Start: 2018-02-03 07:53:07 UTC [wheezy] Package: theseus Version: 1.6.2-2 Installed-Size: 2381 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.7), libgsl0ldbl (>= 1.9), muscle Suggests: clustlaw, mafft, t-coffee, kalign, dialign Description: superimpose macromolecules using maximum likelihood Homepage: http://www.theseus3d.org Description-md5: 91517695c1e9e5cdc2a87ff78d5403a8 Tag: biology::peptidic, field::biology, field::biology:bioinformatics, field::biology:structural, implemented-in::c, interface::commandline, role::program, use::analysing, use::comparing, works-with-format::plaintext Section: science Priority: optional Filename: pool/main/t/theseus/theseus_1.6.2-2_amd64.deb Size: 1506734 MD5sum: 6792b429489dc95117f2ad05ab137074 SHA1: 76e6e5b76b24737e4cd019b5fa799d2b4c21a415 SHA256: d57c79b9f04d034dea23d71aa6901151e62d50a46aba7c64106208cada11afe5 [wheezy-lts] Package: theseus Version: 1.6.2-2 Installed-Size: 2381 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.7), libgsl0ldbl (>= 1.9), muscle Suggests: clustlaw, mafft, t-coffee, kalign, dialign Description: superimpose macromolecules using maximum likelihood Homepage: http://www.theseus3d.org Description-md5: 91517695c1e9e5cdc2a87ff78d5403a8 Tag: biology::peptidic, field::biology, field::biology:bioinformatics, field::biology:structural, implemented-in::c, interface::commandline, role::program, use::analysing, use::comparing, works-with-format::plaintext Section: science Priority: optional Filename: pool/main/t/theseus/theseus_1.6.2-2_amd64.deb Size: 1506734 MD5sum: 6792b429489dc95117f2ad05ab137074 SHA1: 76e6e5b76b24737e4cd019b5fa799d2b4c21a415 SHA256: d57c79b9f04d034dea23d71aa6901151e62d50a46aba7c64106208cada11afe5 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 theseus=1.6.2-2 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 0.84~201801121530~0.83-4-g6e16ed9a 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 theseus=1.6.2-2 0m0.0s INFO: Running on: Linux piu-slave-bm-a 4.9.0-5-amd64 #1 SMP Debian 4.9.65-3+deb9u2 (2018-01-04) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp3rsGak 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp3rsGak 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp3rsGak', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz'] 0m2.0s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp3rsGak', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz'] 0m2.0s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp3rsGak/proc'] 0m2.0s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp3rsGak/proc'] 0m2.0s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp3rsGak/dev/pts'] 0m2.0s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp3rsGak/dev/pts'] 0m2.0s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp3rsGak/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp3rsGak/dev/ptmx'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp3rsGak/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp3rsGak/dev/ptmx'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp3rsGak/dev/console'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp3rsGak/dev/console'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp3rsGak/run/shm'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp3rsGak/run/shm'] 0m2.1s DEBUG: sources.list: deb http://mirror.bm.debian.org/debian/ wheezy main 0m2.1s DEBUG: Created policy-rc.d and chmodded it. 0m2.1s DEBUG: Created resolv.conf. 0m2.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp3rsGak/tmp/scripts/ 0m2.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts-wheezy to /srv/piuparts.debian.org/tmp/tmp3rsGak/tmp/scripts/ 0m2.2s INFO: Running scripts post_chroot_unpack 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-get', 'update'] 0m4.9s 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... 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-get', 'update'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', '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/tmp3rsGak', 'apt-get', '-yf', 'dist-upgrade'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.8s DUMP: 0c96df6df725ee7ec7aebd2b6a77fb72 - 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.8s INFO: Running scripts post_setup 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_setup_dummy_users'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_setup_dummy_users'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_setup_experimental'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_setup_experimental'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_setup_forbid_home'] 0m7.2s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_setup_forbid_home'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.2s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' `/bin/sync' -> `true' 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_setup_minimize'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_setup_minimize'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_setup_wheezy-fake-essential'] 0m8.6s 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 (20.3 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) ... 