] Underfull \hbox (badness 4429) in paragraph at lines 14553--14556 []\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 [225] [226] Underfull \hbox (badness 10000) in paragraph at lines 14653--14655 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14659--14663 []\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 10000) in paragraph at lines 14698--14702 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 4156) in paragraph at lines 14698--14702 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] Underfull \hbox (badness 2452) in paragraph at lines 15287--15291 []\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 15287--15291 \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 [237] [238] [239] Underfull \hbox (badness 1092) in paragraph at lines 15460--15465 [][]\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 [240] [241] [242] Underfull \hbox (badness 6741) in paragraph at lines 15708--15712 \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 , [243] [244] [245] [246] [247] Underfull \hbox (badness 1867) in paragraph at lines 16014--16021 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [248] [249] [250] [251] Underfull \vbox (badness 10000) has occurred while \output is active [252] [253] [254] Underfull \hbox (badness 3679) in paragraph at lines 16424--16426 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [255] [256] [257] [258] [259] [260] [261] [262] Underfull \hbox (badness 1478) in paragraph at lines 16979--16982 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [263] [264] [265] Underfull \hbox (badness 10000) in paragraph at lines 17232--17234 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] Underfull \hbox (badness 1442) in paragraph at lines 17822--17824 []\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 [276] Underfull \hbox (badness 2452) in paragraph at lines 17914--17930 [][][]\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 , [277] [278] [279] [280] [281] [282] [283] Underfull \hbox (badness 1248) in paragraph at lines 18328--18331 []\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 , [284] [285] [286] [287] Underfull \hbox (badness 4739) in paragraph at lines 18586--18588 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] Underfull \hbox (badness 2469) in paragraph at lines 19603--19608 []\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 19617--19624 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [305] Underfull \hbox (badness 10000) in paragraph at lines 19691--19695 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 19691--19695 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$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 ' [306] [307] Underfull \hbox (badness 1509) in paragraph at lines 19826--19833 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 19826--19833 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 19842--19847 []\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 [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] Underfull \hbox (badness 1264) in paragraph at lines 20575--20580 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: [319] Underfull \hbox (badness 4441) in paragraph at lines 20604--20607 []\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 , [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] Underfull \hbox (badness 10000) in paragraph at lines 21330--21332 []\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 [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] Underfull \hbox (badness 1077) in paragraph at lines 22365--22371 \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 . [347] [348] [349] Underfull \hbox (badness 1484) in paragraph at lines 22526--22534 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [350] [351] [352] [353] Underfull \hbox (badness 2790) in paragraph at lines 22797--22800 []\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 22797--22800 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [354] [355] [356] [357] Underfull \hbox (badness 1194) in paragraph at lines 23079--23082 []\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 [358] [359] [360] [361] Underfull \hbox (badness 10000) in paragraph at lines 23285--23291 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23285--23291 \T1/ptm/m/n/10 list, i.e., \T1/zi4/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23295--23298 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23295--23298 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] [373] [374] [375] Underfull \hbox (badness 10000) in paragraph at lines 24245--24247 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [376] [377] [378] [379] Underfull \hbox (badness 1199) in paragraph at lines 24489--24495 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24489--24495 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [380] [381] [382] [383] [384] [385] [386] [387] [388] Underfull \hbox (badness 1038) in paragraph at lines 25068--25076 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially Underfull \hbox (badness 1881) in paragraph at lines 25077--25080 []\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 25096--25098 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [389] Underfull \hbox (badness 10000) in paragraph at lines 25205--25215 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25216--25222 []\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 [390] Underfull \hbox (badness 1968) in paragraph at lines 25252--25257 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 25262--25264 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [391] [392] [393] Underfull \hbox (badness 10000) in paragraph at lines 25521--25527 []\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 25521--25527 \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 25521--25527 \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 25534--25537 []\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 25558--25560 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [394] Underfull \hbox (badness 10000) in paragraph at lines 25590--25595 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 25596--25607 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 25608--25611 []\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 3713) in paragraph at lines 25618--25630 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 25618--25630 \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). Underfull \hbox (badness 2351) in paragraph at lines 25618--25630 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25632--25639 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/zi4/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 25632--25639 \T1/zi4/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 25632--25639 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Underfull \hbox (badness 1874) in paragraph at lines 25632--25639 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [395] [396] [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 25979--25983 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 25979--25983 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [400] [401] [402] [403] [404] Underfull \hbox (badness 1735) in paragraph at lines 26297--26301 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [405] [406] [407] [408] [409] [410] [411] [412] [413] [414] Underfull \hbox (badness 2726) in paragraph at lines 26868--26871 []\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 [415] [416] [417] [418] [419] [420] [421] [422] [423] [424] [425] [426] [427] Underfull \hbox (badness 1052) in paragraph at lines 27695--27700 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [428] [429] [430] [431] [432] Underfull \vbox (badness 10000) has occurred while \output is active [433] [434] [435] [436] [437] [438] [439] Underfull \hbox (badness 1533) in paragraph at lines 28504--28507 []\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 [440] [441] [442] Underfull \hbox (badness 1163) in paragraph at lines 28666--28677 []\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 [443] [444] [445] [446] [447] [448] [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] Underfull \hbox (badness 10000) in paragraph at lines 30189--30193 []\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 30189--30193 \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 30211--30213 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [467] [468] [469] [470] [471] [472] [473] [474] [475] Underfull \hbox (badness 1655) in paragraph at lines 30759--30761 []\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 [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] Underfull \hbox (badness 10000) in paragraph at lines 31434--31438 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [487] [488] [489] [490] Underfull \hbox (badness 2302) in paragraph at lines 31674--31681 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 31674--31681 