Start: 2014-04-16 17:47:57 UTC Package: shogun-r Priority: optional Section: science Installed-Size: 704 Maintainer: Soeren Sonnenburg Architecture: amd64 Source: shogun Version: 0.9.3-4 Depends: libatlas3gf-base, libc6 (>= 2.2.5), libgcc1 (>= 1:4.1.1), libglpk0 (>= 4.30), libhdf5-serial-1.8.4 | libhdf5-1.8.4, liblzma2 (>= 4.999.9beta), liblzo2-2, libshogun8 (= 0.9.3-4), libshogunui5 (= 0.9.3-4), libstdc++6 (>= 4.1.1), zlib1g (>= 1:1.1.4), r-base-core Filename: pool/main/s/shogun/shogun-r_0.9.3-4_amd64.deb Size: 67812 MD5sum: 509e13d250b914935628f7d150582120 SHA1: 8ca17ff0883c498de4cc29fd59947b85fdf9e975 SHA256: a948df4180dfe53c35480f4d1637e0daa9fa7c2ebb89e66bc8a24d64762b38d1 Description: Large Scale Machine Learning Toolbox SHOGUN - is a new machine learning toolbox with focus on large scale kernel methods and especially on Support Vector Machines (SVM) with focus to bioinformatics. It provides a generic SVM object interfacing to several different SVM implementations. Each of the SVMs can be combined with a variety of the many kernels implemented. It can deal with weighted linear combination of a number of sub-kernels, each of which not necessarily working on the same domain, where an optimal sub-kernel weighting can be learned using Multiple Kernel Learning. Apart from SVM 2-class classification and regression problems, a number of linear methods like Linear Discriminant Analysis (LDA), Linear Programming Machine (LPM), (Kernel) Perceptrons and also algorithms to train hidden markov models are implemented. The input feature-objects can be dense, sparse or strings and of type int/short/double/char and can be converted into different feature types. Chains of preprocessors (e.g. substracting the mean) can be attached to each feature object allowing for on-the-fly pre-processing. . SHOGUN comes in different flavours, a stand-a-lone version and also with interfaces to Matlab(tm), R, Octave, Readline and Python. This is the R package. Homepage: http://www.shogun-toolbox.org Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python2.7/dist-packages timeout -s INT -k 5m 35m /srv/piuparts.debian.org/sbin/piuparts --skip-logrotatefiles-test --warn-on-others --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge -i /etc/shells --scriptsdir /etc/piuparts/scripts-squeeze --warn-on-debsums-errors --mirror 'http://mirror.bm.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz -d squeeze --no-upgrade-test --apt shogun-r=0.9.3-4 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at http://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 0.57.1~201403012113~0.57-23-gfd8571c starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --skip-logrotatefiles-test --warn-on-others --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge -i /etc/shells --scriptsdir /etc/piuparts/scripts-squeeze --warn-on-debsums-errors --mirror 'http://mirror.bm.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz -d squeeze --no-upgrade-test --apt shogun-r=0.9.3-4 0m0.0s INFO: Running on: Linux piu-slave-bm-a 3.2.0-4-amd64 #1 SMP Debian 3.2.54-2 x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpnr4pjk 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpnr4pjk 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz'] 0m1.8s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'mount', '-t', 'proc', 'proc', '/proc'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'mount', '-t', 'proc', 'proc', '/proc'] 0m1.8s DEBUG: sources.list: deb http://mirror.bm.debian.org/debian/ squeeze main 0m1.8s DEBUG: Created policy-rc.d and chmodded it. 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-get', 'update'] 0m1.9s DUMP: Hit http://mirror.bm.debian.org squeeze Release.gpg Ign http://mirror.bm.debian.org/debian/ squeeze/main Translation-en Hit http://mirror.bm.debian.org squeeze Release Hit http://mirror.bm.debian.org squeeze/main amd64 Packages Reading package lists... 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-get', 'update'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DUMP: Reading package lists... Building dependency tree... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpnr4pjk/tmp/scripts/ 0m2.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts-squeeze to /srv/piuparts.debian.org/tmp/tmpnr4pjk/tmp/scripts/ 0m2.2s INFO: Running scripts post_setup 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/post_setup_experimental'] 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/post_setup_experimental'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/post_setup_forbid_home'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/post_setup_forbid_home'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/post_setup_squeeze-fake-essential'] 0m3.1s DUMP: *** Adding fake essential packages *** Reading package lists... Building dependency tree... Suggested packages: perl-modules The following NEW packages will be installed: adduser ucf 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 320 kB of archives. After this operation, 1532 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ squeeze/main adduser all 3.112+nmu2 [250 kB] Get:2 http://mirror.bm.debian.org/debian/ squeeze/main ucf all 3.0025+nmu1 [69.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 320 kB in 0s (23.3 MB/s) Selecting previously deselected package adduser. (Reading database ... 6135 files and directories currently installed.) Unpacking adduser (from .../adduser_3.112+nmu2_all.deb) ... Selecting previously deselected package ucf. Unpacking ucf (from .../ucf_3.0025+nmu1_all.deb) ... Moving old data out of the way Setting up adduser (3.112+nmu2) ... Setting up ucf (3.0025+nmu1) ... 