Start: 2014-07-02 18:26:54 UTC Package: med-bio-dev Priority: extra Section: misc Installed-Size: 120 Maintainer: Debian Med Packaging Team Architecture: all Source: debian-med Version: 1.8 Depends: med-tasks (= 1.8), med-config (= 1.8) Recommends: bioperl, bioperl-run, biosquid, libace-perl, libajax6-dev, libbio-graphics-perl, libbio-mage-perl, libbio-mage-utils-perl, libbio-primerdesigner-perl, libbio-ruby, libbiojava-java, libgenome-1.3-0-dev, libgo-perl, libncbi6-dev, libnucleus6-dev, libqsearch-dev, libsrf-dev, libstaden-read-dev, libtfbs-perl, libvibrant6-dev, mcl, octave-bioinfo, python-biopython, r-cran-genetics, r-cran-haplo.stats, seqan-dev Suggests: bioclipse, bioconductor, libajax5-dev, libbio-das-perl, libbiococoa-dev, libgff-perl, libmems-1.5-1, libnucleus5-dev, libsbml1, limma, python-cogent, r-cran-rocr Filename: pool/main/d/debian-med/med-bio-dev_1.8_all.deb Size: 11604 MD5sum: b82ad7e05066ab0c8fce8f7562e9965f SHA1: f2e7f18937814a661ed47dffb19d49729d0d6d9d SHA256: fc60039e3894cc03a26c91ad77ef3f9211f88bd4285280d926ee1cf7df95e2ba Description: Debian Med packages for development of micro-biology applications This metapackage will install Debian packages which might be helpful for development of applications for micro-biological research. Tag: field::biology, role::metapackage, suite::debian 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 med-bio-dev=1.8 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 0.59~201405301115~0.58-62-g352dac2 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 med-bio-dev=1.8 0m0.0s INFO: Running on: Linux piu-slave-bm-a 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3+deb7u2 x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpYfyRPk 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpYfyRPk 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz'] 0m1.7s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz'] 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'mount', '-t', 'proc', 'proc', '/proc'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', '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/tmpYfyRPk', 'apt-get', 'update'] 0m1.8s 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... 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'apt-get', 'update'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DUMP: Reading package lists... Building dependency tree... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpYfyRPk/tmp/scripts/ 0m2.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts-squeeze to /srv/piuparts.debian.org/tmp/tmpYfyRPk/tmp/scripts/ 0m2.1s INFO: Running scripts post_setup 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/post_setup_experimental'] 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/post_setup_experimental'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/post_setup_forbid_home'] 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/post_setup_forbid_home'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/post_setup_squeeze-fake-essential'] 0m2.9s 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 (18.0 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) ... 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/post_setup_squeeze-fake-essential'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'apt-get', 'clean'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'apt-get', 'clean'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg', '--get-selections', '*'] 0m3.4s 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 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg', '--get-selections', '*'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg-divert', '--list'] 0m3.4s 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 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg-divert', '--list'] 0m3.4s INFO: apt-cache does not know about any of the requested packages 0m3.4s INFO: Running scripts pre_test 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/pre_test_root_password'] 0m3.4s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/pre_test_root_password'] 0m3.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYfyRPk'] 0m3.