Start: 2014-10-12 19:06:33 UTC Package: exonerate Priority: optional Section: science Installed-Size: 8952 Maintainer: Debian Med Packaging Team Architecture: amd64 Version: 2.2.0-2 Depends: libc6 (>= 2.3), libglib2.0-0 (>= 2.12.0) Suggests: wise Filename: pool/main/e/exonerate/exonerate_2.2.0-2_amd64.deb Size: 3321532 MD5sum: b86ac66371bf3fc29056bb4464318238 SHA1: 7524fde59a8f7b59888bcd3f70ec3aabd0462aa4 SHA256: 374723ac29aa5ab8182f89dc7ce418890542d7d6077d9fe5954613ed5ee36918 Description: generic tool for pairwise sequence comparison Exonerate allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. Much of the functionality of the Wise dynamic programming suite was reimplemented in C for better efficiency. Exonerate is an intrinsic component of the building of the Ensembl genome databases, providing similarity scores between RNA and DNA sequences and thus determining splice variants and coding sequences in general. . An In-silico PCR Experiment Simulation System (see the ipcress man page) is packaged with exonerate. . This package also comes with a selection of utilities for performing simple manipulations quickly on fasta files beyond 2Gb Enhances: bioperl-run Homepage: http://www.ebi.ac.uk/~guy/exonerate/ Tag: field::biology, field::biology:bioinformatics, implemented-in::c, interface::commandline, role::program, scope::utility, use::searching, works-with-format::plaintext 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 exonerate=2.2.0-2 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 https://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 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 exonerate=2.2.0-2 0m0.0s INFO: Running on: Linux piu-slave-bm-a 3.2.0-4-amd64 #1 SMP Debian 3.2.60-1+deb7u3 x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp_oL7Zh 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp_oL7Zh 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz'] 0m1.7s DUMP: tar: ./proc: time stamp 2014-10-15 13:49:47 is 240193.151531362 s in the future 0m1.7s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz'] 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'mount', '-t', 'proc', 'proc', '/proc'] 0m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'mount', '-t', 'proc', 'proc', '/proc'] 0m1.7s DEBUG: sources.list: deb http://mirror.bm.debian.org/debian/ squeeze main 0m1.7s DEBUG: Created policy-rc.d and chmodded it. 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', '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/tmp_oL7Zh', 'apt-get', 'update'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', '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/tmp_oL7Zh', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp_oL7Zh/tmp/scripts/ 0m2.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts-squeeze to /srv/piuparts.debian.org/tmp/tmp_oL7Zh/tmp/scripts/ 0m2.1s INFO: Running scripts post_setup 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/post_setup_experimental'] 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/post_setup_experimental'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/post_setup_forbid_home'] 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/post_setup_forbid_home'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/post_setup_squeeze-fake-essential'] 0m2.8s 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 (27.1 MB/s) Selecting previously deselected package adduser. (Reading database ... 6138 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) ... 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/post_setup_squeeze-fake-essential'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'apt-get', 'clean'] 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'apt-get', 'clean'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg', '--get-selections', '*'] 0m3.3s 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 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 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg', '--get-selections', '*'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg-divert', '--list'] 0m3.3s 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 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg-divert', '--list'] 0m3.3s INFO: apt-cache does not know about any of the requested packages 0m3.3s INFO: Running scripts pre_test 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', '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/tmp_oL7Zh', 'tmp/scripts/pre_test_root_password'] 0m3.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh'] 0m3.