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 3333) in paragraph at lines 31674--31681 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 31674--31681 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [491] [492] Underfull \hbox (badness 2261) in paragraph at lines 31830--31835 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if Underfull \hbox (badness 10000) in paragraph at lines 31857--31863 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters [493] Underfull \hbox (badness 10000) in paragraph at lines 31933--31938 []\T1/ptm/m/n/10 Note that since \T1/zi4/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by [494] [495] [496] [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] Underfull \vbox (badness 3803) has occurred while \output is active [533] [534] [535] [536] [537] [538] [539] [540] Underfull \hbox (badness 1072) in paragraph at lines 34971--34975 []\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 34976--34980 []\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 35004--35010 []\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 35004--35010 \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 35004--35010 \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 [541] Underfull \hbox (badness 3343) in paragraph at lines 35016--35023 \T1/ptm/m/n/10 early in the start-up pro-cess-ing. It con-tains en-vi-ron-ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 35016--35023 \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 35016--35023 \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 [542] [543] [544] [545] Underfull \hbox (badness 10000) in paragraph at lines 35314--35320 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35314--35320 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [546] [547] [548] [549] [550] [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] Underfull \hbox (badness 3333) in paragraph at lines 37158--37163 []\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 [576] [577] [578] [579] [580] [581] Underfull \vbox (badness 10000) has occurred while \output is active [582] [583] [584] [585] Underfull \hbox (badness 1472) in paragraph at lines 37781--37784 []\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 [586] [587] [588] [589] [590] [591] [592] [593] [594] [595] [596] [597] [598] Underfull \vbox (badness 3803) has occurred while \output is active [599] Underfull \hbox (badness 10000) in paragraph at lines 38646--38650 []\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., [600] [601] [602] [603] Underfull \hbox (badness 10000) in paragraph at lines 38894--38897 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [604] [605] Underfull \hbox (badness 10000) in paragraph at lines 39012--39016 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [606] Underfull \hbox (badness 10000) in paragraph at lines 39074--39078 [][][]\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 \ [][]$\T1/zi4/m/n/10 https : / / developer . [607] [608] [609] [610] [611] [612] [613] [614] Underfull \hbox (badness 4013) in paragraph at lines 39619--39621 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [615] [616] [617] [618] [619] [620] Underfull \vbox (badness 10000) has occurred while \output is active [621] [622] [623] [624] [625] [626] [627] Underfull \hbox (badness 3460) in paragraph at lines 40480--40483 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via [628] Underfull \hbox (badness 1990) in paragraph at lines 40487--40495 []\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 40487--40495 \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 [629] [630] [631] [632] Underfull \hbox (badness 10000) in paragraph at lines 40764--40767 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [633] [634] [635] Underfull \hbox (badness 1917) in paragraph at lines 40992--40999 []\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 [636] [637] [638] [639] [640] [641] [642] [643] [644] [645] [646] Underfull \hbox (badness 3668) in paragraph at lines 41671--41673 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [647] Underfull \hbox (badness 2401) in paragraph at lines 41777--41781 []\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 [648] [649] [650] Underfull \hbox (badness 2111) in paragraph at lines 41953--41958 \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. [651] Underfull \hbox (badness 7362) in paragraph at lines 41969--41974 []\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 [652] [653] [654] [655] [656] [657] [658] [659] [660] Underfull \hbox (badness 5417) in paragraph at lines 42526--42530 []\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 [661] Underfull \hbox (badness 10000) in paragraph at lines 42587--42591 []\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 [662]) (./compiler-pkg.tex Chapter 2. [663] [664] [665] [666]) (./datasets-pkg.tex Chapter 3. [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] Underfull \vbox (badness 1515) has occurred while \output is active [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] Underfull \hbox (badness 6658) in paragraph at lines 3954--3956 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/zi4/m/n/10 h ttp : / / www . ltrr . arizona . edu / ~hallman / [734] Underfull \vbox (badness 10000) has occurred while \output is active [735] [736] [737] [738] Underfull \vbox (badness 10000) has occurred while \output is active [739] [740] [741] [742] [743] [744] Overfull \vbox (18.9959pt too high) has occurred while \output is active [745] [746] [747]) (./grDevices-pkg.tex [748] Chapter 4. [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] Underfull \hbox (badness 5175) in paragraph at lines 1069--1071 []\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 [766] [767] [768] [769] Underfull \hbox (badness 1852) in paragraph at lines 1266--1269 []\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 [770] [771] [772] Underfull \hbox (badness 1490) in paragraph at lines 1472--1477 \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 [773] [774] Underfull \hbox (badness 10000) in paragraph at lines 1595--1599 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [775] [776] [777] [778] Underfull \hbox (badness 1325) in paragraph at lines 1878--1888 \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 , [779] [780] Underfull \hbox (badness 10000) in paragraph at lines 1983--1985 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [781] [782] [783] Underfull \hbox (badness 6758) in paragraph at lines 2144--2147 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [784] [785] [786] [787] [788] [789] [790] [791] [792] Underfull \hbox (badness 10000) in paragraph at lines 2737--2738 [793] [794] [795] [796] [797] [798] [799] [800] Underfull \hbox (badness 10000) in paragraph at lines 3235--3240 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [801] [802] [803] [804] Underfull \hbox (badness 3302) in paragraph at lines 3494--3497 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3508--3510 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] [816] [817] Underfull \hbox (badness 1067) in paragraph at lines 4331--4338 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [818] [819] Underfull \hbox (badness 3364) in paragraph at lines 4491--4493 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$ \T1/zi4/m/n/10 https : / / partners . adobe . com / public / [820] Underfull \hbox (badness 1789) in paragraph at lines 4568--4570 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [821] Underfull \hbox (badness 1377) in paragraph at lines 4618--4623 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [822] Underfull \hbox (badness 2671) in paragraph at lines 4645--4653 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4694--4701 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4702--4711 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4702--4711 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, Underfull \hbox (badness 1755) in paragraph at lines 4712--4714 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [823] [824] Underfull \hbox (badness 1377) in paragraph at lines 4823--4828 []\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 [825] Underfull \hbox (badness 7344) in paragraph at lines 4883--4885 []\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 [826] [827] Underfull \hbox (badness 2035) in paragraph at lines 5007--5016 []\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 5007--5016 \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 5007--5016 \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 , [828] Underfull \hbox (badness 10000) in paragraph at lines 5075--5082 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5075--5082 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [829] [830] [831] Underfull \hbox (badness 1546) in paragraph at lines 5217--5225 []\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 , [832] Underfull \hbox (badness 1648) in paragraph at lines 5294--5298 