Start: 2018-07-07 00:35:44 UTC [wheezy] Package: exonerate Version: 2.2.0-6 Installed-Size: 8144 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.7), libglib2.0-0 (>= 2.24.0) Suggests: wise Enhances: bioperl-run Description: generic tool for pairwise sequence comparison Homepage: http://www.ebi.ac.uk/~guy/exonerate/ Description-md5: 61984be320e7cae47c75d879b270d329 Tag: field::biology, field::biology:bioinformatics, implemented-in::c, interface::commandline, role::program, scope::utility, use::TODO, use::searching, works-with-format::TODO, works-with-format::plaintext, works-with::TODO Section: science Priority: optional Filename: pool/main/e/exonerate/exonerate_2.2.0-6_amd64.deb Size: 3053402 MD5sum: 83a75a82a555aa601d874aa671baaaa7 SHA1: e39d7fd387145d78abde21e06ae0ffef36f81850 SHA256: 628a9b8ead0dee7bcacf0abae2a9fca3cf7d9805633b1e4df1a1b4fa450cf608 [wheezy-lts] Package: exonerate Version: 2.2.0-6 Installed-Size: 8144 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.7), libglib2.0-0 (>= 2.24.0) Suggests: wise Enhances: bioperl-run Description: generic tool for pairwise sequence comparison Homepage: http://www.ebi.ac.uk/~guy/exonerate/ Description-md5: 61984be320e7cae47c75d879b270d329 Tag: field::biology, field::biology:bioinformatics, implemented-in::c, interface::commandline, role::program, scope::utility, use::TODO, use::searching, works-with-format::TODO, works-with-format::plaintext, works-with::TODO Section: science Priority: optional Filename: pool/main/e/exonerate/exonerate_2.2.0-6_amd64.deb Size: 3053402 MD5sum: 83a75a82a555aa601d874aa671baaaa7 SHA1: e39d7fd387145d78abde21e06ae0ffef36f81850 SHA256: 628a9b8ead0dee7bcacf0abae2a9fca3cf7d9805633b1e4df1a1b4fa450cf608 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python2.7/dist-packages timeout -s INT -k 5m 80m /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 --scriptsdir /etc/piuparts/scripts-wheezy --warn-on-debsums-errors --warn-on-install-over-symlink --mirror 'http://mirror.bm.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz -d wheezy -d wheezy-lts -B reference-chroot-metadata.dat --apt exonerate=2.2.0-6 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 0.90~201806121501~0.89-1-g6355f063 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 --scriptsdir /etc/piuparts/scripts-wheezy --warn-on-debsums-errors --warn-on-install-over-symlink --mirror 'http://mirror.bm.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz -d wheezy -d wheezy-lts -B reference-chroot-metadata.dat --apt exonerate=2.2.0-6 0m0.0s INFO: Running on: Linux piu-slave-bm-a 4.9.0-6-amd64 #1 SMP Debian 4.9.88-1+deb9u1 (2018-05-07) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpYp_V1s 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpYp_V1s 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz'] 0m2.1s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/proc'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/proc'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/dev/pts'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/dev/pts'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/dev/ptmx'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/dev/ptmx'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/dev/console'] 0m2.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/dev/console'] 0m2.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/run/shm'] 0m2.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/run/shm'] 0m2.2s DEBUG: sources.list: deb http://mirror.bm.debian.org/debian/ wheezy main 0m2.2s DEBUG: Created policy-rc.d and chmodded it. 0m2.2s DEBUG: Created resolv.conf. 0m2.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpYp_V1s/tmp/scripts/ 0m2.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts-wheezy to /srv/piuparts.debian.org/tmp/tmpYp_V1s/tmp/scripts/ 0m2.2s INFO: Running scripts post_chroot_unpack 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-get', 'update'] 0m5.0s DUMP: Hit http://mirror.bm.debian.org wheezy Release.gpg Hit http://mirror.bm.debian.org wheezy Release Hit http://mirror.bm.debian.org wheezy/main amd64 Packages Hit http://mirror.bm.debian.org wheezy/main Translation-en Reading package lists... 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-get', 'update'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-get', '-yf', 'dist-upgrade'] 0m5.4s DUMP: Reading package lists... Building dependency tree... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-get', '-yf', 'dist-upgrade'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.8s DUMP: 0c96df6df725ee7ec7aebd2b6a77fb72 - 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.8s INFO: Running scripts post_setup 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_setup_dummy_users'] 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_setup_dummy_users'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_setup_experimental'] 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_setup_experimental'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_setup_forbid_home'] 0m7.1s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_setup_forbid_home'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.1s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' `/bin/sync' -> `true' 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_setup_minimize'] 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_setup_minimize'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_setup_wheezy-fake-essential'] 0m8.4s 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 335 kB of archives. After this operation, 1327 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ wheezy/main adduser all 3.113+nmu3 [264 kB] Get:2 http://mirror.bm.debian.org/debian/ wheezy/main ucf all 3.0025+nmu3 [70.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 335 kB in 0s (19.5 MB/s) Selecting previously unselected package adduser. (Reading database ... 6639 files and directories currently installed.) Unpacking adduser (from .../adduser_3.113+nmu3_all.deb) ... Selecting previously unselected package ucf. Unpacking ucf (from .../ucf_3.0025+nmu3_all.deb) ... Moving old data out of the way Setting up adduser (3.113+nmu3) ... Setting up ucf (3.0025+nmu3) ... 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_setup_wheezy-fake-essential'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_setup_zz_backports'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_setup_zz_backports'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.4s DUMP: install ok installed adduser adduser 3.113+nmu3 install ok installed apt apt 0.9.7.9+deb7u7 install ok installed base-files base-files 7.1wheezy11 install ok installed base-passwd base-passwd 3.5.26 install ok installed bash bash 4.2+dfsg-0.1+deb7u3 install ok installed bsdutils bsdutils 1:2.20.1-5.3 install ok installed coreutils coreutils 8.13-3.5 install ok installed dash dash 0.5.7-3 install ok installed debconf debconf 1.5.49 install ok installed debconf-i18n debconf-i18n 1.5.49 install ok installed debian-archive-keyring debian-archive-keyring 2014.3~deb7u1 install ok installed debianutils debianutils 4.3.2 install ok installed diffutils diffutils 1:3.2-6 install ok installed dpkg dpkg 1.16.18 install ok installed e2fslibs:amd64 e2fslibs 1.42.5-1.1+deb7u1 install ok installed e2fsprogs e2fsprogs 1.42.5-1.1+deb7u1 install ok installed findutils findutils 4.4.2-4 install ok installed gcc-4.7-base:amd64 gcc-4.7-base 4.7.2-5 install ok installed gnupg gnupg 1.4.12-7+deb7u7 install ok installed gpgv gpgv 1.4.12-7+deb7u7 install ok installed grep grep 2.12-2 install ok installed gzip gzip 1.5-1.1 install ok installed hostname hostname 3.11 install ok installed initscripts initscripts 2.88dsf-41+deb7u1 install ok installed insserv insserv 1.14.0-5 install ok installed libacl1:amd64 libacl1 2.2.51-8 install ok installed libapt-pkg4.12:amd64 libapt-pkg4.12 0.9.7.9+deb7u7 install ok installed libattr1:amd64 libattr1 1:2.4.46-8 install ok installed libblkid1:amd64 libblkid1 2.20.1-5.3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-4 install ok installed libc-bin libc-bin 2.13-38+deb7u10 install ok installed libc6:amd64 libc6 2.13-38+deb7u10 install ok installed libcomerr2:amd64 libcomerr2 1.42.5-1.1+deb7u1 install ok installed libdb5.1:amd64 libdb5.1 5.1.29-5 install ok installed libgcc1:amd64 libgcc1 1:4.7.2-5 install ok installed liblocale-gettext-perl liblocale-gettext-perl 1.05-7+b1 install ok installed liblzma5:amd64 liblzma5 5.1.1alpha+20120614-2 install ok installed libmount1 libmount1 2.20.1-5.3 install ok installed libncurses5:amd64 libncurses5 5.9-10 install ok installed libpam-modules:amd64 libpam-modules 1.1.3-7.1 install ok installed libpam-modules-bin libpam-modules-bin 1.1.3-7.1 install ok installed libpam-runtime libpam-runtime 1.1.3-7.1 install ok installed libpam0g:amd64 libpam0g 1.1.3-7.1 install ok installed libreadline6:amd64 libreadline6 6.2+dfsg-0.1 install ok installed libselinux1:amd64 libselinux1 2.1.9-5 install ok installed libsemanage-common libsemanage-common 2.1.6-6 install ok installed libsemanage1:amd64 libsemanage1 2.1.6-6 install ok installed libsepol1:amd64 libsepol1 2.1.4-3 install ok installed libslang2:amd64 libslang2 2.2.4-15 install ok installed libss2:amd64 libss2 1.42.5-1.1+deb7u1 install ok installed libstdc++6:amd64 libstdc++6 4.7.2-5 install ok installed libtext-charwidth-perl libtext-charwidth-perl 0.04-7+b1 install ok installed libtext-iconv-perl libtext-iconv-perl 1.7-5 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-7 install ok installed libtinfo5:amd64 libtinfo5 5.9-10 install ok installed libusb-0.1-4:amd64 libusb-0.1-4 2:0.1.12-20+nmu1 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-3 install ok installed libuuid1:amd64 libuuid1 2.20.1-5.3 install ok installed login login 1:4.1.5.1-1 install ok installed lsb-base lsb-base 4.1+Debian8+deb7u1 install ok