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/post_setup_squeeze-fake-essential'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-get', 'clean'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-get', 'clean'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg', '--get-selections', '*'] 0m3.6s DUMP: adduser install apt install base-files install base-passwd install bash install bsdutils install coreutils install dash install debconf install debconf-i18n install debian-archive-keyring install debianutils install diffutils install dpkg install e2fslibs install e2fsprogs install findutils install gcc-4.4-base install gnupg install gpgv install grep install gzip install hostname install initscripts install insserv install libacl1 install libattr1 install libblkid1 install libbz2-1.0 install libc-bin install libc6 install libcomerr2 install libdb4.8 install libgcc1 install liblocale-gettext-perl install liblzma2 install libncurses5 install libpam-modules install libpam-runtime install libpam0g install libreadline6 install libselinux1 install libsepol1 install libslang2 install libss2 install libstdc++6 install libtext-charwidth-perl install libtext-iconv-perl install libtext-wrapi18n-perl install libusb-0.1-4 install libuuid1 install login install lsb-base install mawk install mount install ncurses-base install ncurses-bin install passwd install perl-base install readline-common install sed install sensible-utils install sysv-rc install sysvinit install sysvinit-utils install tar install tzdata install ucf install util-linux install xz-utils install zlib1g install 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg', '--get-selections', '*'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg-divert', '--list'] 0m3.6s DUMP: diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /bin/sync to /bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg-divert', '--list'] 0m3.6s INFO: apt-cache does not know about any of the requested packages 0m3.6s INFO: Running scripts pre_test 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/pre_test_root_password'] 0m3.6s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/pre_test_root_password'] 0m3.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnr4pjk'] 0m3.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnr4pjk'] 0m4.6s DEBUG: No broken symlinks as far as we can find. 0m4.6s INFO: Running scripts pre_install 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/pre_install_database-server'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/pre_install_database-server'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/pre_install_exceptions'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/pre_install_exceptions'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/pre_install_extras'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/pre_install_extras'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-cache', 'show', 'shogun-r=0.9.3-4'] 0m4.7s DUMP: Package: shogun-r Priority: optional Section: science Installed-Size: 704 Maintainer: Soeren Sonnenburg Architecture: amd64 Source: shogun Version: 0.9.3-4 Depends: libatlas3gf-base, libc6 (>= 2.2.5), libgcc1 (>= 1:4.1.1), libglpk0 (>= 4.30), libhdf5-serial-1.8.4 | libhdf5-1.8.4, liblzma2 (>= 4.999.9beta), liblzo2-2, libshogun8 (= 0.9.3-4), libshogunui5 (= 0.9.3-4), libstdc++6 (>= 4.1.1), zlib1g (>= 1:1.1.4), r-base-core Filename: pool/main/s/shogun/shogun-r_0.9.3-4_amd64.deb Size: 67812 MD5sum: 509e13d250b914935628f7d150582120 SHA1: 8ca17ff0883c498de4cc29fd59947b85fdf9e975 SHA256: a948df4180dfe53c35480f4d1637e0daa9fa7c2ebb89e66bc8a24d64762b38d1 Description: Large Scale Machine Learning Toolbox SHOGUN - is a new machine learning toolbox with focus on large scale kernel methods and especially on Support Vector Machines (SVM) with focus to bioinformatics. It provides a generic SVM object interfacing to several different SVM implementations. Each of the SVMs can be combined with a variety of the many kernels implemented. It can deal with weighted linear combination of a number of sub-kernels, each of which not necessarily working on the same domain, where an optimal sub-kernel weighting can be learned using Multiple Kernel Learning. Apart from SVM 2-class classification and regression problems, a number of linear methods like Linear Discriminant Analysis (LDA), Linear Programming Machine (LPM), (Kernel) Perceptrons and also algorithms to train hidden markov models are implemented. The input feature-objects can be dense, sparse or strings and of type int/short/double/char and can be converted into different feature types. Chains of preprocessors (e.g. substracting the mean) can be attached to each feature object allowing for on-the-fly pre-processing. . SHOGUN comes in different flavours, a stand-a-lone version and also with interfaces to Matlab(tm), R, Octave, Readline and Python. This is the R package. Homepage: http://www.shogun-toolbox.org 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-cache', 'show', 'shogun-r=0.9.3-4'] 0m4.7s DEBUG: metapackage: Package: piuparts-depends-dummy Version: 0.invalid.0 Architecture: all Maintainer: piuparts developers team Description: Dummy package to satisfy dependencies - created by piuparts This package was created automatically by piuparts and can safely be removed Depends: libatlas3gf-base, libc6 (>= 2.2.5), libgcc1 (>= 1:4.1.1), libglpk0 (>= 4.30), libhdf5-serial-1.8.4 | libhdf5-1.8.4, liblzma2 (>= 4.999.9beta), liblzo2-2, libshogun8 (= 0.9.3-4), libshogunui5 (= 0.9.3-4), libstdc++6 (>= 4.1.1), zlib1g (>= 1:1.1.4), r-base-core 0m4.7s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmp3wsjn8/piuparts-depends-dummy'] 0m4.8s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmp3wsjn8/piuparts-depends-dummy.deb'. 0m4.8s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmp3wsjn8/piuparts-depends-dummy'] 0m4.8s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmp3wsjn8/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmpnr4pjk/tmp 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m4.8s DUMP: Selecting previously deselected package piuparts-depends-dummy. (Reading database ... 6258 files and directories currently installed.) Unpacking piuparts-depends-dummy (from tmp/piuparts-depends-dummy.deb) ... dpkg: dependency problems prevent configuration of piuparts-depends-dummy: piuparts-depends-dummy depends on libatlas3gf-base; however: Package libatlas3gf-base is not installed. piuparts-depends-dummy depends on libglpk0 (>= 4.30); however: Package libglpk0 is not installed. piuparts-depends-dummy depends on libhdf5-serial-1.8.4 | libhdf5-1.8.4; however: Package libhdf5-serial-1.8.4 is not installed. Package libhdf5-1.8.4 is not installed. piuparts-depends-dummy depends on liblzo2-2; however: Package liblzo2-2 is not installed. piuparts-depends-dummy depends on libshogun8 (= 0.9.3-4); however: Package libshogun8 is not installed. piuparts-depends-dummy depends on libshogunui5 (= 0.9.3-4); however: Package libshogunui5 is not installed. piuparts-depends-dummy depends on r-base-core; however: Package r-base-core is not installed. dpkg: error processing piuparts-depends-dummy (--install): dependency problems - leaving unconfigured Errors were encountered while processing: piuparts-depends-dummy 0m4.8s DEBUG: Command failed (status=1), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-get', '-yf', 'install'] 0m13.