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [833] [834] [835] [836] [837] [838] [839] Underfull \hbox (badness 10000) in paragraph at lines 5746--5749 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [840] [841] [842] [843] [844] [845] Underfull \hbox (badness 1189) in paragraph at lines 6143--6145 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [846] [847] Underfull \hbox (badness 10000) in paragraph at lines 6241--6243 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [848] [849] [850] [851] Underfull \hbox (badness 3780) in paragraph at lines 6532--6538 []\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 , [852] [853] [854] Underfull \hbox (badness 2680) in paragraph at lines 6733--6735 []\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 [855] [856] [857]) (./graphics-pkg.tex [858] Chapter 5. [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] [869] Underfull \hbox (badness 10000) in paragraph at lines 683--690 []\T1/zi4/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [870] [871] [872] [873] Underfull \vbox (badness 3803) has occurred while \output is active [874] [875] [876] [877] [878] [879] Underfull \hbox (badness 4634) in paragraph at lines 1255--1258 [][][]\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 , [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] [892] [893] [894] [895] [896] Underfull \hbox (badness 1009) in paragraph at lines 2289--2296 \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 [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] Underfull \vbox (badness 10000) has occurred while \output is active [919] [920] [921] [922] Underfull \hbox (badness 1867) in paragraph at lines 3931--3935 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [923] [924] [925] [926] [927] [928] [929] [930] Underfull \hbox (badness 1924) in paragraph at lines 4378--4383 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain Underfull \hbox (badness 2529) in paragraph at lines 4409--4412 []\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 [931] [932] [933] [934] [935] Underfull \hbox (badness 10000) in paragraph at lines 4759--4765 []\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 4759--4765 \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 [936] [937] Underfull \hbox (badness 10000) in paragraph at lines 4890--4893 [938 >/library/graphics/help/figures/mai.pdf>] Underfull \hbox (badness 10000) in paragraph at lines 4951--4953 Underfull \vbox (badness 10000) has occurred while \output is active [939] [940 >/library/graphics/help/figures/oma.pdf>] [941] Underfull \hbox (badness 10000) in paragraph at lines 5141--5143 []\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 [942] Underfull \vbox (badness 3803) has occurred while \output is active [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6612--6613 [][] [965] [966 >/library/graphics/help/figures/pch .pdf>] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] Underfull \hbox (badness 1048) in paragraph at lines 7321--7326 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [977] [978] Underfull \hbox (badness 1102) in paragraph at lines 7437--7440 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] [989] [990] [991] [992] Underfull \hbox (badness 1043) in paragraph at lines 8272--8276 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [993] [994] [995] [996] [997] [998] [999] Underfull \hbox (badness 10000) in paragraph at lines 8675--8677 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8677--8679 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color [1000]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8757 \HeaderA{units}{Graphical Units}{units} [1001] [1002] [1003] [1004]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1005] [1006] [1007] [1008] [1009] [1010] Underfull \hbox (badness 2680) in paragraph at lines 390--393 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] Underfull \hbox (badness 4279) in paragraph at lines 970--979 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] Underfull \vbox (badness 3803) has occurred while \output is active [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] Underfull \hbox (badness 1067) in paragraph at lines 4340--4343 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1078] [1079] [1080] [1081] Underfull \hbox (badness 7256) in paragraph at lines 4585--4587 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] Underfull \hbox (badness 10000) in paragraph at lines 5862--5868 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] Underfull \hbox (badness 7649) in paragraph at lines 6341--6344 []\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 [1112] [1113] [1114] [1115]) (./methods-pkg.tex [1116] Chapter 7. [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] Underfull \vbox (badness 3803) has occurred while \output is active [1125] Underfull \vbox (badness 10000) has occurred while \output is active [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] Underfull \hbox (badness 2237) in paragraph at lines 1386--1388 []\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 [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] Underfull \hbox (badness 1077) in paragraph at lines 1933--1940 []\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 [1144] Underfull \hbox (badness 10000) in paragraph at lines 1982--1987 []\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 1982--1987 \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 [1145] [1146] [1147] Underfull \hbox (badness 1242) in paragraph at lines 2215--2220 []\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 = [1148] [1149] [1150] [1151] [1152] Underfull \hbox (badness 10000) in paragraph at lines 2575--2578 []\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 [1153] [1154] Underfull \hbox (badness 1132) in paragraph at lines 2715--2719 []\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 [1155] Underfull \hbox (badness 1033) in paragraph at lines 2747--2752 \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 [1156] [1157] [1158] [1159] [1160] [1161] [1162] Underfull \hbox (badness 1102) in paragraph at lines 3304--3306 []\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 [1163] [1164] [1165] [1166] [1167] [1168] Underfull \hbox (badness 10000) in paragraph at lines 3637--3642 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Underfull \hbox (badness 10000) in paragraph at lines 3645--3654 []\T1/ptm/m/n/10 The [1169] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3765--3766 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3765--3766 [1170] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3849--3850 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180] Underfull \hbox (badness 1436) in paragraph at lines 4446--4449 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4475--4481 []\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 4475--4481 \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 [1181] Underfull \hbox (badness 1092) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4534--4541 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] Underfull \vbox (badness 10000) has occurred while \output is active [1191] [1192] Underfull \hbox (badness 10000) in paragraph at lines 5358--5359 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1193] Underfull \hbox (badness 4036) in paragraph at lines 5440--5443 []\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 [1194] Underfull \hbox (badness 3803) in paragraph at lines 5515--5517 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1195] [1196] [1197] [1198] Underfull \hbox (badness 1087) in paragraph at lines 5747--5752 []\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 [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] Underfull \hbox (badness 1675) in paragraph at lines 6454--6460 \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 [1207] [1208] [1209] [1210] Underfull \vbox (badness 10000) has occurred while \output is active [1211] [1212] [1213] [1214]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6976 \aliasA{S4}{S3Part}{S4} [1215] [1216] [1217]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate ignored \relax l.7232 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7234 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7235 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7237 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7238 \aliasA{Summary}{S4groupGeneric}{Summary} [1218] Underfull \hbox (badness 2050) in paragraph at lines 7299--7303 []\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 [1219] [1220] [1221] Underfull \hbox (badness 1286) in paragraph at lines 7487--7489 []\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 [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] Underfull \vbox (badness 10000) has occurred while \output is active [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] [1261] [1262] [1263] Underfull \hbox (badness 1852) in paragraph at lines 10567--10571 []\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., [1264] [1265] [1266] [1267]) (./parallel-pkg.tex [1268] 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 [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] Underfull \hbox (badness 3386) in paragraph at lines 1268--1271 []\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 [1289] [1290] [1291]) (./splines-pkg.tex [1292] 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 [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] [1306] [1307]) (./stats-pkg.tex [1308] Chapter 10. [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] Underfull \hbox (badness 1412) in paragraph at lines 848--850 []\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 [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] Underfull \hbox (badness 2503) in paragraph at lines 1329--1332 []\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 , [1330] [1331] [1332] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1333] [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] Underfull \hbox (badness 3965) in paragraph at lines 2168--2170 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1344] [1345] [1346] [1347] [1348] Underfull \hbox (badness 3965) in paragraph at lines 2510--2512 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] Underfull \hbox (badness 2726) in paragraph at lines 3224--3240 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1360] [1361] Underfull \hbox (badness 2503) in paragraph at lines 3354--3357 []\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 , [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] Underfull \hbox (badness 3989) in paragraph at lines 4582--4589 []\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 = [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] Underfull \hbox (badness 2556) in paragraph at lines 5193--5196 []\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 5210--5212 []\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 [1392] [1393] [1394] [1395] Underfull \hbox (badness 1142) in paragraph at lines 5451--5463 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1396] [1397] [1398] Underfull \hbox (badness 2503) in paragraph at lines 5599--5603 []\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 , [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] Underfull \hbox (badness 8132) in paragraph at lines 6102--6107 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1407] [1408] [1409] [1410] [1411] Underfull \hbox (badness 7081) in paragraph at lines 6380--6383 []\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 6384--6386 []\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 [1412] [1413] [1414] [1415] [1416] Underfull \vbox (badness 3803) has occurred while \output is active [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 10000) in paragraph at lines 7225--7228 []\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 [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] Underfull \hbox (badness 2626) in paragraph at lines 8860--8863 []\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 [1452] Underfull \hbox (badness 2503) in paragraph at lines 8960--8964 []\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 , [1453] [1454] [1455] [1456] [1457] [1458] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9309--9311 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] Underfull \hbox (badness 4518) in paragraph at lines 10235--10240 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1473] [1474] [1475] [1476] [1477] Underfull \hbox (badness 2142) in paragraph at lines 10577--10580 []\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 10596--10599 []\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, [1478] Underfull \hbox (badness 1708) in paragraph at lines 10658--10662 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1479] [1480] [1481] [1482] [1483] [1484] Underfull \hbox (badness 1694) in paragraph at lines 11054--11057 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1485] Underfull \hbox (badness 1867) in paragraph at lines 11073--11082 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1486] [1487] [1488] [1489] [1490] Underfull \hbox (badness 10000) in paragraph at lines 11380--11383 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1491] [1492]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.hat}) has been already used, duplicate ignored \relax l.11534 \aliasA{hat}{influence.measures}{hat} [1493] [1494] Underfull \hbox (badness 1484) in paragraph at lines 11665--11667 []\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 [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] Underfull \hbox (badness 4441) in paragraph at lines 12248--12250 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12255--12257 []\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 [1505] [1506] [1507] [1508] [1509] [1510] Underfull \hbox (badness 2894) in paragraph at lines 12589--12593 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] Underfull \hbox (badness 4518) in paragraph at lines 13287--13292 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1523] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] Underfull \hbox (badness 4518) in paragraph at lines 13934--13939 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1532] [1533] [1534] Underfull \hbox (badness 10000) in paragraph at lines 14072--14076 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14079--14081 []\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 [1535] [1536] [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] Underfull \hbox (badness 2503) in paragraph at lines 15141--15145 []\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 , [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] Underfull \hbox (badness 1584) in paragraph at lines 15653--15659 []\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 [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] Underfull \hbox (badness 2359) in paragraph at lines 17290--17292 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1587] Underfull \vbox (badness 3803) has occurred while \output is active [1588] Underfull \vbox (badness 10000) has occurred while \output is active [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] Underfull \hbox (badness 1377) in paragraph at lines 18201--18206 []\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 18206--18209 []\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 [1602] Underfull \hbox (badness 1454) in paragraph at lines 18219--18223 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18227--18231 []\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 [1603] [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] Underfull \hbox (badness 1337) in paragraph at lines 18843--18846 []\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 [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] [1621] Underfull \hbox (badness 3049) in paragraph at lines 19329--19333 []\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 [1622] [1623] [1624] [1625] Underfull \hbox (badness 5563) in paragraph at lines 19579--19581 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19582--19585 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1626] [1627] [1628] [1629] [1630] [1631] Underfull \hbox (badness 2503) in paragraph at lines 19957--19960 []\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 , [1632] Underfull \hbox (badness 10000) in paragraph at lines 19984--19986 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1633] [1634] [1635] [1636] [1637] [1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648] [1649] [1650] Underfull \hbox (badness 10000) in paragraph at lines 21047--21053 []\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 , [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] Underfull \hbox (badness 1337) in paragraph at lines 22385--22391 []\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 [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] Overfull \hbox (27.74408pt too wide) in paragraph at lines 22930--22930 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1681] [1682] [1683] [1684] [1685] Underfull \hbox (badness 10000) in paragraph at lines 23180--23183 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1686] [1687] [1688] [1689] [1690] [1691] [1692] [1693] [1694] Underfull \hbox (badness 10000) in paragraph at lines 23765--23768 []\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 [1695] Underfull \hbox (badness 3690) in paragraph at lines 23816--23820 [][][]\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 [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] Underfull \hbox (badness 3439) in paragraph at lines 24286--24292 [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSasympO rig[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSbiexp[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSfpl[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 