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_setup_wheezy-fake-essential'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_setup_zz_backports'] 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_setup_zz_backports'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.6s 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 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.6s DEBUG: Loading chroot meta data from reference-chroot-metadata.dat 0m9.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3rsGak'] 0m10.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3rsGak'] 0m10.7s INFO: Running scripts is_testable 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/is_testable_uninstallable'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/is_testable_uninstallable'] 0m10.7s INFO: Running scripts pre_test 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_test_exceptions'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_test_exceptions'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_test_root_password'] 0m10.8s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_test_root_password'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-cache', 'show', 'theseus'] 0m10.8s DUMP: Package: theseus Version: 1.6.2-2 Installed-Size: 2381 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.7), libgsl0ldbl (>= 1.9), muscle Suggests: clustlaw, mafft, t-coffee, kalign, dialign Description-en: superimpose macromolecules using maximum likelihood Theseus is a program that simultaneously superimposes multiple macromolecular structures. Theseus finds the optimal solution to the superposition problem using the method of maximum likelihood. By down-weighting variable regions of the superposition and by correcting for correlations among atoms, the ML superposition method produces very accurate structural alignments. . When macromolecules with different residue sequences are superimposed, other programs and algorithms discard residues that are aligned with gaps. Theseus, however, uses a novel superimposition algorithm that includes all of the data. Homepage: http://www.theseus3d.org Description-md5: 91517695c1e9e5cdc2a87ff78d5403a8 Tag: biology::peptidic, field::biology, field::biology:bioinformatics, field::biology:structural, implemented-in::c, interface::commandline, role::program, use::analysing, use::comparing, works-with-format::plaintext Section: science Priority: optional Filename: pool/main/t/theseus/theseus_1.6.2-2_amd64.deb Size: 1506734 MD5sum: 6792b429489dc95117f2ad05ab137074 SHA1: 76e6e5b76b24737e4cd019b5fa799d2b4c21a415 SHA256: d57c79b9f04d034dea23d71aa6901151e62d50a46aba7c64106208cada11afe5 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-cache', 'show', 'theseus'] 0m10.8s INFO: apt-cache knows about the following packages: theseus 0m10.8s INFO: Running scripts pre_install 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_database-server'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_database-server'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_exceptions'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_exceptions'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_extras'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_extras'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', '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/tmp3rsGak', 'apt-cache', 'policy'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-cache', 'policy', 'theseus'] 0m11.0s DUMP: theseus: Installed: (none) Candidate: 1.6.2-2 Version table: 1.6.2-2 0 500 http://mirror.bm.debian.org/debian/ wheezy/main amd64 Packages 0m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-cache', 'policy', 'theseus'] 0m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-get', '-y', 'install', 'theseus'] 0m12.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libgsl0ldbl muscle Suggested packages: gsl-ref-psdoc gsl-doc-pdf gsl-doc-info gsl-ref-html clustlaw mafft t-coffee kalign dialign The following NEW packages will be installed: libgsl0ldbl muscle theseus 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 2808 kB of archives. After this operation, 5780 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ wheezy/main libgsl0ldbl amd64 1.15+dfsg.2-2 [1132 kB] Get:2 http://mirror.bm.debian.org/debian/ wheezy/main muscle amd64 1:3.8.31-1 [169 kB] Get:3 http://mirror.bm.debian.org/debian/ wheezy/main theseus amd64 1.6.2-2 [1507 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 2808 kB in 0s (8096 kB/s) Selecting previously unselected package libgsl0ldbl. (Reading database ... 6768 files and directories currently installed.) Unpacking libgsl0ldbl (from .../libgsl0ldbl_1.15+dfsg.2-2_amd64.deb) ... Selecting previously unselected package muscle. Unpacking muscle (from .../muscle_1%3a3.8.31-1_amd64.deb) ... Selecting previously unselected package theseus. Unpacking theseus (from .../theseus_1.6.2-2_amd64.deb) ... Setting up libgsl0ldbl (1.15+dfsg.2-2) ... Setting up muscle (1:3.8.31-1) ... Setting up theseus (1.6.2-2) ... 0m12.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-get', '-y', 'install', 'theseus'] 0m12.4s INFO: Running scripts post_install 0m12.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_install_exceptions'] 0m12.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_install_exceptions'] 0m12.