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Correcting dependencies... Done The following extra packages will be installed: defoma file fontconfig fontconfig-config libatlas3gf-base libcairo2 libdatrie1 libdb4.7 libexpat1 libfontconfig1 libfreetype6 libgdbm3 libgfortran3 libglib2.0-0 libglpk0 libgmp3c2 libhdf5-serial-1.8.4 libice6 libjpeg62 libltdl7 liblzo2-2 libmagic1 libnewt0.52 libpango1.0-0 libpango1.0-common libpaper-utils libpaper1 libpcre3 libpixman-1-0 libpng12-0 libpopt0 libshogun8 libshogunui5 libsm6 libthai-data libthai0 libtiff4 libx11-6 libx11-data libxau6 libxcb-render-util0 libxcb-render0 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1 libxss1 libxt6 perl perl-modules r-base-core tcl8.5 tk8.5 ttf-dejavu-core unzip whiptail x11-common xdg-utils zip Suggested packages: defoma-doc psfontmgr x-ttcidfont-conf dfontmgr libblas3gf liblapack3gf libiodbc2-dev libmysqlclient-dev ttf-japanese-gothic ttf-japanese-mincho ttf-thryomanes ttf-baekmuk ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp ttf-arphic-bkai00mp perl-doc libterm-readline-gnu-perl libterm-readline-perl-perl make ess r-doc-info r-doc-pdf r-mathlib r-base-html tclreadline gvfs-bin Recommended packages: libfont-freetype-perl libglib2.0-data shared-mime-info libfribidi0 netbase r-recommended r-base-dev r-doc-html xterm x-terminal-emulator iceweasel www-browser x11-utils x11-xserver-utils mime-support The following NEW packages will be installed: defoma file fontconfig fontconfig-config libatlas3gf-base libcairo2 libdatrie1 libdb4.7 libexpat1 libfontconfig1 libfreetype6 libgdbm3 libgfortran3 libglib2.0-0 libglpk0 libgmp3c2 libhdf5-serial-1.8.4 libice6 libjpeg62 libltdl7 liblzo2-2 libmagic1 libnewt0.52 libpango1.0-0 libpango1.0-common libpaper-utils libpaper1 libpcre3 libpixman-1-0 libpng12-0 libpopt0 libshogun8 libshogunui5 libsm6 libthai-data libthai0 libtiff4 libx11-6 libx11-data libxau6 libxcb-render-util0 libxcb-render0 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1 libxss1 libxt6 perl perl-modules r-base-core tcl8.5 tk8.5 ttf-dejavu-core unzip whiptail x11-common xdg-utils zip 0 upgraded, 60 newly installed, 0 to remove and 0 not upgraded. 1 not fully installed or removed. Need to get 44.7 MB of archives. After this operation, 125 MB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ squeeze/main libgfortran3 amd64 4.4.5-8 [291 kB] Get:2 http://mirror.bm.debian.org/debian/ squeeze/main libatlas3gf-base amd64 3.8.3-27 [6200 kB] Get:3 http://mirror.bm.debian.org/debian/ squeeze/main libgmp3c2 amd64 2:4.3.2+dfsg-1 [313 kB] Get:4 http://mirror.bm.debian.org/debian/ squeeze/main libltdl7 amd64 2.2.6b-2 [296 kB] Get:5 http://mirror.bm.debian.org/debian/ squeeze/main libglpk0 amd64 4.43-1 [446 kB] Get:6 http://mirror.bm.debian.org/debian/ squeeze/main libhdf5-serial-1.8.4 amd64 1.8.4-patch1-2 [1479 kB] Get:7 http://mirror.bm.debian.org/debian/ squeeze/main liblzo2-2 amd64 2.03-2 [59.6 kB] Get:8 http://mirror.bm.debian.org/debian/ squeeze/main libshogun8 amd64 0.9.3-4 [844 kB] Get:9 http://mirror.bm.debian.org/debian/ squeeze/main libshogunui5 amd64 0.9.3-4 [233 kB] Get:10 http://mirror.bm.debian.org/debian/ squeeze/main perl-modules all 5.10.1-17squeeze6 [3482 kB] Get:11 http://mirror.bm.debian.org/debian/ squeeze/main libdb4.7 amd64 4.7.25-9 [662 kB] Get:12 http://mirror.bm.debian.org/debian/ squeeze/main libgdbm3 amd64 1.8.3-9 [46.2 kB] Get:13 http://mirror.bm.debian.org/debian/ squeeze/main perl amd64 5.10.1-17squeeze6 [4462 kB] Get:14 http://mirror.bm.debian.org/debian/ squeeze/main zip amd64 3.0-3 [334 kB] Get:15 http://mirror.bm.debian.org/debian/ squeeze/main unzip amd64 6.0-4 [190 kB] Get:16 http://mirror.bm.debian.org/debian/ squeeze/main libpaper1 amd64 1.1.24 [21.5 kB] Get:17 http://mirror.bm.debian.org/debian/ squeeze/main libpaper-utils amd64 1.1.24 [18.2 kB] Get:18 http://mirror.bm.debian.org/debian/ squeeze/main xdg-utils all 1.0.2+cvs20100307-2 [65.8 kB] Get:19 http://mirror.bm.debian.org/debian/ squeeze/main libexpat1 amd64 2.0.1-7+squeeze1 [138 kB] Get:20 http://mirror.bm.debian.org/debian/ squeeze/main libfreetype6 amd64 2.4.2-2.1+squeeze4 [377 kB] Get:21 http://mirror.bm.debian.org/debian/ squeeze/main ttf-dejavu-core all 2.31-1 [1451 kB] Get:22 http://mirror.bm.debian.org/debian/ squeeze/main fontconfig-config all 2.8.0-2.1 [217 kB] Get:23 http://mirror.bm.debian.org/debian/ squeeze/main libfontconfig1 amd64 2.8.0-2.1 [281 kB] Get:24 http://mirror.bm.debian.org/debian/ squeeze/main libpixman-1-0 amd64 0.16.4-1+deb6u1 [237 kB] Get:25 http://mirror.bm.debian.org/debian/ squeeze/main libpng12-0 amd64 1.2.44-1+squeeze4 [180 kB] Get:26 http://mirror.bm.debian.org/debian/ squeeze/main libxau6 amd64 1:1.0.6-1 [16.8 kB] Get:27 http://mirror.bm.debian.org/debian/ squeeze/main libxdmcp6 amd64 1:1.0.3-2 [19.3 kB] Get:28 http://mirror.bm.debian.org/debian/ squeeze/main libxcb1 amd64 1.6-1+squeeze1 [44.3 kB] Get:29 http://mirror.bm.debian.org/debian/ squeeze/main libx11-data all 2:1.3.3-4+squeeze1 [184 kB] Get:30 http://mirror.bm.debian.org/debian/ squeeze/main libx11-6 amd64 2:1.3.3-4+squeeze1 [847 kB] Get:31 http://mirror.bm.debian.org/debian/ squeeze/main libxcb-render0 amd64 1.6-1+squeeze1 [15.9 kB] Get:32 http://mirror.bm.debian.org/debian/ squeeze/main libxcb-render-util0 amd64 0.3.6-1 [9772 B] Get:33 http://mirror.bm.debian.org/debian/ squeeze/main libxrender1 amd64 1:0.9.6-1+squeeze1 [31.2 kB] Get:34 http://mirror.bm.debian.org/debian/ squeeze/main libcairo2 amd64 1.8.10-6 [520 kB] Get:35 http://mirror.bm.debian.org/debian/ squeeze/main libpcre3 amd64 8.02-1.1 [234 kB] Get:36 http://mirror.bm.debian.org/debian/ squeeze/main libglib2.0-0 amd64 2.24.2-1 [1122 kB] Get:37 http://mirror.bm.debian.org/debian/ squeeze/main x11-common all 1:7.5+8+squeeze1 [279 kB] Get:38 http://mirror.bm.debian.org/debian/ squeeze/main libice6 amd64 2:1.0.6-2 [53.8 kB] Get:39 http://mirror.bm.debian.org/debian/ squeeze/main libjpeg62 amd64 6b1-1 [94.0 kB] Get:40 http://mirror.bm.debian.org/debian/ squeeze/main libnewt0.52 amd64 0.52.11-1 [71.8 kB] Get:41 http://mirror.bm.debian.org/debian/ squeeze/main libpopt0 amd64 1.16-1 [54.1 kB] Get:42 http://mirror.bm.debian.org/debian/ squeeze/main whiptail amd64 0.52.11-1 [40.2 kB] Get:43 http://mirror.bm.debian.org/debian/ squeeze/main libmagic1 amd64 5.04-5+squeeze2 [235 kB] Get:44 http://mirror.bm.debian.org/debian/ squeeze/main file amd64 5.04-5+squeeze2 [50.0 kB] Get:45 http://mirror.bm.debian.org/debian/ squeeze/main defoma all 0.11.11 [101 kB] Get:46 http://mirror.bm.debian.org/debian/ squeeze/main fontconfig amd64 2.8.0-2.1 [334 kB] Get:47 http://mirror.bm.debian.org/debian/ squeeze/main libpango1.0-common all 1.28.3-1+squeeze2 [114 kB] Get:48 http://mirror.bm.debian.org/debian/ squeeze/main libdatrie1 amd64 0.2.4-1 [26.8 kB] Get:49 http://mirror.bm.debian.org/debian/ squeeze/main libthai-data all 0.1.14-2 [198 kB] Get:50 http://mirror.bm.debian.org/debian/ squeeze/main libthai0 amd64 0.1.14-2 [41.5 kB] Get:51 http://mirror.bm.debian.org/debian/ squeeze/main libxft2 amd64 2.1.14-2 [55.7 kB] Get:52 http://mirror.bm.debian.org/debian/ squeeze/main libpango1.0-0 amd64 1.28.3-1+squeeze2 [330 kB] Get:53 http://mirror.bm.debian.org/debian/ squeeze/main libsm6 amd64 2:1.1.1-1 [25.0 kB] Get:54 http://mirror.bm.debian.org/debian/ squeeze/main libtiff4 amd64 3.9.4-5+squeeze10 [195 kB] Get:55 http://mirror.bm.debian.org/debian/ squeeze/main libxext6 amd64 2:1.1.2-1+squeeze1 [45.5 kB] Get:56 http://mirror.bm.debian.org/debian/ squeeze/main libxss1 amd64 1:1.2.0-2 [13.8 kB] Get:57 http://mirror.bm.debian.org/debian/ squeeze/main libxt6 amd64 1:1.0.7-1+squeeze1 [195 kB] Get:58 http://mirror.bm.debian.org/debian/ squeeze/main tcl8.5 amd64 8.5.8-2 [1599 kB] Get:59 http://mirror.bm.debian.org/debian/ squeeze/main tk8.5 amd64 8.5.8-1 [1182 kB] Get:60 http://mirror.bm.debian.org/debian/ squeeze/main r-base-core amd64 2.11.1-6 [14.0 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 44.7 MB in 2s (21.7 MB/s) Selecting previously deselected package libgfortran3. (Reading database ... 6258 files and directories currently installed.) Unpacking libgfortran3 (from .../libgfortran3_4.4.5-8_amd64.deb) ... Selecting previously deselected package libatlas3gf-base. Unpacking libatlas3gf-base (from .../libatlas3gf-base_3.8.3-27_amd64.deb) ... Selecting previously deselected package libgmp3c2. Unpacking libgmp3c2 (from .../libgmp3c2_2%3a4.3.2+dfsg-1_amd64.deb) ... Selecting previously deselected package libltdl7. Unpacking libltdl7 (from .../libltdl7_2.2.6b-2_amd64.deb) ... Selecting previously deselected package libglpk0. Unpacking libglpk0 (from .../libglpk0_4.43-1_amd64.deb) ... Selecting previously deselected package libhdf5-serial-1.8.4. Unpacking libhdf5-serial-1.8.4 (from .../libhdf5-serial-1.8.4_1.8.4-patch1-2_amd64.deb) ... Selecting previously deselected package liblzo2-2. Unpacking liblzo2-2 (from .../liblzo2-2_2.03-2_amd64.deb) ... Selecting previously deselected package libshogun8. Unpacking libshogun8 (from .../libshogun8_0.9.3-4_amd64.deb) ... Selecting previously deselected package libshogunui5. Unpacking libshogunui5 (from .../libshogunui5_0.9.3-4_amd64.deb) ... Selecting previously deselected package perl-modules. Unpacking perl-modules (from .../perl-modules_5.10.1-17squeeze6_all.deb) ... Selecting previously deselected package libdb4.7. Unpacking libdb4.7 (from .../libdb4.7_4.7.25-9_amd64.deb) ... Selecting previously deselected package libgdbm3. Unpacking libgdbm3 (from .../libgdbm3_1.8.3-9_amd64.deb) ... Selecting previously deselected package perl. Unpacking perl (from .../perl_5.10.1-17squeeze6_amd64.deb) ... Selecting previously deselected package zip. Unpacking zip (from .../archives/zip_3.0-3_amd64.deb) ... Selecting previously deselected package unzip. Unpacking unzip (from .../archives/unzip_6.0-4_amd64.deb) ... Selecting previously deselected package libpaper1. Unpacking libpaper1 (from .../libpaper1_1.1.24_amd64.deb) ... Selecting previously deselected package libpaper-utils. Unpacking libpaper-utils (from .../libpaper-utils_1.1.24_amd64.deb) ... Selecting previously deselected package xdg-utils. Unpacking xdg-utils (from .../xdg-utils_1.0.2+cvs20100307-2_all.deb) ... Selecting previously deselected package libexpat1. Unpacking libexpat1 (from .../libexpat1_2.0.1-7+squeeze1_amd64.deb) ... Selecting previously deselected package libfreetype6. Unpacking libfreetype6 (from .../libfreetype6_2.4.2-2.1+squeeze4_amd64.deb) ... Selecting previously deselected package ttf-dejavu-core. Unpacking ttf-dejavu-core (from .../ttf-dejavu-core_2.31-1_all.deb) ... Selecting previously deselected package fontconfig-config. Unpacking fontconfig-config (from .../fontconfig-config_2.8.0-2.1_all.deb) ... Selecting previously deselected package libfontconfig1. Unpacking libfontconfig1 (from .../libfontconfig1_2.8.0-2.1_amd64.deb) ... Selecting previously deselected package libpixman-1-0. Unpacking libpixman-1-0 (from .../libpixman-1-0_0.16.4-1+deb6u1_amd64.deb) ... Selecting previously deselected package libpng12-0. Unpacking libpng12-0 (from .../libpng12-0_1.2.44-1+squeeze4_amd64.deb) ... Selecting previously deselected package libxau6. Unpacking libxau6 (from .../libxau6_1%3a1.0.6-1_amd64.deb) ... Selecting previously deselected package libxdmcp6. Unpacking libxdmcp6 (from .../libxdmcp6_1%3a1.0.3-2_amd64.deb) ... Selecting previously deselected package libxcb1. Unpacking libxcb1 (from .../libxcb1_1.6-1+squeeze1_amd64.deb) ... Selecting previously deselected package libx11-data. Unpacking libx11-data (from .../libx11-data_2%3a1.3.3-4+squeeze1_all.deb) ... Selecting previously deselected package libx11-6. Unpacking libx11-6 (from .../libx11-6_2%3a1.3.3-4+squeeze1_amd64.deb) ... Selecting previously deselected package libxcb-render0. Unpacking libxcb-render0 (from .../libxcb-render0_1.6-1+squeeze1_amd64.deb) ... Selecting previously deselected package libxcb-render-util0. Unpacking libxcb-render-util0 (from .../libxcb-render-util0_0.3.6-1_amd64.deb) ... Selecting previously deselected package libxrender1. Unpacking libxrender1 (from .../libxrender1_1%3a0.9.6-1+squeeze1_amd64.deb) ... Selecting previously deselected package libcairo2. Unpacking libcairo2 (from .../libcairo2_1.8.10-6_amd64.deb) ... Selecting previously deselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_8.02-1.1_amd64.deb) ... Selecting previously deselected package libglib2.0-0. Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_amd64.deb) ... Selecting previously deselected package x11-common. Unpacking x11-common (from .../x11-common_1%3a7.5+8+squeeze1_all.deb) ... Selecting previously deselected package libice6. Unpacking libice6 (from .../libice6_2%3a1.0.6-2_amd64.deb) ... Selecting previously deselected package libjpeg62. Unpacking libjpeg62 (from .../libjpeg62_6b1-1_amd64.deb) ... Selecting previously deselected package libnewt0.52. Unpacking libnewt0.52 (from .../libnewt0.52_0.52.11-1_amd64.deb) ... Selecting previously deselected package libpopt0. Unpacking libpopt0 (from .../libpopt0_1.16-1_amd64.deb) ... Selecting previously deselected package whiptail. Unpacking whiptail (from .../whiptail_0.52.11-1_amd64.deb) ... Selecting previously deselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.04-5+squeeze2_amd64.deb) ... Selecting previously deselected package file. Unpacking file (from .../file_5.04-5+squeeze2_amd64.deb) ... Selecting previously deselected package defoma. Unpacking defoma (from .../defoma_0.11.11_all.deb) ... Selecting previously deselected package fontconfig. Unpacking fontconfig (from .../fontconfig_2.8.0-2.1_amd64.deb) ... Selecting previously deselected package libpango1.0-common. Unpacking libpango1.0-common (from .../libpango1.0-common_1.28.3-1+squeeze2_all.deb) ... Selecting previously deselected package libdatrie1. Unpacking libdatrie1 (from .../libdatrie1_0.2.4-1_amd64.deb) ... Selecting previously deselected package libthai-data. Unpacking libthai-data (from .../libthai-data_0.1.14-2_all.deb) ... Selecting previously deselected package libthai0. Unpacking libthai0 (from .../libthai0_0.1.14-2_amd64.deb) ... Selecting previously deselected package libxft2. Unpacking libxft2 (from .../libxft2_2.1.14-2_amd64.deb) ... Selecting previously deselected package libpango1.0-0. Unpacking libpango1.0-0 (from .../libpango1.0-0_1.28.3-1+squeeze2_amd64.deb) ... Selecting previously deselected package libsm6. Unpacking libsm6 (from .../libsm6_2%3a1.1.1-1_amd64.deb) ... Selecting previously deselected package libtiff4. Unpacking libtiff4 (from .../libtiff4_3.9.4-5+squeeze10_amd64.deb) ... Selecting previously deselected package libxext6. Unpacking libxext6 (from .../libxext6_2%3a1.1.2-1+squeeze1_amd64.deb) ... Selecting previously deselected package libxss1. Unpacking libxss1 (from .../libxss1_1%3a1.2.0-2_amd64.deb) ... Selecting previously deselected package libxt6. Unpacking libxt6 (from .../libxt6_1%3a1.0.7-1+squeeze1_amd64.deb) ... Selecting previously deselected package tcl8.5. Unpacking tcl8.5 (from .../tcl8.5_8.5.8-2_amd64.deb) ... Selecting previously deselected package tk8.5. Unpacking tk8.5 (from .../tk8.5_8.5.8-1_amd64.deb) ... Selecting previously deselected package r-base-core. Unpacking r-base-core (from .../r-base-core_2.11.1-6_amd64.deb) ... Setting up libgfortran3 (4.4.5-8) ... Setting up libatlas3gf-base (3.8.3-27) ... update-alternatives: using /usr/lib/atlas-base/atlas/libblas.so.3gf to provide /usr/lib/libblas.so.3gf (libblas.so.3gf) in auto mode. update-alternatives: using /usr/lib/atlas-base/atlas/liblapack.so.3gf to provide /usr/lib/liblapack.so.3gf (liblapack.so.3gf) in auto mode. Setting up libgmp3c2 (2:4.3.2+dfsg-1) ... Setting up libltdl7 (2.2.6b-2) ... Setting up libglpk0 (4.43-1) ... Setting up libhdf5-serial-1.8.4 (1.8.4-patch1-2) ... Setting up liblzo2-2 (2.03-2) ... Setting up libshogun8 (0.9.3-4) ... Setting up libshogunui5 (0.9.3-4) ... Setting up libdb4.7 (4.7.25-9) ... Setting up libgdbm3 (1.8.3-9) ... Setting up zip (3.0-3) ... Setting up unzip (6.0-4) ... Setting up libpaper1 (1.1.24) ... Creating config file /etc/papersize with new version Setting up libpaper-utils (1.1.24) ... Setting up xdg-utils (1.0.2+cvs20100307-2) ... Setting up libexpat1 (2.0.1-7+squeeze1) ... Setting up libfreetype6 (2.4.2-2.1+squeeze4) ... Setting up ttf-dejavu-core (2.31-1) ... Setting up fontconfig-config (2.8.0-2.1) ... Setting up libfontconfig1 (2.8.0-2.1) ... Setting up libpixman-1-0 (0.16.4-1+deb6u1) ... Setting up libpng12-0 (1.2.44-1+squeeze4) ... Setting up libxau6 (1:1.0.6-1) ... Setting up libxdmcp6 (1:1.0.3-2) ... Setting up libxcb1 (1.6-1+squeeze1) ... Setting up libx11-data (2:1.3.3-4+squeeze1) ... Setting up libx11-6 (2:1.3.3-4+squeeze1) ... Setting up libxcb-render0 (1.6-1+squeeze1) ... Setting up libxcb-render-util0 (0.3.6-1) ... Setting up libxrender1 (1:0.9.6-1+squeeze1) ... Setting up libcairo2 (1.8.10-6) ... Setting up libpcre3 (8.02-1.1) ... Setting up libglib2.0-0 (2.24.2-1) ... Setting up x11-common (1:7.5+8+squeeze1) ... invoke-rc.d: policy-rc.d denied execution of start. Setting up libice6 (2:1.0.6-2) ... Setting up libjpeg62 (6b1-1) ... Setting up libnewt0.52 (0.52.11-1) ... Setting up libpopt0 (1.16-1) ... Setting up whiptail (0.52.11-1) ... Setting up libmagic1 (5.04-5+squeeze2) ... Setting up file (5.04-5+squeeze2) ... Setting up fontconfig (2.8.0-2.1) ... Updating font configuration of fontconfig... Cleaning up category cid.. Cleaning up category truetype.. Cleaning up category type1.. Updating category type1.. Updating category truetype.. Updating category cid.. Cleaning up old fontconfig caches... done. Regenerating fonts cache... done. Setting up libdatrie1 (0.2.4-1) ... Setting up libthai-data (0.1.14-2) ... Setting up libthai0 (0.1.14-2) ... Setting up libxft2 (2.1.14-2) ... Setting up libsm6 (2:1.1.1-1) ... Setting up libtiff4 (3.9.4-5+squeeze10) ... Setting up libxext6 (2:1.1.2-1+squeeze1) ... Setting up libxss1 (1:1.2.0-2) ... Setting up libxt6 (1:1.0.7-1+squeeze1) ... Setting up tcl8.5 (8.5.8-2) ... update-alternatives: using /usr/bin/tclsh8.5 to provide /usr/bin/tclsh (tclsh) in auto mode. Setting up tk8.5 (8.5.8-1) ... update-alternatives: using /usr/bin/wish8.5 to provide /usr/bin/wish (wish) in auto mode. Setting up perl-modules (5.10.1-17squeeze6) ... Setting up perl (5.10.1-17squeeze6) ... update-alternatives: using /usr/bin/prename to provide /usr/bin/rename (rename) in auto mode. Setting up defoma (0.11.11) ... Setting up libpango1.0-common (1.28.3-1+squeeze2) ... Cleaning up font configuration of pango... Updating font configuration of pango... Cleaning up category xfont.. Updating category xfont.. *** You don't have any defomized font packages. *** So we are trying to force to generate pangox.aliases... Setting up libpango1.0-0 (1.28.3-1+squeeze2) ... Setting up r-base-core (2.11.1-6) ... Setting R_PAPERSIZE_USER default to 'a4' Creating config file /etc/R/Renviron with new version Setting up piuparts-depends-dummy (0.invalid.0) ... 