SSgompertz[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 SSmicmen[][][]\T1/ptm/m/n/1 0 , [1705] [1706] [1707] Underfull \hbox (badness 1867) in paragraph at lines 24483--24485 []\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 24496--24500 \T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 24496--24500 \T1/zi4/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was Underfull \hbox (badness 1132) in paragraph at lines 24496--24500 \T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o f un-de-ter-mined co-ef-fi-cients, e.g., for [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] Underfull \hbox (badness 10000) in paragraph at lines 24968--24973 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732] Underfull \hbox (badness 3514) in paragraph at lines 26010--26015 []\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 [1733] Underfull \hbox (badness 3514) in paragraph at lines 26072--26077 []\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 [1734] Underfull \hbox (badness 3514) in paragraph at lines 26129--26134 []\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 [1735] Underfull \hbox (badness 3514) in paragraph at lines 26190--26196 []\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 [1736] [1737] [1738] [1739] Underfull \hbox (badness 3514) in paragraph at lines 26403--26408 []\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 [1740] Underfull \hbox (badness 3514) in paragraph at lines 26459--26464 []\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 [1741] Underfull \hbox (badness 3514) in paragraph at lines 26517--26522 []\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 [1742] Underfull \hbox (badness 3514) in paragraph at lines 26572--26577 []\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 [1743] Underfull \hbox (badness 6691) in paragraph at lines 26641--26646 []\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 [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751] [1752] Underfull \hbox (badness 10000) in paragraph at lines 27165--27168 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27165--27168 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1753] [1754] [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] Underfull \hbox (badness 5431) in paragraph at lines 27771--27773 []\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 [1763] [1764] [1765] Underfull \hbox (badness 5431) in paragraph at lines 27981--27984 []\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 [1766] [1767] [1768] [1769] [1770] [1771] Underfull \hbox (badness 1337) in paragraph at lines 28295--28299 []\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 [1772] [1773] Underfull \hbox (badness 10000) in paragraph at lines 28412--28415 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1774] [1775] Underfull \hbox (badness 1616) in paragraph at lines 28595--28598 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1776] [1777] [1778] [1779] [1780] [1781] [1782] [1783] [1784] [1785] [1786] [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] Underfull \hbox (badness 10000) in paragraph at lines 29721--29725 []\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 [1795] [1796] [1797] Underfull \vbox (badness 10000) has occurred while \output is active [1798] [1799] [1800] Underfull \hbox (badness 1337) in paragraph at lines 30085--30089 []\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 [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] Underfull \hbox (badness 1337) in paragraph at lines 30569--30573 []\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 [1809] Underfull \hbox (badness 2142) in paragraph at lines 30646--30651 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the [1810] Underfull \hbox (badness 5161) in paragraph at lines 30668--30670 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1811] [1812] [1813] [1814] [1815] [1816] Underfull \hbox (badness 10000) in paragraph at lines 31050--31055 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1817] [1818]) (./stats4-pkg.tex Chapter 11. [1819] [1820] [1821] [1822] [1823] [1824]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} [1825] [1826] [1827] [1828]) (./tcltk-pkg.tex Chapter 12. [1829] [1830] [1831] [1832] [1833] [1834] [1835] Underfull \vbox (badness 10000) has occurred while \output is active [1836] Underfull \vbox (badness 10000) has occurred while \output is active [1837] 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 [1838] [1839] [1840] [1841] [1842] [1843] [1844] [1845] [1846] [1847] [1848] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1849]) (./tools-pkg.tex [1850] Chapter 13. [1851] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1852] 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 [1853] [1854] 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 [1855] [1856] 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 [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] Underfull \hbox (badness 1635) in paragraph at lines 1054--1056 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1868] Underfull \hbox (badness 4441) in paragraph at lines 1132--1142 \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- [1869] Underfull \hbox (badness 1014) in paragraph at lines 1154--1156 []\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 1160--1162 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1197--1200 []\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 1197--1200 \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 , [1870] [1871] [1872] Underfull \hbox (badness 10000) in paragraph at lines 1366--1368 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1873] [1874] [1875] Underfull \hbox (badness 2293) in paragraph at lines 1540--1542 []\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 [1876] [1877] Underfull \hbox (badness 7981) in paragraph at lines 1678--1683 []\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 1685--1687 []\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 [1878] [1879] [1880] [1881]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1882 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1882] [1883] [1884] [1885] [1886] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2184--2184 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1887] [1888] [1889] Underfull \hbox (badness 7981) in paragraph at lines 2353--2359 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of [1890] [1891] [1892] [1893] [1894] [1895] [1896] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2818. [1897] [1898] [1899] [1900] Underfull \hbox (badness 1424) in paragraph at lines 3100--3102 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1901] [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] [1910] [1911] [1912] Underfull \hbox (badness 10000) in paragraph at lines 3800--3802 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1913] [1914] Underfull \hbox (badness 10000) in paragraph at lines 3939--3942 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1915] [1916] Underfull \hbox (badness 1137) in paragraph at lines 4037--4039 []\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 [1917] [1918] [1919] Underfull \hbox (badness 1838) in paragraph at lines 4246--4252 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4246--4252 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1920] Underfull \hbox (badness 5726) in paragraph at lines 4326--4331 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4326--4331 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1921] [1922] [1923] Underfull \hbox (badness 2197) in paragraph at lines 4475--4485 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4475--4485 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1924] Underfull \hbox (badness 1571) in paragraph at lines 4538--4542 []\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 [1925] [1926] [1927]) (./utils-pkg.tex [1928] Chapter 14. [1929] Underfull \hbox (badness 2556) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1930] [1931] [1932] [1933] [1934] [1935] [1936] Underfull \hbox (badness 10000) in paragraph at lines 546--552 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 546--552 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1937] [1938] Underfull \hbox (badness 5847) in paragraph at lines 660--666 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 660--666 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1939] Underfull \hbox (badness 3861) in paragraph at lines 728--733 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1940] [1941] [1942] Underfull \hbox (badness 1430) in paragraph at lines 893--900 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 893--900 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 893--900 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 893--900 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 904--906 