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYfyRPk'] 0m4.4s DEBUG: No broken symlinks as far as we can find. 0m4.4s INFO: Running scripts pre_install 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/pre_install_database-server'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/pre_install_database-server'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/pre_install_exceptions'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/pre_install_exceptions'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/pre_install_extras'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/pre_install_extras'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'apt-cache', 'show', 'med-bio-dev=1.8'] 0m4.6s DUMP: Package: med-bio-dev Priority: extra Section: misc Installed-Size: 120 Maintainer: Debian Med Packaging Team Architecture: all Source: debian-med Version: 1.8 Depends: med-tasks (= 1.8), med-config (= 1.8) Recommends: bioperl, bioperl-run, biosquid, libace-perl, libajax6-dev, libbio-graphics-perl, libbio-mage-perl, libbio-mage-utils-perl, libbio-primerdesigner-perl, libbio-ruby, libbiojava-java, libgenome-1.3-0-dev, libgo-perl, libncbi6-dev, libnucleus6-dev, libqsearch-dev, libsrf-dev, libstaden-read-dev, libtfbs-perl, libvibrant6-dev, mcl, octave-bioinfo, python-biopython, r-cran-genetics, r-cran-haplo.stats, seqan-dev Suggests: bioclipse, bioconductor, libajax5-dev, libbio-das-perl, libbiococoa-dev, libgff-perl, libmems-1.5-1, libnucleus5-dev, libsbml1, limma, python-cogent, r-cran-rocr Filename: pool/main/d/debian-med/med-bio-dev_1.8_all.deb Size: 11604 MD5sum: b82ad7e05066ab0c8fce8f7562e9965f SHA1: f2e7f18937814a661ed47dffb19d49729d0d6d9d SHA256: fc60039e3894cc03a26c91ad77ef3f9211f88bd4285280d926ee1cf7df95e2ba Description: Debian Med packages for development of micro-biology applications This metapackage will install Debian packages which might be helpful for development of applications for micro-biological research. Tag: field::biology, role::metapackage, suite::debian 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'apt-cache', 'show', 'med-bio-dev=1.8'] 0m4.6s 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: med-tasks (= 1.8), med-config (= 1.8) 0m4.6s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpyYgiiy/piuparts-depends-dummy'] 0m4.6s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmpyYgiiy/piuparts-depends-dummy.deb'. 0m4.6s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpyYgiiy/piuparts-depends-dummy'] 0m4.6s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmpyYgiiy/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmpYfyRPk/tmp 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m4.7s 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 med-tasks (= 1.8); however: Package med-tasks is not installed. piuparts-depends-dummy depends on med-config (= 1.8); however: Package med-config is not installed. dpkg: error processing piuparts-depends-dummy (--install): dependency problems - leaving unconfigured Errors were encountered while processing: piuparts-depends-dummy 0m4.7s DEBUG: Command failed (status=1), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'apt-get', '-yf', 'install'] 0m8.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Correcting dependencies... Done The following extra packages will be installed: aptitude blends-common libboost-iostreams1.42.0 libcwidget3 libept1 libncursesw5 libsigc++-2.0-0c2a libsqlite3-0 libxapian22 med-config med-tasks menu tasksel tasksel-data Suggested packages: debtags blends-doc libcwidget-dev xapian-tools menu-l10n gksu kdebase-bin kdebase-runtime ktsuss sux Recommended packages: aptitude-doc-en aptitude-doc apt-xapian-index libparse-debianchangelog-perl libgpm2 laptop-detect The following NEW packages will be installed: aptitude blends-common libboost-iostreams1.42.0 libcwidget3 libept1 libncursesw5 libsigc++-2.0-0c2a libsqlite3-0 libxapian22 med-config med-tasks menu tasksel tasksel-data 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 1 not fully installed or removed. Need to get 7044 kB of archives. After this operation, 22.0 MB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ squeeze/main libboost-iostreams1.42.0 amd64 1.42.0-4 [59.2 kB] Get:2 http://mirror.bm.debian.org/debian/ squeeze/main libncursesw5 amd64 5.7+20100313-5 [390 kB] Get:3 http://mirror.bm.debian.org/debian/ squeeze/main libsigc++-2.0-0c2a amd64 2.2.4.2-1 [39.5 kB] Get:4 http://mirror.bm.debian.org/debian/ squeeze/main libcwidget3 amd64 0.5.16-3 [308 kB] Get:5 http://mirror.bm.debian.org/debian/ squeeze/main libxapian22 amd64 1.2.3-2 [1150 kB] Get:6 http://mirror.bm.debian.org/debian/ squeeze/main libept1 amd64 1.0.4 [149 kB] Get:7 http://mirror.bm.debian.org/debian/ squeeze/main libsqlite3-0 amd64 3.7.3-1 [397 kB] Get:8 http://mirror.bm.debian.org/debian/ squeeze/main aptitude amd64 0.6.3-3.2+squeeze1 [3854 kB] Get:9 http://mirror.bm.debian.org/debian/ squeeze/main tasksel-data all 2.88 [106 kB] Get:10 http://mirror.bm.debian.org/debian/ squeeze/main tasksel all 2.88 [87.9 kB] Get:11 http://mirror.bm.debian.org/debian/ squeeze/main med-tasks all 1.8 [9786 B] Get:12 http://mirror.bm.debian.org/debian/ squeeze/main menu amd64 2.1.44 [459 kB] Get:13 http://mirror.bm.debian.org/debian/ squeeze/main blends-common all 0.6.15 [23.3 kB] Get:14 http://mirror.bm.debian.org/debian/ squeeze/main med-config all 1.8 [10.