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-get', '-yf', 'install'] 0m13.5s INFO: Installation of ['tmp/piuparts-depends-dummy.deb'] ok 0m13.5s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmpnr4pjk/tmp/piuparts-depends-dummy.deb 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m13.6s DUMP: piuparts-depends-dummy install ok installed 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m13.6s DUMP: (Reading database ... 10186 files and directories currently installed.) Removing piuparts-depends-dummy ... 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-get', 'clean'] 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-get', 'clean'] 0m14.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnr4pjk'] 0m14.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnr4pjk'] 0m15.9s ERROR: WARN: Broken symlinks: /etc/fonts/conf.d/30-defoma.conf -> /var/lib/defoma/fontconfig.d/fonts.conf 0m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-cache', 'policy'] 0m15.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror.bm.debian.org/debian/ squeeze/main amd64 Packages release v=6.0.9,o=Debian,a=oldstable,n=squeeze,l=Debian,c=main origin mirror.bm.debian.org Pinned packages: 0m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-cache', 'policy'] 0m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-cache', 'policy', 'shogun-r'] 0m15.9s DUMP: shogun-r: Installed: (none) Candidate: 0.9.3-4 Version table: 0.9.3-4 0 500 http://mirror.bm.debian.org/debian/ squeeze/main amd64 Packages 0m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-cache', 'policy', 'shogun-r'] 0m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-get', '-y', 'install', 'shogun-r=0.9.3-4'] 0m16.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: shogun-r 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 67.8 kB of archives. After this operation, 721 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ squeeze/main shogun-r amd64 0.9.3-4 [67.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 67.8 kB in 0s (1450 kB/s) Selecting previously deselected package shogun-r. (Reading database ... 10186 files and directories currently installed.) Unpacking shogun-r (from .../shogun-r_0.9.3-4_amd64.deb) ... Setting up shogun-r (0.9.3-4) ... 0m16.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-get', '-y', 'install', 'shogun-r=0.9.3-4'] 0m16.6s INFO: Running scripts post_install 0m16.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnr4pjk'] 0m17.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnr4pjk'] 0m18.3s ERROR: WARN: Broken symlinks: /etc/fonts/conf.d/30-defoma.conf -> /var/lib/defoma/fontconfig.d/fonts.conf 0m18.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg', '--get-selections', '*'] 0m18.3s DUMP: adduser install apt install base-files install base-passwd install bash install bsdutils install coreutils install dash install debconf install debconf-i18n install debian-archive-keyring install debianutils install defoma install diffutils install dpkg install e2fslibs install e2fsprogs install file install findutils install fontconfig install fontconfig-config install gcc-4.4-base install gnupg install gpgv install grep install gzip install hostname install initscripts install insserv install libacl1 install libatlas3gf-base install libattr1 install libblkid1 install libbz2-1.0 install libc-bin install libc6 install libcairo2 install libcomerr2 install libdatrie1 install libdb4.7 install libdb4.8 install libexpat1 install libfontconfig1 install libfreetype6 install libgcc1 install libgdbm3 install libgfortran3 install libglib2.0-0 install libglpk0 install libgmp3c2 install libhdf5-serial-1.8.4 install libice6 install libjpeg62 install liblocale-gettext-perl install libltdl7 install liblzma2 install liblzo2-2 install libmagic1 install libncurses5 install libnewt0.52 install libpam-modules install libpam-runtime install libpam0g install libpango1.0-0 install libpango1.0-common install libpaper-utils install libpaper1 install libpcre3 install libpixman-1-0 install libpng12-0 install libpopt0 install libreadline6 install libselinux1 install libsepol1 install libshogun8 install libshogunui5 install libslang2 install libsm6 install libss2 install libstdc++6 install libtext-charwidth-perl install libtext-iconv-perl install libtext-wrapi18n-perl install libthai-data install libthai0 install libtiff4 install libusb-0.1-4 install libuuid1 install libx11-6 install libx11-data install libxau6 install libxcb-render-util0 install libxcb-render0 install libxcb1 install libxdmcp6 install libxext6 install libxft2 install libxrender1 install libxss1 install libxt6 install login install lsb-base install mawk install mount install ncurses-base install ncurses-bin install passwd install perl install perl-base install perl-modules install r-base-core install readline-common install sed install sensible-utils install shogun-r install sysv-rc install sysvinit install sysvinit-utils install tar install tcl8.5 install tk8.5 install ttf-dejavu-core install tzdata install ucf install unzip install util-linux install whiptail install x11-common install xdg-utils install xz-utils install zip install zlib1g install 0m18.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg', '--get-selections', '*'] 0m19.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', '-ac'] 0m20.3s DUMP: debsums: no md5sums for mawk 0m20.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', '-ac'] 0m20.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m20.3s DUMP: 0.11.3~bpo70+1 0m20.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m20.3s INFO: Running adequate version 0.11.3~bpo70+1 now. 0m20.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'shogun-r'] 0m20.4s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'shogun-r'] 0m20.4s INFO: Running scripts pre_remove 0m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m20.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m20.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m20.