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1943] [1944] [1945] [1946] [1947] [1948] [1949] Underfull \hbox (badness 1371) in paragraph at lines 1375--1377 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 2057) in paragraph at lines 1863--1865 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1958] Underfull \hbox (badness 10000) in paragraph at lines 1958--1960 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1959] [1960] Underfull \hbox (badness 5189) in paragraph at lines 2060--2062 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1961] Underfull \vbox (badness 3803) has occurred while \output is active [1962] [1963] [1964] Underfull \hbox (badness 1661) in paragraph at lines 2278--2285 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2294--2297 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1965] [1966] [1967] [1968] [1969] [1970] Underfull \hbox (badness 10000) in paragraph at lines 2703--2707 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2708--2711 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1971] [1972] [1973] [1974] [1975] [1976] [1977] [1978] [1979] [1980] [1981] Underfull \hbox (badness 1430) in paragraph at lines 3385--3393 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the Underfull \hbox (badness 1231) in paragraph at lines 3434--3440 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1982] [1983] [1984] [1985] [1986] [1987] [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.4274 ...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.4274 ...mat Unordered and Ordered Lists}{format} [1996] [1997] [1998] [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] [2010] [2011] Underfull \hbox (badness 1371) in paragraph at lines 5271--5273 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [2012] Underfull \hbox (badness 1502) in paragraph at lines 5360--5365 []\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 5360--5365 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2013] [2014] [2015] Underfull \hbox (badness 10000) in paragraph at lines 5533--5542 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, [2016] Underfull \hbox (badness 2150) in paragraph at lines 5596--5599 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2017] [2018] Underfull \hbox (badness 3118) in paragraph at lines 5733--5735 []\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 Underfull \hbox (badness 2409) in paragraph at lines 5766--5770 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [2019] [2020] Underfull \hbox (badness 1325) in paragraph at lines 5874--5878 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [2021] Underfull \hbox (badness 10000) in paragraph at lines 5957--5960 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 5957--5960 \T1/ptm/m/n/10 to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2022] Underfull \hbox (badness 3219) in paragraph at lines 6030--6037 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6030--6037 \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 6030--6037 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [2023] Underfull \hbox (badness 10000) in paragraph at lines 6110--6115 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] [2047] Underfull \hbox (badness 10000) in paragraph at lines 7527--7529 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7532--7537 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] Underfull \hbox (badness 1789) in paragraph at lines 8087--8089 []\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 [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] Underfull \hbox (badness 1097) in paragraph at lines 8916--8919 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2069] Underfull \hbox (badness 3000) in paragraph at lines 9052--9057 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] Underfull \hbox (badness 2134) in paragraph at lines 9635--9640 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2079] [2080] [2081] [2082] [2083] [2084] [2085] Underfull \hbox (badness 5077) in paragraph at lines 10060--10064 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10060--10064 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 2469) in paragraph at lines 10072--10076 []\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 10072--10076 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2086] [2087] [2088] [2089] [2090] Overfull \hbox (18.77168pt too wide) in paragraph at lines 10366--10366 []\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 '[] [2091] Underfull \hbox (badness 10000) in paragraph at lines 10429--10431 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][] []\T1/ptm/m/n/10 s are nicely viewed via [2092] [2093] [2094] Underfull \hbox (badness 2150) in paragraph at lines 10605--10607 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2095] [2096] [2097] [2098] Underfull \hbox (badness 10000) in paragraph at lines 10824--10828 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n ow taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 10855--10861 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2099] [2100] Underfull \hbox (badness 2096) in paragraph at lines 10973--10976 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 10977--10980 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether JPEG fig-ures should be gen-er-ated. Ig-nored if [2101] Underfull \hbox (badness 1009) in paragraph at lines 11049--11060 []\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 [2102] [2103] [2104] [2105] [2106] Underfull \hbox (badness 3780) in paragraph at lines 11355--11359 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 11374--11377 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2107] [2108] [2109] [2110] [2111] [2112] Underfull \hbox (badness 2818) in paragraph at lines 11746--11751 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 11755--11758 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2113] [2114] [2115] [2116] [2117] Underfull \hbox (badness 10000) in paragraph at lines 12018--12020 []\T1/ptm/m/n/10 Options other than \T1/zi4/m/sl/10 memory = "none" \T1/ptm/m/n /10 ap-ply only to files pro-duced by [2118] [2119] Underfull \hbox (badness 1057) in paragraph at lines 12175--12182 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in turn, [2120] [2121] [2122] [2123] Underfull \hbox (badness 6510) in paragraph at lines 12434--12438 []\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 is set to t he com-mand \T1/zi4/m/sl/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 12441--12444 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 12441--12444 \T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131] Underfull \hbox (badness 10000) in paragraph at lines 12983--12985 []\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 1052) in paragraph at lines 12986--12988 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2132] Underfull \hbox (badness 10000) in paragraph at lines 13016--13021 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined see Underfull \hbox (badness 10000) in paragraph at lines 13016--13021 [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 av ailable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 1297) in paragraph at lines 13016--13021 \T1/zi4/m/sl/10 available.packages(contriburl = contriburl, method = method) \T 1/ptm/m/n/10 and hence by Underfull \hbox (badness 10000) in paragraph at lines 13045--13048 [][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n /10 , [2133] [2134] [2135] [2136] Overfull \hbox (23.85939pt too wide) in paragraph at lines 13287--13290 [][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi -gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](, package = "") [2137] [2138] Underfull \hbox (badness 1454) in paragraph at lines 13364--13368 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, [2139] Underfull \hbox (badness 10000) in paragraph at lines 13434--13436 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion [2140] [2141] [2142]) (./fullrefman.ind [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187] [2188] [2189] [2190] [2191] Overfull \hbox (33.3567pt too wide) in paragraph at lines 8523--8525 []\T1/zi4/m/it/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] Overfull \hbox (5.8567pt too wide) in paragraph at lines 11513--11515 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_depends Overfull \hbox (5.8567pt too wide) in paragraph at lines 11515--11517 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_results Overfull \hbox (5.8567pt too wide) in paragraph at lines 11517--11519 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_timings [2205] [2206] [2207] [2208] [2209] [2210] [2211] [2212] [2213]) (./fullrefman.aux) LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.write.matrix} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.survreg} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.coxph} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.stepAIC} has