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh'] 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/tmp_oL7Zh', 'tmp/scripts/pre_install_database-server'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/pre_install_database-server'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/pre_install_exceptions'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/pre_install_exceptions'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/pre_install_extras'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/pre_install_extras'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'apt-cache', 'show', 'exonerate=2.2.0-2'] 0m4.5s DUMP: Package: exonerate Priority: optional Section: science Installed-Size: 8952 Maintainer: Debian Med Packaging Team Architecture: amd64 Version: 2.2.0-2 Depends: libc6 (>= 2.3), libglib2.0-0 (>= 2.12.0) Suggests: wise Filename: pool/main/e/exonerate/exonerate_2.2.0-2_amd64.deb Size: 3321532 MD5sum: b86ac66371bf3fc29056bb4464318238 SHA1: 7524fde59a8f7b59888bcd3f70ec3aabd0462aa4 SHA256: 374723ac29aa5ab8182f89dc7ce418890542d7d6077d9fe5954613ed5ee36918 Description: generic tool for pairwise sequence comparison Exonerate allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. Much of the functionality of the Wise dynamic programming suite was reimplemented in C for better efficiency. Exonerate is an intrinsic component of the building of the Ensembl genome databases, providing similarity scores between RNA and DNA sequences and thus determining splice variants and coding sequences in general. . An In-silico PCR Experiment Simulation System (see the ipcress man page) is packaged with exonerate. . This package also comes with a selection of utilities for performing simple manipulations quickly on fasta files beyond 2Gb Enhances: bioperl-run Homepage: http://www.ebi.ac.uk/~guy/exonerate/ Tag: field::biology, field::biology:bioinformatics, implemented-in::c, interface::commandline, role::program, scope::utility, use::searching, works-with-format::plaintext 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'apt-cache', 'show', 'exonerate=2.2.0-2'] 0m4.5s 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: libc6 (>= 2.3), libglib2.0-0 (>= 2.12.0) 0m4.5s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpY7cJxE/piuparts-depends-dummy'] 0m4.5s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmpY7cJxE/piuparts-depends-dummy.deb'. 0m4.5s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpY7cJxE/piuparts-depends-dummy'] 0m4.5s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmpY7cJxE/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmp_oL7Zh/tmp 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m4.5s DUMP: Selecting previously deselected package piuparts-depends-dummy. (Reading database ... 6261 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 libglib2.0-0 (>= 2.12.0); however: Package libglib2.0-0 is not installed. dpkg: error processing piuparts-depends-dummy (--install): dependency problems - leaving unconfigured Errors were encountered while processing: piuparts-depends-dummy 0m4.5s DEBUG: Command failed (status=1), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'apt-get', '-yf', 'install'] 0m5.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Correcting dependencies... Done The following extra packages will be installed: libglib2.0-0 libpcre3 Recommended packages: libglib2.0-data shared-mime-info The following NEW packages will be installed: libglib2.0-0 libpcre3 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 1 not fully installed or removed. Need to get 1357 kB of archives. After this operation, 2937 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ squeeze/main libpcre3 amd64 8.02-1.1 [234 kB] Get:2 http://mirror.bm.debian.org/debian/ squeeze/main libglib2.0-0 amd64 2.24.2-1 [1122 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1357 kB in 0s (13.3 MB/s) Selecting previously deselected package libpcre3. (Reading database ... 6261 files and directories currently installed.) 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) ... Setting up libpcre3 (8.02-1.1) ... Setting up libglib2.0-0 (2.24.2-1) ... Setting up piuparts-depends-dummy (0.invalid.0) ... 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'apt-get', '-yf', 'install'] 0m5.5s INFO: Installation of ['tmp/piuparts-depends-dummy.deb'] ok 0m5.5s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmp_oL7Zh/tmp/piuparts-depends-dummy.deb 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m5.5s DUMP: piuparts-depends-dummy install ok installed 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m5.5s DUMP: (Reading database ... 6299 files and directories currently installed.) Removing piuparts-depends-dummy ... 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'apt-get', 'clean'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'apt-get', 'clean'] 0m6.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh'] 0m6.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh'] 0m7.1s DEBUG: No broken symlinks as far as we can find. 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'apt-cache', 'policy'] 0m7.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror.bm.debian.org/debian/ squeeze/main amd64 Packages release v=6.0.10,o=Debian,a=oldstable,n=squeeze,l=Debian,c=main origin mirror.bm.debian.org Pinned packages: 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'apt-cache', 'policy'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'apt-cache', 'policy', 'exonerate'] 0m7.1s DUMP: exonerate: Installed: (none) Candidate: 2.2.0-2 Version table: 2.2.0-2 0 500 http://mirror.bm.debian.org/debian/ squeeze/main amd64 Packages 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'apt-cache', 'policy', 'exonerate'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'apt-get', '-y', 'install', 'exonerate=2.2.0-2'] 0m7.9s DUMP: Reading package lists... Building dependency tree... Reading state information... Suggested packages: wise The following NEW packages will be installed: exonerate 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 3322 kB of archives. After this operation, 9167 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ squeeze/main exonerate amd64 2.2.0-2 [3322 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3322 kB in 0s (22.7 MB/s) Selecting previously deselected package exonerate. (Reading database ... 