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/pre_remove_exceptions'] 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/pre_remove_exceptions'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-get', 'remove', 'libglib2.0-0', 'libltdl7', 'libxss1', 'libpng12-0', 'libxrender1', 'defoma', 'libhdf5-serial-1.8.4', 'libxext6', 'libthai-data', 'libfreetype6', 'libice6', 'libpango1.0-common', 'file', 'libtiff4', 'libsm6', 'libthai0', 'libx11-data', 'libpaper1', 'libxcb1', 'zip', 'whiptail', 'fontconfig', 'libgmp3c2', 'libnewt0.52', 'libshogun8', 'libgfortran3', 'libcairo2', 'libxau6', 'libpaper-utils', 'xdg-utils', 'libglpk0', 'libx11-6', 'libmagic1', 'unzip', 'libgdbm3', 'libpcre3', 'libjpeg62', 'tk8.5', 'perl', 'perl-modules', 'libxdmcp6', 'x11-common', 'tcl8.5', 'libdatrie1', 'ttf-dejavu-core', 'libxft2', 'r-base-core', 'libshogunui5', 'libxcb-render-util0', 'libpopt0', 'liblzo2-2', 'libatlas3gf-base', 'fontconfig-config', 'libxt6', 'libdb4.7', 'libxcb-render0', 'libpango1.0-0', 'libexpat1', 'libpixman-1-0', 'libfontconfig1', 'shogun-r'] 0m22.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: defoma file fontconfig fontconfig-config libatlas3gf-base libcairo2 libdatrie1 libdb4.7 libexpat1 libfontconfig1 libfreetype6 libgdbm3 libgfortran3 libglib2.0-0 libglpk0 libgmp3c2 libhdf5-serial-1.8.4 libice6 libjpeg62 libltdl7 liblzo2-2 libmagic1 libnewt0.52 libpango1.0-0 libpango1.0-common libpaper-utils libpaper1 libpcre3 libpixman-1-0 libpng12-0 libpopt0 libshogun8 libshogunui5 libsm6 libthai-data libthai0 libtiff4 libx11-6 libx11-data libxau6 libxcb-render-util0 libxcb-render0 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1 libxss1 libxt6 perl perl-modules r-base-core shogun-r tcl8.5 tk8.5 ttf-dejavu-core unzip whiptail x11-common xdg-utils zip 0 upgraded, 0 newly installed, 61 to remove and 0 not upgraded. After this operation, 126 MB disk space will be freed. (Reading database ... 10339 files and directories currently installed.) Removing shogun-r ... Removing r-base-core ... Removing libpango1.0-0 ... Removing libpango1.0-common ... Purging font configuration of pango... Purging category xfont.. Removing defoma ... Removing file ... Removing fontconfig ... Removing tk8.5 ... Removing libxft2 ... Removing libcairo2 ... Removing libfontconfig1 ... Removing fontconfig-config ... Removing libshogunui5 ... Removing libshogun8 ... Removing libatlas3gf-base ... Removing libthai0 ... Removing libdatrie1 ... Removing libexpat1 ... Removing libfreetype6 ... Removing libhdf5-serial-1.8.4 ... Removing libgfortran3 ... Removing libglib2.0-0 ... Removing libglpk0 ... Removing libgmp3c2 ... Removing libxt6 ... Removing libsm6 ... Removing libice6 ... Removing libtiff4 ... Removing libjpeg62 ... Removing libltdl7 ... Removing liblzo2-2 ... Removing libmagic1 ... Removing whiptail ... Removing libnewt0.52 ... Removing libpaper-utils ... Removing libpaper1 ... Removing libpcre3 ... Removing libpixman-1-0 ... Removing libpng12-0 ... Removing libpopt0 ... Removing libthai-data ... Removing libxss1 ... Removing libxrender1 ... Removing libxext6 ... Removing libx11-6 ... Removing libx11-data ... Removing libxcb-render-util0 ... Removing libxcb-render0 ... Removing libxcb1 ... Removing libxau6 ... Removing libxdmcp6 ... Removing tcl8.5 ... Removing ttf-dejavu-core ... Removing unzip ... Removing x11-common ... invoke-rc.d: policy-rc.d denied execution of stop. Removing xdg-utils ... Removing zip ... Removing perl ... Removing perl-modules ... Removing libdb4.7 ... Removing libgdbm3 ... 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-get', 'remove', 'libglib2.0-0', 'libltdl7', 'libxss1', 'libpng12-0', 'libxrender1', 'defoma', 'libhdf5-serial-1.8.4', 'libxext6', 'libthai-data', 'libfreetype6', 'libice6', 'libpango1.0-common', 'file', 'libtiff4', 'libsm6', 'libthai0', 'libx11-data', 'libpaper1', 'libxcb1', 'zip', 'whiptail', 'fontconfig', 'libgmp3c2', 'libnewt0.52', 'libshogun8', 'libgfortran3', 'libcairo2', 'libxau6', 'libpaper-utils', 'xdg-utils', 'libglpk0', 'libx11-6', 'libmagic1', 'unzip', 'libgdbm3', 'libpcre3', 'libjpeg62', 'tk8.5', 'perl', 'perl-modules', 'libxdmcp6', 'x11-common', 'tcl8.5', 'libdatrie1', 'ttf-dejavu-core', 'libxft2', 'r-base-core', 'libshogunui5', 'libxcb-render-util0', 'libpopt0', 'liblzo2-2', 'libatlas3gf-base', 'fontconfig-config', 'libxt6', 'libdb4.7', 'libxcb-render0', 'libpango1.0-0', 'libexpat1', 'libpixman-1-0', 'libfontconfig1', 'shogun-r'] 0m22.0s INFO: Running scripts post_remove 0m22.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/post_remove_exceptions_lenny'] 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/post_remove_exceptions_lenny'] 0m22.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/post_remove_extras'] 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/post_remove_extras'] 0m22.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg', '--purge', 'libglib2.0-0', 'libltdl7', 'libxss1', 'libpng12-0', 'libxrender1', 'defoma', 'libhdf5-serial-1.8.4', 'libxext6', 'libthai-data', 'libfreetype6', 'libice6', 'libpango1.0-common', 'file', 'libtiff4', 'libsm6', 'libthai0', 'libx11-data', 'libpaper1', 'libxcb1', 'zip', 'whiptail', 'fontconfig', 'libgmp3c2', 'libnewt0.52', 'libshogun8', 'libgfortran3', 'libcairo2', 'libxau6', 'libpaper-utils', 'xdg-utils', 'libglpk0', 'libx11-6', 'libmagic1', 'unzip', 'libgdbm3', 'libpcre3', 'libjpeg62', 'tk8.5', 'perl', 'perl-modules', 'libxdmcp6', 'x11-common', 'tcl8.5', 'libdatrie1', 'ttf-dejavu-core', 'libxft2', 'r-base-core', 'libshogunui5', 'libxcb-render-util0', 'libpopt0', 'liblzo2-2', 'libatlas3gf-base', 'fontconfig-config', 'libxt6', 'libdb4.7', 'libxcb-render0', 'libpango1.0-0', 'libexpat1', 'libpixman-1-0', 'libfontconfig1'] 0m22.9s DUMP: (Reading database ... 