been referenced but 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Transcript written on fullrefman.log. make[3]: Leaving directory '/<>/doc/manual' make[2]: Leaving directory '/<>/doc' make[1]: Leaving directory '/<>' /usr/bin/make -k vignettes 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 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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 *** check *** touch check-stamp fakeroot debian/rules binary-arch *** 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/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 touch install-indep-stamp gunzip -9v /<>/debian/r-base-core/usr/share/info/*.gz /<>/debian/r-base-core/usr/share/info/R-FAQ.info.gz: 67.0% -- 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: 69.9% -- 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: 82.9% -- replaced with /<>/debian/r-base-core/usr/share/info/R-exts.info-3 /<>/debian/r-base-core/usr/share/info/R-exts.info.gz: 69.7% -- replaced with /<>/debian/r-base-core/usr/share/info/R-exts.info /<>/debian/r-base-core/usr/share/info/R-intro.info.gz: 70.0% -- replaced with /<>/debian/r-base-core/usr/share/info/R-intro.info /<>/debian/r-base-core/usr/share/info/R-ints.info.gz: 67.7% -- 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' 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 1968 -rw-rw-r-- 1 root root 1242482 Apr 14 03:10 libRmath.a -rwxrwxr-x 1 root root 762312 Apr 14 03:10 libRmath.so drwxr-xr-x 2 root root 4096 Apr 14 03:10 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 43 with fuzz 2 (offset 10 lines). done dh_bash-completion # edd 12 Jan 2016 new location #install -m 0644 debian/R.bash-completion \ # debian/r-base-core/usr/share/bash-completion/completions/R (cd /<>/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 '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 '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' dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package r-base-core: unknown substitution variable ${perl:Depends} dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 136 INFO: pkgstriptranslations version 136 INFO: pkgstriptranslations version 136 pkgstriptranslations: processing r-mathlib (in debian/r-mathlib); do_strip: , oemstrip: 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: debian/r-base-core/usr/share/applications/R.desktop: does not have gettext domain, not stripping pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/r-base-core/DEBIAN/control, package r-base-core, directory debian/r-base-core .. removing usr/share/doc/r-base-core/changelog.gz pkgstripfiles: Truncating usr/share/doc/r-base-core/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-base-core ... oopkgmaintainermangler: 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) ... oINFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... oWARNING: optipng failed on usr/lib/R/library/graphics/help/figures/mai.png, ignoring .WARNING: optipng failed on usr/lib/R/library/graphics/help/figures/pch.png, ignoring INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... oWARNING: optipng failed on usr/lib/R/library/graphics/help/figures/oma.png, ignoring .INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... ooINFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " INFO: pkgstripfiles: waiting for lock (r-base-core-dbg) ... pkgstripfiles: processing control file: debian/r-mathlib/DEBIAN/control, package r-mathlib, directory debian/r-mathlib .. removing usr/share/doc/r-mathlib/changelog.gz pkgstripfiles: Truncating usr/share/doc/r-mathlib/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package r-mathlib ... pkgstripfiles: No PNG files. dpkg-deb: building package 'r-mathlib' in '../r-mathlib_3.4.4-1_armhf.deb'. o pkgstripfiles: PNG optimization (8/0) for package r-base-core took 15 s dpkg-deb: building package 'r-base-core' in '../r-base-core_3.4.4-1_armhf.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_3.4.4-1_armhf.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../r-base_3.4.4-1_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build r-base-3.4.4 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20180414-0312 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ r-base_3.4.4-1_armhf.changes: ----------------------------- Format: 1.8 Date: Thu, 15 Mar 2018 06:28:51 -0500 Source: r-base Binary: r-base r-base-core r-base-dev r-mathlib r-base-html r-doc-pdf r-doc-html r-doc-info r-recommended r-base-core-dbg Architecture: armhf Version: 3.4.4-1 Distribution: bionic-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 (3.4.4-1) unstable; urgency=medium . * New upstream version released this morning Checksums-Sha1: 175e0474f090287057160b2b65c6aa7b33c9b13c 4133292 r-base-core-dbg_3.4.4-1_armhf.deb 3985a9161a0871e21698c52a2b9c228c94e796c6 22879384 r-base-core_3.4.4-1_armhf.deb 5e64bae242335449f1c4955d342533e4666e06d1 16030 r-base_3.4.4-1_armhf.buildinfo 8b39bf6b0eea250e17ff5d550c2ecd64185f42a2 1564288 r-mathlib_3.4.4-1_armhf.deb Checksums-Sha256: 00f40b0e82a3cc4397805adccbdd4b521d520690e9ada652cfe4d5479c9e80b1 4133292 r-base-core-dbg_3.4.4-1_armhf.deb d87c0452755e678f36bbe0802eccfed843da3e81fdb7b52296679e5b04232be2 22879384 r-base-core_3.4.4-1_armhf.deb d707ec6243cc377820b6f36efb9ce197d2b5fa225d518433ede595e63308fa9a 16030 r-base_3.4.4-1_armhf.buildinfo d49f536415abfd13ccea7d23280fa821dc9e48d31f7cf2db6b57e2f7f4e98007 1564288 r-mathlib_3.4.4-1_armhf.deb Files: 7f5a627681eb8787f77d1bdc21bc493d 4133292 debug optional r-base-core-dbg_3.4.4-1_armhf.deb d58e72fe2f86af58d1875c126b5043b5 22879384 gnu-r optional r-base-core_3.4.4-1_armhf.deb a9372c8d292cbd29ecbb6d84bd1ff409 16030 gnu-r optional r-base_3.4.4-1_armhf.buildinfo 2047f3da94e859774e3a22db84b2306a 1564288 gnu-r optional r-mathlib_3.4.4-1_armhf.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ r-base-core-dbg_3.4.4-1_armhf.deb --------------------------------- new debian package, version 2.0. size 4133292 bytes: control archive=2248 bytes. 2636 bytes, 40 lines control 2088 bytes, 20 lines md5sums Package: r-base-core-dbg Source: r-base Version: 3.4.4-1 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Dirk Eddelbuettel Installed-Size: 4662 Depends: r-base-core (= 3.4.4-1), r-base-dev (= 3.4.4-1) Section: debug Priority: optional Homepage: http://www.r-project.org/ Description: GNU R debug symbols for statistical comp. language and environment R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files. . The design of R has been heavily influenced by two existing languages: Becker, Chambers & Wilks' S and Sussman's Scheme. Whereas the resulting language is very similar in appearance to S, the underlying implementation and semantics are derived from Scheme. . The core of R is an interpreted computer language which allows branching and looping as well as modular programming using functions. Most of the user-visible functions in R are written in R. It is possible for the user to interface to procedures written in the C, C++, or FORTRAN languages for efficiency, and many of R's core functions do so. The R distribution contains functionality for a large number of statistical procedures and underlying applied math computations. There is also a large set of functions which provide a flexible graphical environment for creating various kinds of data presentations. . Additionally, several thousand extension "packages" are available from CRAN, the Comprehensive R Archive Network, many also as Debian packages, named 'r-cran-'. . This package contains debugging symbol tables for the binaries and dynamic libraries in the r-base-core package. Build-Ids: 04fb88021d2ee4de042dde7c26018fedd6e085cd 0bebcb3e39e266001434c4f626bc3f4d30edd97d 1024c67d1643a225fdd3042a71593bde39b239c9 1adef7aeade916f9c3c100558303d84b6d7f1180 26755f8aa5847236185b888c76bab11335172c7e 54ae6ea02c0d9a62ef854217e42bdfe7200ed5b9 5a552805100eb593b6a6fb7330c96caafb2c99fc 7c64a28471bede9ddeea52d3fa318bb4af08b0f2 7dc32f74ada430a0f3f7b1d0def34b242d9c6d6d 7f7869258d65bb61357246ed4a4fceec92ce0bcd 88ce9f8a2ff7bb00098985057f80260d552e2731 964159c7d7fa7f790fcce3ee3696d65a12ce321f b5ccdadc3881c92ed62687a94544a20461cf1ff8 b6bbf929cc92e25db1e0e1e926bc08f6b36b312d bc5bb49530c511b697879fa925ff4fa96c84c5a3 c177fb6df405fa31e3f585573fe2029b74fa54af d20d077ca888b095e2eee1f8976517e0f50ab016 e4979d803a8e377ac36504599d23ff5c548f030b fff478329b6e1f213ce5fbf126ec434e5644866d drwxr-xr-x root/root 0 2018-03-15 11:28 ./ drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/ drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/lib/ drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/lib/debug/ drwxr-xr-x 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2018-03-15 11:28 ./usr/lib/debug/.build-id/c1/77fb6df405fa31e3f585573fe2029b74fa54af.debug drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/lib/debug/.build-id/d2/ -rw-r--r-- root/root 133156 2018-03-15 11:28 ./usr/lib/debug/.build-id/d2/0d077ca888b095e2eee1f8976517e0f50ab016.debug drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/lib/debug/.build-id/e4/ -rw-r--r-- root/root 122724 2018-03-15 11:28 ./usr/lib/debug/.build-id/e4/979d803a8e377ac36504599d23ff5c548f030b.debug drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/lib/debug/.build-id/ff/ -rw-r--r-- root/root 2525960 2018-03-15 11:28 ./usr/lib/debug/.build-id/ff/f478329b6e1f213ce5fbf126ec434e5644866d.debug drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/share/ drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/share/doc/r-base-core-dbg/ lrwxrwxrwx root/root 0 2018-03-15 11:28 ./usr/share/doc/r-base-core-dbg/NEWS.gz -> changelog.gz lrwxrwxrwx root/root 0 2018-03-15 11:28 ./usr/share/doc/r-base-core-dbg/changelog.Debian.gz -> ../r-base-core/changelog.Debian.gz -rw-r--r-- root/root 20761 2010-08-05 18:01 ./usr/share/doc/r-base-core-dbg/copyright drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/share/lintian/ drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/share/lintian/overrides/ r-base-core_3.4.4-1_armhf.deb ----------------------------- new debian package, version 2.0. size 22879384 bytes: control archive=23936 bytes. 