installed mawk mawk 1.3.3-17 install ok installed mount mount 2.20.1-5.3 install ok installed multiarch-support multiarch-support 2.13-38+deb7u10 install ok installed ncurses-base ncurses-base 5.9-10 install ok installed ncurses-bin ncurses-bin 5.9-10 install ok installed passwd passwd 1:4.1.5.1-1 install ok installed perl-base perl-base 5.14.2-21+deb7u3 install ok installed readline-common readline-common 6.2+dfsg-0.1 install ok installed sed sed 4.2.1-10 install ok installed sensible-utils sensible-utils 0.0.7 install ok installed sysv-rc sysv-rc 2.88dsf-41+deb7u1 install ok installed sysvinit sysvinit 2.88dsf-41+deb7u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-41+deb7u1 install ok installed tar tar 1.26+dfsg-0.1 install ok installed tzdata tzdata 2016d-0+deb7u1 install ok installed ucf ucf 3.0025+nmu3 install ok installed util-linux util-linux 2.20.1-5.3 install ok installed xz-utils xz-utils 5.1.1alpha+20120614-2 install ok installed zlib1g:amd64 zlib1g 1:1.2.7.dfsg-13 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.4s DEBUG: Loading chroot meta data from reference-chroot-metadata.dat 0m9.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYp_V1s'] 0m10.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYp_V1s'] 0m10.7s INFO: Running scripts is_testable 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/is_testable_uninstallable'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/is_testable_uninstallable'] 0m10.7s INFO: Running scripts pre_test 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_test_exceptions'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_test_exceptions'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_test_root_password'] 0m10.7s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_test_root_password'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-cache', 'show', '--no-all-versions', 'exonerate'] 0m10.8s DUMP: Package: exonerate Version: 2.2.0-6 Installed-Size: 8144 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.7), libglib2.0-0 (>= 2.24.0) Suggests: wise Enhances: bioperl-run Description-en: 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 Homepage: http://www.ebi.ac.uk/~guy/exonerate/ Description-md5: 61984be320e7cae47c75d879b270d329 Tag: field::biology, field::biology:bioinformatics, implemented-in::c, interface::commandline, role::program, scope::utility, use::TODO, use::searching, works-with-format::TODO, works-with-format::plaintext, works-with::TODO Section: science Priority: optional Filename: pool/main/e/exonerate/exonerate_2.2.0-6_amd64.deb Size: 3053402 MD5sum: 83a75a82a555aa601d874aa671baaaa7 SHA1: e39d7fd387145d78abde21e06ae0ffef36f81850 SHA256: 628a9b8ead0dee7bcacf0abae2a9fca3cf7d9805633b1e4df1a1b4fa450cf608 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-cache', 'show', '--no-all-versions', 'exonerate'] 0m10.8s INFO: apt-cache knows about the following packages: exonerate 0m10.8s INFO: Running scripts pre_install 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_database-server'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_database-server'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_exceptions'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_exceptions'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_extras'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_extras'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-cache', 'policy'] 0m10.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror.bm.debian.org/debian/ wheezy/main Translation-en 500 http://mirror.bm.debian.org/debian/ wheezy/main amd64 Packages release v=7.11,o=Debian,a=oldoldstable,n=wheezy,l=Debian,c=main origin mirror.bm.debian.org Pinned packages: 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-cache', 'policy'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-cache', 'policy', 'exonerate'] 0m10.9s DUMP: exonerate: Installed: (none) Candidate: 2.2.0-6 Version table: 2.2.0-6 0 500 http://mirror.bm.debian.org/debian/ wheezy/main amd64 Packages 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-cache', 'policy', 'exonerate'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-get', '-y', 'install', 'exonerate'] 0m12.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libffi5 libglib2.0-0 libpcre3 Suggested packages: wise Recommended packages: libglib2.0-data shared-mime-info The following NEW packages will be installed: exonerate libffi5 libglib2.0-0 libpcre3 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 5158 kB of archives. After this operation, 12.8 MB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ wheezy/main libpcre3 amd64 1:8.30-5 [242 kB] Get:2 http://mirror.bm.debian.org/debian/ wheezy/main libffi5 amd64 3.0.10-3 [24.8 kB] Get:3 http://mirror.bm.debian.org/debian/ wheezy/main libglib2.0-0 amd64 2.33.12+really2.32.4-5 [1838 kB] Get:4 http://mirror.bm.debian.org/debian/ wheezy/main exonerate amd64 2.2.0-6 [3053 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 5158 kB in 0s (18.0 MB/s) Selecting previously unselected package libpcre3:amd64. (Reading database ... 