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3rsGak'] 0m13.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3rsGak'] 0m13.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp3rsGak to wheezy-lts 0m13.5s DEBUG: sources.list: deb http://mirror.bm.debian.org/debian/ wheezy main deb http://security.debian.org wheezy/updates main 0m13.5s INFO: Running scripts pre_distupgrade 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_distupgrade_exceptions'] 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_distupgrade_exceptions'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_distupgrade_wheezy'] 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_distupgrade_wheezy'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-get', 'update'] 0m16.6s 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 Get:1 http://security.debian.org wheezy/updates Release.gpg [1601 B] Get:2 http://security.debian.org wheezy/updates Release [39.0 kB] Get:3 http://security.debian.org wheezy/updates/main amd64 Packages [605 kB] Get:4 http://security.debian.org wheezy/updates/main Translation-en [330 kB] Fetched 976 kB in 1s (733 kB/s) Reading package lists... 0m16.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-get', 'update'] 0m16.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-get', '-yf', 'dist-upgrade'] 0m23.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: bash gnupg gpgv libc-bin libc6 libdb5.1 login multiarch-support passwd perl-base sensible-utils tar tzdata 13 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 15.3 MB of archives. After this operation, 663 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+deb7u5 [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 gpgv amd64 1.4.12-7+deb7u9 [229 kB] Get:9 http://security.debian.org/ wheezy/updates/main gnupg amd64 1.4.12-7+deb7u9 [1954 kB] Get:10 http://security.debian.org/ wheezy/updates/main passwd amd64 1:4.1.5.1-1+deb7u1 [1262 kB] Get:11 http://security.debian.org/ wheezy/updates/main sensible-utils all 0.0.7+deb7u1 [9000 B] Get:12 http://security.debian.org/ wheezy/updates/main tzdata all 2017c-0+deb7u1 [493 kB] Get:13 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 15.3 MB in 1s (12.7 MB/s) (Reading database ... 6817 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 ... 6817 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 ... 6817 files and directories currently installed.) Preparing to replace perl-base 5.14.2-21+deb7u3 (using .../perl-base_5.14.2-21+deb7u5_amd64.deb) ... Unpacking replacement perl-base ... Setting up perl-base (5.14.2-21+deb7u5) ... (Reading database ... 6817 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 ... 6817 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 ... 6817 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 ... 6817 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 ... 6817 files and directories currently installed.) 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 ... 6817 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 ... 6817 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 ... 6817 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 ... 6817 files and directories currently installed.) Preparing to replace tzdata 2016d-0+deb7u1 (using .../tzdata_2017c-0+deb7u1_all.deb) ... Unpacking replacement tzdata ... Setting up tzdata (2017c-0+deb7u1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Feb 3 07:53:30 UTC 2018. Universal Time is now: Sat Feb 3 07:53:30 UTC 2018. Run 'dpkg-reconfigure tzdata' if you wish to change it. (Reading database ... 6829 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) ... 0m23.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-get', '-yf', 'dist-upgrade'] 0m23.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m23.6s DUMP: 4c169f7d24c584d4e8d5c8875d926be1 - 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-cache', 'show', 'theseus'] 0m23.6s DUMP: Package: theseus Version: 1.6.2-2 Installed-Size: 2381 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.7), libgsl0ldbl (>= 1.9), muscle Suggests: clustlaw, mafft, t-coffee, kalign, dialign Description-en: superimpose macromolecules using maximum likelihood Theseus is a program that simultaneously superimposes multiple macromolecular structures. Theseus finds the optimal solution to the superposition problem using the method of maximum likelihood. By down-weighting variable regions of the superposition and by correcting for correlations among atoms, the ML superposition method produces very accurate structural alignments. . When macromolecules with different residue sequences are superimposed, other programs and algorithms discard residues that are aligned with gaps. Theseus, however, uses a novel superimposition algorithm that includes all of the data. Homepage: http://www.theseus3d.org Description-md5: 91517695c1e9e5cdc2a87ff78d5403a8 Tag: biology::peptidic, field::biology, field::biology:bioinformatics, field::biology:structural, implemented-in::c, interface::commandline, role::program, use::analysing, use::comparing, works-with-format::plaintext Section: science Priority: optional Filename: pool/main/t/theseus/theseus_1.6.2-2_amd64.deb Size: 1506734 MD5sum: 6792b429489dc95117f2ad05ab137074 SHA1: 76e6e5b76b24737e4cd019b5fa799d2b4c21a415 