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7044 kB in 0s (27.0 MB/s) Selecting previously deselected package libboost-iostreams1.42.0. (Reading database ... 6258 files and directories currently installed.) Unpacking libboost-iostreams1.42.0 (from .../libboost-iostreams1.42.0_1.42.0-4_amd64.deb) ... Selecting previously deselected package libncursesw5. Unpacking libncursesw5 (from .../libncursesw5_5.7+20100313-5_amd64.deb) ... Selecting previously deselected package libsigc++-2.0-0c2a. Unpacking libsigc++-2.0-0c2a (from .../libsigc++-2.0-0c2a_2.2.4.2-1_amd64.deb) ... Selecting previously deselected package libcwidget3. Unpacking libcwidget3 (from .../libcwidget3_0.5.16-3_amd64.deb) ... Selecting previously deselected package libxapian22. Unpacking libxapian22 (from .../libxapian22_1.2.3-2_amd64.deb) ... Selecting previously deselected package libept1. Unpacking libept1 (from .../libept1_1.0.4_amd64.deb) ... Selecting previously deselected package libsqlite3-0. Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.3-1_amd64.deb) ... Selecting previously deselected package aptitude. Unpacking aptitude (from .../aptitude_0.6.3-3.2+squeeze1_amd64.deb) ... Selecting previously deselected package tasksel-data. Unpacking tasksel-data (from .../tasksel-data_2.88_all.deb) ... Selecting previously deselected package tasksel. Unpacking tasksel (from .../archives/tasksel_2.88_all.deb) ... Selecting previously deselected package med-tasks. Unpacking med-tasks (from .../archives/med-tasks_1.8_all.deb) ... Selecting previously deselected package menu. Unpacking menu (from .../archives/menu_2.1.44_amd64.deb) ... Selecting previously deselected package blends-common. Unpacking blends-common (from .../blends-common_0.6.15_all.deb) ... Selecting previously deselected package med-config. Unpacking med-config (from .../med-config_1.8_all.deb) ... Setting up libboost-iostreams1.42.0 (1.42.0-4) ... Setting up libncursesw5 (5.7+20100313-5) ... Setting up libsigc++-2.0-0c2a (2.2.4.2-1) ... Setting up libcwidget3 (0.5.16-3) ... Setting up libxapian22 (1.2.3-2) ... Setting up libept1 (1.0.4) ... Setting up libsqlite3-0 (3.7.3-1) ... Setting up aptitude (0.6.3-3.2+squeeze1) ... update-alternatives: using /usr/bin/aptitude-curses to provide /usr/bin/aptitude (aptitude) in auto mode. Setting up menu (2.1.44) ... Processing triggers for menu ... Setting up blends-common (0.6.15) ... Setting up med-config (1.8) ... Adding group `med' (GID 102) ... Done. Setting up tasksel-data (2.88) ... Setting up tasksel (2.88) ... Setting up med-tasks (1.8) ... Setting up piuparts-depends-dummy (0.invalid.0) ... Processing triggers for menu ... 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'apt-get', '-yf', 'install'] 0m8.3s INFO: Installation of ['tmp/piuparts-depends-dummy.deb'] ok 0m8.3s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmpYfyRPk/tmp/piuparts-depends-dummy.deb 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m8.3s DUMP: piuparts-depends-dummy install ok installed 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m8.4s DUMP: (Reading database ... 6837 files and directories currently installed.) Removing piuparts-depends-dummy ... 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'apt-get', 'clean'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'apt-get', 'clean'] 0m8.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYfyRPk'] 0m9.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYfyRPk'] 0m10.0s DEBUG: No broken symlinks as far as we can find. 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'apt-cache', 'policy'] 0m10.0s 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: 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'apt-cache', 'policy'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'apt-cache', 'policy', 'med-bio-dev'] 0m10.0s DUMP: med-bio-dev: Installed: (none) Candidate: 1.8 Version table: 1.8 0 500 http://mirror.bm.debian.org/debian/ squeeze/main amd64 Packages 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'apt-cache', 'policy', 'med-bio-dev'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'apt-get', '-y', 'install', 'med-bio-dev=1.8'] 0m10.7s DUMP: Reading package lists... Building dependency tree... Reading state