6768 files and directories currently installed.) Unpacking libpcre3:amd64 (from .../libpcre3_1%3a8.30-5_amd64.deb) ... Selecting previously unselected package libffi5:amd64. Unpacking libffi5:amd64 (from .../libffi5_3.0.10-3_amd64.deb) ... Selecting previously unselected package libglib2.0-0:amd64. Unpacking libglib2.0-0:amd64 (from .../libglib2.0-0_2.33.12+really2.32.4-5_amd64.deb) ... Selecting previously unselected package exonerate. Unpacking exonerate (from .../exonerate_2.2.0-6_amd64.deb) ... Setting up libpcre3:amd64 (1:8.30-5) ... Setting up libffi5:amd64 (3.0.10-3) ... Setting up libglib2.0-0:amd64 (2.33.12+really2.32.4-5) ... No schema files found: doing nothing. Setting up exonerate (2.2.0-6) ... 0m12.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-get', '-y', 'install', 'exonerate'] 0m12.6s INFO: Running scripts post_install 0m12.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_install_exceptions'] 0m12.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_install_exceptions'] 0m12.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYp_V1s'] 0m13.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYp_V1s'] 0m13.9s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpYp_V1s to wheezy-lts 0m13.9s DEBUG: sources.list: deb http://mirror.bm.debian.org/debian/ wheezy main deb http://security.debian.org wheezy/updates main 0m13.9s INFO: Running scripts pre_distupgrade 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_distupgrade_exceptions'] 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_distupgrade_exceptions'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_distupgrade_wheezy'] 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_distupgrade_wheezy'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-get', 'update'] 0m17.0s DUMP: Hit http://mirror.bm.debian.org wheezy Release.gpg Hit http://mirror.bm.debian.org wheezy Release Hit http://mirror.bm.debian.org wheezy/main amd64 Packages Get:1 http://security.debian.org wheezy/updates Release.gpg [1601 B] Hit http://mirror.bm.debian.org wheezy/main Translation-en Get:2 http://security.debian.org wheezy/updates Release [52.3 kB] Get:3 http://security.debian.org wheezy/updates/main amd64 Packages [589 kB] Get:4 http://security.debian.org wheezy/updates/main Translation-en [338 kB] Fetched 981 kB in 1s (716 kB/s) Reading package lists... 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-get', 'update'] 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-get', '-yf', 'dist-upgrade'] 0m23.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: bash gnupg gpgv libc-bin libc6 libdb5.1 libffi5 login multiarch-support passwd perl-base sensible-utils tar tzdata 14 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 15.4 MB of archives. After this operation, 665 kB of additional disk space will be used. Get:1 http://security.debian.org/ wheezy/updates/main bash amd64 4.2+dfsg-0.1+deb7u4 [1499 kB] Get:2 http://security.debian.org/ wheezy/updates/main login amd64 1:4.1.5.1-1+deb7u1 [984 kB] Get:3 http://security.debian.org/ wheezy/updates/main perl-base amd64 5.14.2-21+deb7u6 [1534 kB] Get:4 http://security.debian.org/ wheezy/updates/main tar amd64 1.26+dfsg-0.1+deb7u1 [984 kB] Get:5 http://security.debian.org/ wheezy/updates/main libc-bin amd64 2.13-38+deb7u12 [1275 kB] Get:6 http://security.debian.org/ wheezy/updates/main libc6 amd64 2.13-38+deb7u12 [4226 kB] Get:7 http://security.debian.org/ wheezy/updates/main libdb5.1 amd64 5.1.29-5+deb7u1 [723 kB] Get:8 http://security.debian.org/ wheezy/updates/main libffi5 amd64 3.0.10-3+deb7u2 [25.5 kB] Get:9 http://security.debian.org/ wheezy/updates/main gpgv amd64 1.4.12-7+deb7u9 [229 kB] Get:10 http://security.debian.org/ wheezy/updates/main gnupg amd64 1.4.12-7+deb7u9 [1954 kB] Get:11 http://security.debian.org/ wheezy/updates/main passwd amd64 1:4.1.5.1-1+deb7u1 [1262 kB] Get:12 http://security.debian.org/ wheezy/updates/main sensible-utils all 0.0.7+deb7u1 [9000 B] Get:13 http://security.debian.org/ wheezy/updates/main tzdata all 2018e-0+deb7u1 [496 kB] Get:14 http://security.debian.org/ wheezy/updates/main multiarch-support amd64 2.13-38+deb7u12 [152 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 15.4 MB in 1s (13.9 MB/s) (Reading database ... 6881 files and directories currently installed.) Preparing to replace bash 4.2+dfsg-0.1+deb7u3 (using .../bash_4.2+dfsg-0.1+deb7u4_amd64.deb) ... Unpacking replacement bash ... Setting up bash (4.2+dfsg-0.1+deb7u4) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 6881 files and directories currently installed.) Preparing to replace login 1:4.1.5.1-1 (using .../login_1%3a4.1.5.1-1+deb7u1_amd64.deb) ... Unpacking replacement login ... Setting up login (1:4.1.5.1-1+deb7u1) ... (Reading database ... 