6299 files and directories currently installed.) Unpacking exonerate (from .../exonerate_2.2.0-2_amd64.deb) ... Setting up exonerate (2.2.0-2) ... 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'apt-get', '-y', 'install', 'exonerate=2.2.0-2'] 0m7.9s INFO: Running scripts post_install 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/post_install_exceptions'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/post_install_exceptions'] 0m7.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh'] 0m8.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh'] 0m9.0s DEBUG: No broken symlinks as far as we can find. 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg', '--get-selections', '*'] 0m9.0s 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 exonerate 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 libglib2.0-0 install liblocale-gettext-perl install liblzma2 install libncurses5 install libpam-modules install libpam-runtime install libpam0g install libpcre3 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 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg', '--get-selections', '*'] 0m9.5s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', '-ac'] 0m10.1s DUMP: debsums: no md5sums for mawk 0m10.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', '-ac'] 0m10.1s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m10.1s DUMP: 0.12~bpo70+1 0m10.1s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m10.1s INFO: Running adequate version 0.12~bpo70+1 now. 0m10.1s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'exonerate'] 0m10.3s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'exonerate'] 0m10.3s INFO: Running scripts pre_remove 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/pre_remove_exceptions'] 0m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/pre_remove_exceptions'] 0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'apt-get', 'remove', 'libglib2.0-0', 'libpcre3', 'exonerate'] 0m11.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: exonerate libglib2.0-0 libpcre3 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. After this operation, 12.1 MB disk space will be freed. (Reading database ... 6363 files and directories currently installed.) Removing exonerate ... Removing libglib2.0-0 ... Removing libpcre3 ... 0m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'apt-get', 'remove', 'libglib2.0-0', 'libpcre3', 'exonerate'] 0m11.0s INFO: Running scripts post_remove 0m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/post_remove_exceptions_lenny'] 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/post_remove_exceptions_lenny'] 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/post_remove_extras'] 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/post_remove_extras'] 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg', '--purge', 'libglib2.0-0', 'libpcre3'] 0m11.1s DUMP: (Reading database ... 6262 files and directories currently installed.) Removing libglib2.0-0 ... Purging configuration files for libglib2.0-0 ... Removing libpcre3 ... Purging configuration files for libpcre3 ... 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg', '--purge', 'libglib2.0-0', 'libpcre3'] 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg', '--purge', 'exonerate'] 0m11.1s DUMP: dpkg: warning: ignoring request to remove exonerate which isn't installed. 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg', '--purge', 'exonerate'] 0m11.1s INFO: Running scripts post_purge 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/post_purge_exceptions'] 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'tmp/scripts/post_purge_exceptions'] 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg', '--purge', '--pending'] 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg', '--purge', '--pending'] 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg', '--remove', '--pending'] 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg', '--remove', '--pending'] 0m11.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh'] 0m11.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh'] 0m12.2s DEBUG: No broken symlinks as far as we can find. 0m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg-divert', '--list'] 0m12.2s 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 0m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'dpkg-divert', '--list'] 0m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'apt-get', 'clean'] 0m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'apt-get', 'clean'] 0m13.1s INFO: PASS: Installation and purging test. 0m13.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'umount', '/proc'] 0m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh', 'umount', '/proc'] 0m13.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh'] 0m13.5s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp_oL7Zh'] 0m13.5s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp_oL7Zh 0m13.5s INFO: PASS: All tests. 0m13.5s INFO: piuparts run ends. ret=0 End: 2014-10-12 19:06:47 UTC