93 bytes, 5 lines conffiles 2781 bytes, 45 lines control 73358 bytes, 931 lines md5sums 2433 bytes, 68 lines * postinst #!/bin/sh 214 bytes, 5 lines * postrm #!/bin/sh 864 bytes, 37 lines * preinst #!/bin/sh 886 bytes, 29 lines * prerm #!/bin/sh Package: r-base-core Source: r-base Version: 3.4.4-1 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Dirk Eddelbuettel Installed-Size: 34437 Depends: zip, unzip, libpaper-utils, xdg-utils, libblas3 | libblas.so.3, libbz2-1.0, libc6 (>= 2.27), libcairo2 (>= 1.6.0), libcurl4 (>= 7.28.0), libglib2.0-0 (>= 2.12.0), libgomp1 (>= 4.9), libicu60 (>= 60.1-1~), 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), libreadline7 (>= 6.0), libtcl8.6 (>= 8.6.0), libtiff5 (>= 4.0.3), libtk8.6 (>= 8.6.0), libx11-6, libxt6, zlib1g (>= 1:1.1.4), ucf (>= 3.0), ca-certificates Recommends: r-recommended, r-base-dev, r-doc-html Suggests: ess, r-doc-info | r-doc-pdf, r-mathlib, r-base-html Conflicts: r-base-latex, r-cran-rcompgen, r-gnome Replaces: r-base (<= 1.4.1-1), r-base-latex (<= 2.9.2-4), r-cran-rcompgen (<= 0.1-17-1), r-gnome (<= 2.3.1), r-recommended (<< 1.9.0) Provides: r-api-3.4, r-base-latex, r-cran-rcompgen, r-gnome Section: gnu-r Priority: optional Homepage: http://www.r-project.org/ Description: GNU R core of statistical computation and graphics system R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files. . The design of R has been heavily influenced by two existing languages: Becker, Chambers & Wilks' S and Sussman's Scheme. Whereas the resulting language is very similar in appearance to S, the underlying implementation and semantics are derived from Scheme. . The core of R is an interpreted computer language which allows branching and looping as well as modular programming using functions. Most of the user-visible functions in R are written in R. It is possible for the user to interface to procedures written in the C, C++, or FORTRAN languages for efficiency, and many of R's core functions do so. The R distribution contains functionality for a large number of statistical procedures and underlying applied math computations. There is also a large set of functions which provide a flexible graphical environment for creating various kinds of data presentations. . Additionally, several thousand extension "packages" are available from CRAN, the Comprehensive R Archive Network, many also as Debian packages, named 'r-cran-'. . This package provides the core GNU R system from which only the optional documentation packages r-base-html, r-doc-html, r-doc-pdf and r-doc-info have been split off to somewhat reduce the size of this package. drwxr-xr-x root/root 0 2018-03-15 11:28 ./ drwxr-xr-x root/root 0 2018-03-15 11:28 ./etc/ drwxr-xr-x root/root 0 2018-03-15 11:28 ./etc/R/ -rw-r--r-- root/root 7957 2018-03-15 11:28 ./etc/R/Makeconf -rw-r--r-- root/root 934 2018-03-15 11:28 ./etc/R/Renviron.site -rw-r--r-- root/root 988 2018-03-15 11:28 ./etc/R/Rprofile.site -rw-r--r-- root/root 797 2018-03-15 11:28 ./etc/R/ldpaths -rw-r--r-- root/root 1161 2018-03-15 11:28 ./etc/R/repositories drwxr-xr-x root/root 0 2018-03-15 11:28 ./etc/ld.so.conf.d/ drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/ drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/bin/ -rwxr-xr-x root/root 8728 2018-03-15 11:28 ./usr/bin/R -rwxr-xr-x root/root 9648 2018-03-15 11:28 ./usr/bin/Rscript drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/lib/ drwxr-xr-x 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2018-03-11 13:59 ./usr/share/lintian/overrides/r-base-core drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/share/man/ drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/share/man/man1/ -rw-r--r-- root/root 2587 2018-03-15 11:28 ./usr/share/man/man1/R.1.gz -rw-r--r-- root/root 659 2018-03-15 11:28 ./usr/share/man/man1/Rscript.1.gz drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/share/texmf/ drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/share/texmf/tex/ drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/share/texmf/tex/latex/ lrwxrwxrwx root/root 0 2018-03-15 11:28 ./usr/share/texmf/tex/latex/R -> ../../../R/share/texmf r-mathlib_3.4.4-1_armhf.deb --------------------------- new debian package, version 2.0. size 1564288 bytes: control archive=2080 bytes. 1839 bytes, 40 lines control 1148 bytes, 17 lines md5sums 369 bytes, 27 lines * postinst #!/bin/sh 21 bytes, 1 lines shlibs 74 bytes, 2 lines triggers Package: r-mathlib Source: r-base Version: 3.4.4-1 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Dirk Eddelbuettel Installed-Size: 1980 Depends: libc6 (>= 2.23) Recommends: r-base-core (= 3.4.4-1), r-base-dev (= 3.4.4-1) 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 2018-03-15 11:28 ./ drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/ drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/include/ -rw-r--r-- root/root 18138 2018-03-15 11:28 ./usr/include/Rmath.h drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/lib/ -rw-r--r-- root/root 257970 2018-03-15 11:28 ./usr/lib/libRmath.a lrwxrwxrwx root/root 0 2018-03-15 11:28 ./usr/lib/libRmath.so -> libRmath.so.1 lrwxrwxrwx root/root 0 2018-03-15 11:28 ./usr/lib/libRmath.so.1 -> libRmath.so.1.0.0 -rw-r--r-- root/root 124428 2018-03-15 11:28 ./usr/lib/libRmath.so.1.0.0 drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/lib/pkgconfig/ -rw-r--r-- root/root 173 2018-03-15 11:28 ./usr/lib/pkgconfig/libRmath.pc drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/share/ drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/share/doc/r-mathlib/ -rw-r--r-- root/root 35933 2014-03-12 23:03 ./usr/share/doc/r-mathlib/NEWS.0.gz -rw-r--r-- root/root 108753 2014-03-12 23:03 ./usr/share/doc/r-mathlib/NEWS.1.gz -rw-r--r-- root/root 96630 2018-03-07 23:02 ./usr/share/doc/r-mathlib/NEWS.2.Rd.gz -rw-r--r-- root/root 229656 2014-03-12 23:03 ./usr/share/doc/r-mathlib/NEWS.2.gz -rw-r--r-- root/root 93734 2018-03-07 23:02 ./usr/share/doc/r-mathlib/NEWS.Rd.gz lrwxrwxrwx root/root 0 2018-03-15 11:28 ./usr/share/doc/r-mathlib/NEWS.gz -> changelog.gz -rw-r--r-- root/root 488518 2018-03-15 11:28 ./usr/share/doc/r-mathlib/NEWS.pdf.gz -rw-r--r-- root/root 399187 2018-03-15 11:28 ./usr/share/doc/r-mathlib/NEWS.rds.gz -rw-r--r-- root/root 2107 2016-10-04 09:14 ./usr/share/doc/r-mathlib/README.gz -rw-r--r-- root/root 3026 2010-08-05 18:01 ./usr/share/doc/r-mathlib/README.mathlib -rw-r--r-- root/root 943 2018-03-15 11:28 ./usr/share/doc/r-mathlib/changelog.Debian.gz -rw-r--r-- root/root 20761 2010-08-05 18:01 ./usr/share/doc/r-mathlib/copyright drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/share/doc/r-mathlib/examples/ -rw-r--r-- root/root 1371 2015-08-25 22:18 ./usr/share/doc/r-mathlib/examples/test.c drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/share/lintian/ drwxr-xr-x root/root 0 2018-03-15 11:28 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 364 2018-03-11 13:59 ./usr/share/lintian/overrides/r-mathlib +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 299968 Build-Time: 2049 Distribution: bionic-proposed Host Architecture: armhf Install-Time: 479 Job: r-base_3.4.4-1.dsc Machine Architecture: arm64 Package: r-base Package-Time: 2536 Source-Version: 3.4.4-1 Space: 299968 Status: successful Version: 3.4.4-1 -------------------------------------------------------------------------------- Finished at 20180414-0312 Build needed 00:42:16, 299968k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-14757513 Scanning for processes to kill in build PACKAGEBUILD-14757513 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-14757513 Stopping target for build PACKAGEBUILD-14757513 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-14757513 Removing build PACKAGEBUILD-14757513