6881 files and directories currently installed.) Preparing to replace perl-base 5.14.2-21+deb7u3 (using .../perl-base_5.14.2-21+deb7u6_amd64.deb) ... Unpacking replacement perl-base ... Setting up perl-base (5.14.2-21+deb7u6) ... (Reading database ... 6881 files and directories currently installed.) Preparing to replace tar 1.26+dfsg-0.1 (using .../tar_1.26+dfsg-0.1+deb7u1_amd64.deb) ... Unpacking replacement tar ... Setting up tar (1.26+dfsg-0.1+deb7u1) ... (Reading database ... 6881 files and directories currently installed.) Preparing to replace libc-bin 2.13-38+deb7u10 (using .../libc-bin_2.13-38+deb7u12_amd64.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.13-38+deb7u12) ... (Reading database ... 6881 files and directories currently installed.) Preparing to replace libc6:amd64 2.13-38+deb7u10 (using .../libc6_2.13-38+deb7u12_amd64.deb) ... Unpacking replacement libc6:amd64 ... Setting up libc6:amd64 (2.13-38+deb7u12) ... (Reading database ... 6881 files and directories currently installed.) Preparing to replace libdb5.1:amd64 5.1.29-5 (using .../libdb5.1_5.1.29-5+deb7u1_amd64.deb) ... Unpacking replacement libdb5.1:amd64 ... Setting up libdb5.1:amd64 (5.1.29-5+deb7u1) ... (Reading database ... 6881 files and directories currently installed.) Preparing to replace libffi5:amd64 3.0.10-3 (using .../libffi5_3.0.10-3+deb7u2_amd64.deb) ... Unpacking replacement libffi5:amd64 ... Preparing to replace gpgv 1.4.12-7+deb7u7 (using .../gpgv_1.4.12-7+deb7u9_amd64.deb) ... Unpacking replacement gpgv ... Setting up gpgv (1.4.12-7+deb7u9) ... (Reading database ... 6881 files and directories currently installed.) Preparing to replace gnupg 1.4.12-7+deb7u7 (using .../gnupg_1.4.12-7+deb7u9_amd64.deb) ... Unpacking replacement gnupg ... Setting up gnupg (1.4.12-7+deb7u9) ... (Reading database ... 6881 files and directories currently installed.) Preparing to replace passwd 1:4.1.5.1-1 (using .../passwd_1%3a4.1.5.1-1+deb7u1_amd64.deb) ... Unpacking replacement passwd ... Setting up passwd (1:4.1.5.1-1+deb7u1) ... (Reading database ... 6881 files and directories currently installed.) Preparing to replace sensible-utils 0.0.7 (using .../sensible-utils_0.0.7+deb7u1_all.deb) ... Unpacking replacement sensible-utils ... Setting up sensible-utils (0.0.7+deb7u1) ... (Reading database ... 6881 files and directories currently installed.) Preparing to replace tzdata 2016d-0+deb7u1 (using .../tzdata_2018e-0+deb7u1_all.deb) ... Unpacking replacement tzdata ... Setting up tzdata (2018e-0+deb7u1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Jul 7 00:36:08 UTC 2018. Universal Time is now: Sat Jul 7 00:36:08 UTC 2018. Run 'dpkg-reconfigure tzdata' if you wish to change it. (Reading database ... 6893 files and directories currently installed.) Preparing to replace multiarch-support 2.13-38+deb7u10 (using .../multiarch-support_2.13-38+deb7u12_amd64.deb) ... Unpacking replacement multiarch-support ... Setting up multiarch-support (2.13-38+deb7u12) ... Setting up libffi5:amd64 (3.0.10-3+deb7u2) ... 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-get', '-yf', 'dist-upgrade'] 0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m24.0s DUMP: c16ce146adddf40566e495d132dec083 - 0m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-cache', 'show', '--no-all-versions', 'exonerate'] 0m24.1s DUMP: Package: exonerate Version: 2.2.0-6 Installed-Size: 8144 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.7), libglib2.0-0 (>= 2.24.0) Suggests: wise Enhances: bioperl-run Description-en: 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 Homepage: http://www.ebi.ac.uk/~guy/exonerate/ Description-md5: 61984be320e7cae47c75d879b270d329 Tag: field::biology, field::biology:bioinformatics, implemented-in::c, interface::commandline, role::program, scope::utility, use::TODO, use::searching, works-with-format::TODO, works-with-format::plaintext, works-with::TODO Section: science Priority: optional Filename: pool/main/e/exonerate/exonerate_2.2.0-6_amd64.deb Size: 3053402 MD5sum: 83a75a82a555aa601d874aa671baaaa7 SHA1: e39d7fd387145d78abde21e06ae0ffef36f81850 SHA256: 628a9b8ead0dee7bcacf0abae2a9fca3cf7d9805633b1e4df1a1b4fa450cf608 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-cache', 'show', '--no-all-versions', 'exonerate'] 0m24.1s INFO: apt-cache knows about the following packages: exonerate 0m24.1s INFO: Running scripts pre_install 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_database-server'] 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_database-server'] 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_exceptions'] 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_exceptions'] 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_extras'] 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_extras'] 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_foreign_architecture'] 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_foreign_architecture'] 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m24.