information... Suggested packages: bioclipse bioconductor libajax5-dev libbio-das-perl libbiococoa-dev libgff-perl libmems-1.5-1 libnucleus5-dev libsbml1 limma python-cogent r-cran-rocr Recommended packages: bioperl bioperl-run biosquid libace-perl libajax6-dev libbio-graphics-perl libbio-mage-perl libbio-mage-utils-perl libbio-primerdesigner-perl libbio-ruby libbiojava-java libgenome-1.3-0-dev libgo-perl libncbi6-dev libnucleus6-dev libqsearch-dev libsrf-dev libstaden-read-dev libtfbs-perl libvibrant6-dev mcl octave-bioinfo python-biopython r-cran-genetics r-cran-haplo.stats seqan-dev The following NEW packages will be installed: med-bio-dev 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 11.6 kB of archives. After this operation, 123 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ squeeze/main med-bio-dev all 1.8 [11.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 11.6 kB in 0s (660 kB/s) Selecting previously deselected package med-bio-dev. (Reading database ... 6837 files and directories currently installed.) Unpacking med-bio-dev (from .../med-bio-dev_1.8_all.deb) ... Setting up med-bio-dev (1.8) ... 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'apt-get', '-y', 'install', 'med-bio-dev=1.8'] 0m10.7s INFO: Running scripts post_install 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/post_install_exceptions'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/post_install_exceptions'] 0m10.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYfyRPk'] 0m11.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYfyRPk'] 0m11.9s DEBUG: No broken symlinks as far as we can find. 0m11.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg', '--get-selections', '*'] 0m12.0s DUMP: adduser install apt install aptitude install base-files install base-passwd install bash install blends-common 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 libboost-iostreams1.42.0 install libbz2-1.0 install libc-bin install libc6 install libcomerr2 install libcwidget3 install libdb4.8 install libept1 install libgcc1 install liblocale-gettext-perl install liblzma2 install libncurses5 install libncursesw5 install libpam-modules install libpam-runtime install libpam0g install libreadline6 install libselinux1 install libsepol1 install libsigc++-2.0-0c2a install libslang2 install libsqlite3-0 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 libxapian22 install login install lsb-base install mawk install med-bio-dev install med-config install med-tasks install menu 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 tasksel install tasksel-data install tzdata install ucf install util-linux install xz-utils install zlib1g install 0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg', '--get-selections', '*'] 0m12.6s DEBUG: Starting command: ['/home/piupartss/bin/debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', '-ac'] 0m13.2s DUMP: This is debsums 2.0.52+nmu2 installed manually. debsums: no md5sums for mawk 0m13.2s DEBUG: Command ok: ['/home/piupartss/bin/debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', '-ac'] 0m13.2s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m13.2s DUMP: 0.11.6~bpo70+1 0m13.2s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m13.2s INFO: Running adequate version 0.11.6~bpo70+1 now. 0m13.2s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'med-bio-dev'] 0m13.3s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'med-bio-dev'] 0m13.3s INFO: Running scripts pre_remove 0m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m13.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m13.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m13.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/pre_remove_exceptions'] 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/pre_remove_exceptions'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'apt-get', 'remove', 'libcwidget3', 'libsigc++-2.0-0c2a', 'libncursesw5', 'menu', 'med-tasks', 'med-config', 'libept1', 'tasksel', 'libboost-iostreams1.42.0', 'libsqlite3-0', 'aptitude', 'libxapian22', 'tasksel-data', 'blends-common', 'med-bio-dev'] 0m14.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: aptitude blends-common libboost-iostreams1.42.0 libcwidget3 libept1 libncursesw5 libsigc++-2.0-0c2a libsqlite3-0 libxapian22 med-bio-dev med-config med-tasks menu tasksel tasksel-data 0 upgraded, 0 newly installed, 15 to remove and 0 not upgraded. After this operation, 22.1 MB disk space will be freed. (Reading database ... 