6335 files and directories currently installed.) Removing libglib2.0-0 ... Purging configuration files for libglib2.0-0 ... Removing libltdl7 ... Purging configuration files for libltdl7 ... Removing libxss1 ... Purging configuration files for libxss1 ... Removing libpng12-0 ... Purging configuration files for libpng12-0 ... Removing libxrender1 ... Purging configuration files for libxrender1 ... Removing defoma ... Purging configuration files for defoma ... Removing libhdf5-serial-1.8.4 ... Purging configuration files for libhdf5-serial-1.8.4 ... Removing libxext6 ... Purging configuration files for libxext6 ... dpkg: warning: ignoring request to remove libthai-data which isn't installed. Removing libfreetype6 ... Purging configuration files for libfreetype6 ... Removing libice6 ... Purging configuration files for libice6 ... Removing libpango1.0-common ... Purging configuration files for libpango1.0-common ... dpkg: warning: while removing libpango1.0-common, directory '/etc/defoma' not empty so not removed. dpkg: warning: ignoring request to remove file which isn't installed. Removing libtiff4 ... Purging configuration files for libtiff4 ... Removing libsm6 ... Purging configuration files for libsm6 ... Removing libthai0 ... Purging configuration files for libthai0 ... dpkg: warning: ignoring request to remove libx11-data which isn't installed. Removing libpaper1 ... Purging configuration files for libpaper1 ... Removing libxcb1 ... Purging configuration files for libxcb1 ... dpkg: warning: ignoring request to remove zip which isn't installed. dpkg: warning: ignoring request to remove whiptail which isn't installed. Removing fontconfig ... Purging configuration files for fontconfig ... Removing libgmp3c2 ... Purging configuration files for libgmp3c2 ... Removing libnewt0.52 ... Purging configuration files for libnewt0.52 ... Removing libshogun8 ... Purging configuration files for libshogun8 ... Removing libgfortran3 ... Purging configuration files for libgfortran3 ... Removing libcairo2 ... Purging configuration files for libcairo2 ... Removing libxau6 ... Purging configuration files for libxau6 ... dpkg: warning: ignoring request to remove libpaper-utils which isn't installed. dpkg: warning: ignoring request to remove xdg-utils which isn't installed. Removing libglpk0 ... Purging configuration files for libglpk0 ... Removing libx11-6 ... Purging configuration files for libx11-6 ... Removing libmagic1 ... Purging configuration files for libmagic1 ... Removing unzip ... Purging configuration files for unzip ... Removing libgdbm3 ... Purging configuration files for libgdbm3 ... Removing libpcre3 ... Purging configuration files for libpcre3 ... dpkg: warning: ignoring request to remove libjpeg62 which isn't installed. Removing tk8.5 ... Purging configuration files for tk8.5 ... dpkg: warning: ignoring request to remove perl which isn't installed. Removing perl-modules ... Purging configuration files for perl-modules ... Removing libxdmcp6 ... Purging configuration files for libxdmcp6 ... Removing x11-common ... Purging configuration files for x11-common ... Removing tcl8.5 ... Purging configuration files for tcl8.5 ... Removing libdatrie1 ... Purging configuration files for libdatrie1 ... dpkg: warning: ignoring request to remove ttf-dejavu-core which isn't installed. Removing libxft2 ... Purging configuration files for libxft2 ... Removing r-base-core ... Purging configuration files for r-base-core ... Removing libshogunui5 ... Purging configuration files for libshogunui5 ... Removing libxcb-render-util0 ... Purging configuration files for libxcb-render-util0 ... Removing libpopt0 ... Purging configuration files for libpopt0 ... Removing liblzo2-2 ... Purging configuration files for liblzo2-2 ... Removing libatlas3gf-base ... Purging configuration files for libatlas3gf-base ... Removing fontconfig-config ... Purging configuration files for fontconfig-config ... Removing libxt6 ... Purging configuration files for libxt6 ... dpkg: warning: ignoring request to remove libdb4.7 which isn't installed. Removing libxcb-render0 ... Purging configuration files for libxcb-render0 ... Removing libpango1.0-0 ... Purging configuration files for libpango1.0-0 ... Removing libexpat1 ... Purging configuration files for libexpat1 ... Removing libpixman-1-0 ... Purging configuration files for libpixman-1-0 ... Removing libfontconfig1 ... Purging configuration files for libfontconfig1 ... 0m22.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg', '--purge', 'libglib2.0-0', 'libltdl7', 'libxss1', 'libpng12-0', 'libxrender1', 'defoma', 'libhdf5-serial-1.8.4', 'libxext6', 'libthai-data', 'libfreetype6', 'libice6', 'libpango1.0-common', 'file', 'libtiff4', 'libsm6', 'libthai0', 'libx11-data', 'libpaper1', 'libxcb1', 'zip', 'whiptail', 'fontconfig', 'libgmp3c2', 'libnewt0.52', 'libshogun8', 'libgfortran3', 'libcairo2', 'libxau6', 'libpaper-utils', 'xdg-utils', 'libglpk0', 'libx11-6', 'libmagic1', 'unzip', 'libgdbm3', 'libpcre3', 'libjpeg62', 'tk8.5', 'perl', 'perl-modules', 'libxdmcp6', 'x11-common', 'tcl8.5', 'libdatrie1', 'ttf-dejavu-core', 'libxft2', 'r-base-core', 'libshogunui5', 'libxcb-render-util0', 'libpopt0', 'liblzo2-2', 'libatlas3gf-base', 'fontconfig-config', 'libxt6', 'libdb4.7', 'libxcb-render0', 'libpango1.0-0', 'libexpat1', 'libpixman-1-0', 'libfontconfig1'] 0m22.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg', '--purge', 'shogun-r'] 0m22.9s DUMP: dpkg: warning: ignoring request to remove shogun-r which isn't installed. 0m22.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg', '--purge', 'shogun-r'] 0m22.9s INFO: Running scripts post_purge 0m22.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/post_purge_exceptions'] 0m22.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'tmp/scripts/post_purge_exceptions'] 0m22.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg', '--purge', '--pending'] 0m22.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg', '--purge', '--pending'] 0m22.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg', '--remove', '--pending'] 0m22.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg', '--remove', '--pending'] 0m22.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnr4pjk'] 0m23.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnr4pjk'] 0m24.0s DEBUG: No broken symlinks as far as we can find. 0m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg-divert', '--list'] 0m24.0s DUMP: diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /bin/sync to /bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'dpkg-divert', '--list'] 0m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-get', 'clean'] 0m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'apt-get', 'clean'] 0m25.1s INFO: PASS: Installation and purging test. 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'umount', '/proc'] 0m25.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnr4pjk', 'umount', '/proc'] 0m25.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpnr4pjk'] 0m25.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpnr4pjk'] 0m25.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpnr4pjk 0m25.4s INFO: PASS: All tests. 0m25.4s INFO: piuparts run ends. ret=0 End: 2014-04-16 17:48:23 UTC