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m24.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-cache', 'policy'] 0m24.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://security.debian.org/ wheezy/updates/main Translation-en 500 http://security.debian.org/ wheezy/updates/main amd64 Packages release v=7.0,o=Debian,a=oldoldstable,n=wheezy,l=Debian-Security,c=main origin security.debian.org 500 http://mirror.bm.debian.org/debian/ wheezy/main Translation-en 500 http://mirror.bm.debian.org/debian/ wheezy/main amd64 Packages release v=7.11,o=Debian,a=oldoldstable,n=wheezy,l=Debian,c=main origin mirror.bm.debian.org Pinned packages: 0m24.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-cache', 'policy'] 0m24.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-cache', 'policy', 'exonerate'] 0m24.2s DUMP: exonerate: Installed: 2.2.0-6 Candidate: 2.2.0-6 Version table: *** 2.2.0-6 0 500 http://mirror.bm.debian.org/debian/ wheezy/main amd64 Packages 100 /var/lib/dpkg/status 0m24.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-cache', 'policy', 'exonerate'] 0m24.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-get', '-y', 'install', 'exonerate'] 0m24.9s DUMP: Reading package lists... Building dependency tree... Reading state information... exonerate is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-get', '-y', 'install', 'exonerate'] 0m24.9s INFO: Running scripts post_install 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_install_exceptions'] 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_install_exceptions'] 0m24.9s INFO: Running scripts post_distupgrade 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_distupgrade_exceptions'] 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_distupgrade_exceptions'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_distupgrade_experimental'] 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_distupgrade_experimental'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_distupgrade_hack_debsums'] 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_distupgrade_hack_debsums'] 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_distupgrade_zz_backports'] 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_distupgrade_zz_backports'] 0m25.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYp_V1s'] 0m26.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYp_V1s'] 0m26.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYp_V1s'] 0m27.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYp_V1s'] 0m27.6s INFO: Running scripts pre_install 0m27.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_database-server'] 0m27.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_database-server'] 0m27.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_exceptions'] 0m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_exceptions'] 0m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_extras'] 0m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_extras'] 0m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_foreign_architecture'] 0m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_foreign_architecture'] 0m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-cache', 'policy'] 0m27.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://security.debian.org/ wheezy/updates/main Translation-en 500 http://security.debian.org/ wheezy/updates/main amd64 Packages release v=7.0,o=Debian,a=oldoldstable,n=wheezy,l=Debian-Security,c=main origin security.debian.org 500 http://mirror.bm.debian.org/debian/ wheezy/main Translation-en 500 http://mirror.bm.debian.org/debian/ wheezy/main amd64 Packages release v=7.11,o=Debian,a=oldoldstable,n=wheezy,l=Debian,c=main origin mirror.bm.debian.org Pinned packages: 0m27.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-cache', 'policy'] 0m27.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-cache', 'policy', 'exonerate'] 0m27.9s DUMP: exonerate: Installed: 2.2.0-6 Candidate: 2.2.0-6 Version table: *** 2.2.0-6 0 500 http://mirror.bm.debian.org/debian/ wheezy/main amd64 Packages 100 /var/lib/dpkg/status 0m27.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-cache', 'policy', 'exonerate'] 0m27.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-get', '-y', 'install', 'exonerate=2.2.0-6'] 0m28.4s DUMP: Reading package lists... Building dependency tree... Reading state information... exonerate is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m28.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-get', '-y', 'install', 'exonerate=2.2.0-6'] 0m28.4s INFO: Running scripts post_install 0m28.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_install_exceptions'] 0m28.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_install_exceptions'] 0m28.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYp_V1s'] 0m29.