6855 files and directories currently installed.) Removing med-bio-dev ... Removing med-tasks ... Removing med-config ... Removing blends-common ... Removing menu ... Removing tasksel ... Removing tasksel-data ... Removing aptitude ... Removing libboost-iostreams1.42.0 ... Removing libcwidget3 ... Removing libept1 ... Removing libncursesw5 ... Removing libsigc++-2.0-0c2a ... Removing libsqlite3-0 ... Removing libxapian22 ... 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'apt-get', 'remove', 'libcwidget3', 'libsigc++-2.0-0c2a', 'libncursesw5', 'menu', 'med-tasks', 'med-config', 'libept1', 'tasksel', 'libboost-iostreams1.42.0', 'libsqlite3-0', 'aptitude', 'libxapian22', 'tasksel-data', 'blends-common', 'med-bio-dev'] 0m14.3s INFO: Running scripts post_remove 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/post_remove_exceptions_lenny'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/post_remove_exceptions_lenny'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/post_remove_extras'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/post_remove_extras'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg', '--purge', 'libcwidget3', 'libsigc++-2.0-0c2a', 'libncursesw5', 'menu', 'med-tasks', 'med-config', 'libept1', 'tasksel', 'libboost-iostreams1.42.0', 'libsqlite3-0', 'aptitude', 'libxapian22', 'tasksel-data', 'blends-common'] 0m14.5s DUMP: (Reading database ... 6272 files and directories currently installed.) Removing libcwidget3 ... Purging configuration files for libcwidget3 ... Removing libsigc++-2.0-0c2a ... Purging configuration files for libsigc++-2.0-0c2a ... Removing libncursesw5 ... Purging configuration files for libncursesw5 ... Removing menu ... Purging configuration files for menu ... dpkg: warning: ignoring request to remove med-tasks which isn't installed. Removing med-config ... Purging configuration files for med-config ... Removing libept1 ... Purging configuration files for libept1 ... Removing tasksel ... Purging configuration files for tasksel ... Removing libboost-iostreams1.42.0 ... Purging configuration files for libboost-iostreams1.42.0 ... Removing libsqlite3-0 ... Purging configuration files for libsqlite3-0 ... Removing aptitude ... Purging configuration files for aptitude ... Removing libxapian22 ... Purging configuration files for libxapian22 ... dpkg: warning: ignoring request to remove tasksel-data which isn't installed. Removing blends-common ... Purging configuration files for blends-common ... 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg', '--purge', 'libcwidget3', 'libsigc++-2.0-0c2a', 'libncursesw5', 'menu', 'med-tasks', 'med-config', 'libept1', 'tasksel', 'libboost-iostreams1.42.0', 'libsqlite3-0', 'aptitude', 'libxapian22', 'tasksel-data', 'blends-common'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg', '--purge', 'med-bio-dev'] 0m14.5s DUMP: (Reading database ... 6260 files and directories currently installed.) Removing med-bio-dev ... Purging configuration files for med-bio-dev ... 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg', '--purge', 'med-bio-dev'] 0m14.5s INFO: Running scripts post_purge 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/post_purge_exceptions'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'tmp/scripts/post_purge_exceptions'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg', '--purge', '--pending'] 0m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg', '--purge', '--pending'] 0m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg', '--remove', '--pending'] 0m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg', '--remove', '--pending'] 0m14.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYfyRPk'] 0m14.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYfyRPk'] 0m15.6s DEBUG: No broken symlinks as far as we can find. 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg-divert', '--list'] 0m15.6s 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 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'dpkg-divert', '--list'] 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'apt-get', 'clean'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'apt-get', 'clean'] 0m16.6s INFO: PASS: Installation and purging test. 0m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'umount', '/proc'] 0m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYfyRPk', 'umount', '/proc'] 0m16.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpYfyRPk'] 0m16.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpYfyRPk'] 0m16.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpYfyRPk 0m17.0s INFO: PASS: All tests. 0m17.0s INFO: piuparts run ends. ret=0 End: 2014-07-02 18:27:11 UTC