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYp_V1s'] 0m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m29.8s DUMP: install ok installed adduser adduser 3.113+nmu3 install ok installed apt apt 0.9.7.9+deb7u7 install ok installed base-files base-files 7.1wheezy11 install ok installed base-passwd base-passwd 3.5.26 install ok installed bash bash 4.2+dfsg-0.1+deb7u4 install ok installed bsdutils bsdutils 1:2.20.1-5.3 install ok installed coreutils coreutils 8.13-3.5 install ok installed dash dash 0.5.7-3 install ok installed debconf debconf 1.5.49 install ok installed debconf-i18n debconf-i18n 1.5.49 install ok installed debian-archive-keyring debian-archive-keyring 2014.3~deb7u1 install ok installed debianutils debianutils 4.3.2 install ok installed diffutils diffutils 1:3.2-6 install ok installed dpkg dpkg 1.16.18 install ok installed e2fslibs:amd64 e2fslibs 1.42.5-1.1+deb7u1 install ok installed e2fsprogs e2fsprogs 1.42.5-1.1+deb7u1 install ok installed exonerate exonerate 2.2.0-6 install ok installed findutils findutils 4.4.2-4 install ok installed gcc-4.7-base:amd64 gcc-4.7-base 4.7.2-5 install ok installed gnupg gnupg 1.4.12-7+deb7u9 install ok installed gpgv gpgv 1.4.12-7+deb7u9 install ok installed grep grep 2.12-2 install ok installed gzip gzip 1.5-1.1 install ok installed hostname hostname 3.11 install ok installed initscripts initscripts 2.88dsf-41+deb7u1 install ok installed insserv insserv 1.14.0-5 install ok installed libacl1:amd64 libacl1 2.2.51-8 install ok installed libapt-pkg4.12:amd64 libapt-pkg4.12 0.9.7.9+deb7u7 install ok installed libattr1:amd64 libattr1 1:2.4.46-8 install ok installed libblkid1:amd64 libblkid1 2.20.1-5.3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-4 install ok installed libc-bin libc-bin 2.13-38+deb7u12 install ok installed libc6:amd64 libc6 2.13-38+deb7u12 install ok installed libcomerr2:amd64 libcomerr2 1.42.5-1.1+deb7u1 install ok installed libdb5.1:amd64 libdb5.1 5.1.29-5+deb7u1 install ok installed libffi5:amd64 libffi5 3.0.10-3+deb7u2 install ok installed libgcc1:amd64 libgcc1 1:4.7.2-5 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.33.12+really2.32.4-5 install ok installed liblocale-gettext-perl liblocale-gettext-perl 1.05-7+b1 install ok installed liblzma5:amd64 liblzma5 5.1.1alpha+20120614-2 install ok installed libmount1 libmount1 2.20.1-5.3 install ok installed libncurses5:amd64 libncurses5 5.9-10 install ok installed libpam-modules:amd64 libpam-modules 1.1.3-7.1 install ok installed libpam-modules-bin libpam-modules-bin 1.1.3-7.1 install ok installed libpam-runtime libpam-runtime 1.1.3-7.1 install ok installed libpam0g:amd64 libpam0g 1.1.3-7.1 install ok installed libpcre3:amd64 libpcre3 1:8.30-5 install ok installed libreadline6:amd64 libreadline6 6.2+dfsg-0.1 install ok installed libselinux1:amd64 libselinux1 2.1.9-5 install ok installed libsemanage-common libsemanage-common 2.1.6-6 install ok installed libsemanage1:amd64 libsemanage1 2.1.6-6 install ok installed libsepol1:amd64 libsepol1 2.1.4-3 install ok installed libslang2:amd64 libslang2 2.2.4-15 install ok installed libss2:amd64 libss2 1.42.5-1.1+deb7u1 install ok installed libstdc++6:amd64 libstdc++6 4.7.2-5 install ok installed libtext-charwidth-perl libtext-charwidth-perl 0.04-7+b1 install ok installed libtext-iconv-perl libtext-iconv-perl 1.7-5 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-7 install ok installed libtinfo5:amd64 libtinfo5 5.9-10 install ok installed libusb-0.1-4:amd64 libusb-0.1-4 2:0.1.12-20+nmu1 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-3 install ok installed libuuid1:amd64 libuuid1 2.20.1-5.3 install ok installed login login 1:4.1.5.1-1+deb7u1 install ok installed lsb-base lsb-base 4.1+Debian8+deb7u1 install ok installed mawk mawk 1.3.3-17 install ok installed mount mount 2.20.1-5.3 install ok installed multiarch-support multiarch-support 2.13-38+deb7u12 install ok installed ncurses-base ncurses-base 5.9-10 install ok installed ncurses-bin ncurses-bin 5.9-10 install ok installed passwd passwd 1:4.1.5.1-1+deb7u1 install ok installed perl-base perl-base 5.14.2-21+deb7u6 install ok installed readline-common readline-common 6.2+dfsg-0.1 install ok installed sed sed 4.2.1-10 install ok installed sensible-utils sensible-utils 0.0.7+deb7u1 install ok installed sysv-rc sysv-rc 2.88dsf-41+deb7u1 install ok installed sysvinit sysvinit 2.88dsf-41+deb7u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-41+deb7u1 install ok installed tar tar 1.26+dfsg-0.1+deb7u1 install ok installed tzdata tzdata 2018e-0+deb7u1 install ok installed ucf ucf 3.0025+nmu3 install ok installed util-linux util-linux 2.20.1-5.3 install ok installed xz-utils xz-utils 5.1.1alpha+20120614-2 install ok installed zlib1g:amd64 zlib1g 1:1.2.7.dfsg-13 0m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m30.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', '-ac', '--ignore-obsolete'] 0m32.2s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', '-ac', '--ignore-obsolete'] 0m32.2s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m32.3s DUMP: 0.15.1 0m32.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m32.3s INFO: Running adequate version 0.15.1 now. 0m32.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'exonerate'] 0m32.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'exonerate'] 0m32.9s INFO: Running scripts pre_remove 0m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m33.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m33.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_remove_exceptions'] 0m34.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/pre_remove_exceptions'] 0m34.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-get', 'remove', 'libpcre3:amd64', 'libffi5:amd64', 'libglib2.0-0:amd64', 'exonerate'] 0m35.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: exonerate libffi5 libglib2.0-0 libpcre3 0 upgraded, 0 newly installed, 4 to remove and 0 not upgraded. After this operation, 12.8 MB disk space will be freed. (Reading database ... 6893 files and directories currently installed.) Removing exonerate ... Removing libglib2.0-0:amd64 ... Removing libffi5:amd64 ... Removing libpcre3:amd64 ... 0m35.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-get', 'remove', 'libpcre3:amd64', 'libffi5:amd64', 'libglib2.0-0:amd64', 'exonerate'] 0m35.4s INFO: Running scripts post_remove 0m35.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_remove_exceptions'] 0m35.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_remove_exceptions'] 0m35.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_remove_extras'] 0m35.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_remove_extras'] 0m35.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'dpkg', '--purge', 'libpcre3:amd64', 'libffi5:amd64', 'libglib2.0-0:amd64'] 0m35.4s DUMP: (Reading database ... 6780 files and directories currently installed.) Removing libpcre3:amd64 ... Purging configuration files for libpcre3:amd64 ... Removing libffi5:amd64 ... Purging configuration files for libffi5:amd64 ... Removing libglib2.0-0:amd64 ... Purging configuration files for libglib2.0-0:amd64 ... 0m35.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'dpkg', '--purge', 'libpcre3:amd64', 'libffi5:amd64', 'libglib2.0-0:amd64'] 0m35.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'dpkg', '--purge', 'exonerate'] 0m35.5s DUMP: dpkg: warning: ignoring request to remove exonerate which isn't installed 0m35.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'dpkg', '--purge', 'exonerate'] 0m35.5s INFO: Running scripts post_purge 0m35.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_purge_exceptions'] 0m35.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_purge_exceptions'] 0m35.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'dpkg', '--purge', '--pending'] 0m35.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'dpkg', '--purge', '--pending'] 0m35.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'dpkg', '--remove', '--pending'] 0m35.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'dpkg', '--remove', '--pending'] 0m35.6s INFO: Running scripts post_test 0m35.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_test_exceptions'] 0m35.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'tmp/scripts/post_test_exceptions'] 0m35.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYp_V1s'] 0m36.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYp_V1s'] 0m36.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'dpkg-divert', '--list'] 0m36.9s 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 local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m36.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'dpkg-divert', '--list'] 0m36.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-get', 'clean'] 0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYp_V1s', 'apt-get', 'clean'] 0m37.0s DEBUG: Recording chroot state 0m41.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/run/shm'] 0m41.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/run/shm'] 0m41.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/dev/console'] 0m41.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/dev/console'] 0m41.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/dev/ptmx'] 0m41.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/dev/ptmx'] 0m41.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/dev/pts'] 0m41.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/dev/pts'] 0m41.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/proc'] 0m41.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpYp_V1s/proc'] 0m41.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpYp_V1s'] 0m41.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpYp_V1s'] 0m41.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpYp_V1s 0m41.6s INFO: PASS: Upgrading between Debian distributions. 0m41.6s INFO: PASS: All tests. 0m41.6s INFO: piuparts run ends. ret=0 End: 2018-07-07 00:36:26 UTC