SHA256: d57c79b9f04d034dea23d71aa6901151e62d50a46aba7c64106208cada11afe5 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-cache', 'show', 'theseus'] 0m23.6s INFO: apt-cache knows about the following packages: theseus 0m23.6s INFO: Running scripts pre_install 0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_database-server'] 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_database-server'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_exceptions'] 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_exceptions'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_extras'] 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_extras'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_foreign_architecture'] 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_foreign_architecture'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-cache', 'policy'] 0m23.8s 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: 0m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-cache', 'policy'] 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-cache', 'policy', 'theseus'] 0m23.8s DUMP: theseus: Installed: 1.6.2-2 Candidate: 1.6.2-2 Version table: *** 1.6.2-2 0 500 http://mirror.bm.debian.org/debian/ wheezy/main amd64 Packages 100 /var/lib/dpkg/status 0m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-cache', 'policy', 'theseus'] 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-get', '-y', 'install', 'theseus'] 0m24.3s DUMP: Reading package lists... Building dependency tree... Reading state information... theseus is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m24.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-get', '-y', 'install', 'theseus'] 0m24.3s INFO: Running scripts post_install 0m24.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_install_exceptions'] 0m24.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_install_exceptions'] 0m24.3s INFO: Running scripts post_distupgrade 0m24.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m24.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m24.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_distupgrade_exceptions'] 0m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_distupgrade_exceptions'] 0m24.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_distupgrade_experimental'] 0m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_distupgrade_experimental'] 0m24.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m24.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_distupgrade_hack_debsums'] 0m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_distupgrade_hack_debsums'] 0m24.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m24.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_distupgrade_zz_backports'] 0m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_distupgrade_zz_backports'] 0m24.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3rsGak'] 0m25.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3rsGak'] 0m25.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3rsGak'] 0m26.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3rsGak'] 0m26.8s INFO: Running scripts pre_install 0m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_database-server'] 0m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_database-server'] 0m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_exceptions'] 0m26.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_exceptions'] 0m26.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_extras'] 0m26.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_extras'] 0m26.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_foreign_architecture'] 0m26.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_foreign_architecture'] 0m26.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m26.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m26.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-cache', 'policy'] 0m27.0s 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: 0m27.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-cache', 'policy'] 0m27.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-cache', 'policy', 'theseus'] 0m27.0s DUMP: theseus: Installed: 1.6.2-2 Candidate: 1.6.2-2 Version table: *** 1.6.2-2 0 500 http://mirror.bm.debian.org/debian/ wheezy/main amd64 Packages 100 /var/lib/dpkg/status 0m27.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-cache', 'policy', 'theseus'] 0m27.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-get', '-y', 'install', 'theseus=1.6.2-2'] 0m27.7s DUMP: Reading package lists... Building dependency tree... Reading state information... theseus is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-get', '-y', 'install', 'theseus=1.6.2-2'] 0m27.7s INFO: Running scripts post_install 0m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_install_exceptions'] 0m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_install_exceptions'] 0m27.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3rsGak'] 0m28.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3rsGak'] 0m28.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m28.9s 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 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 libgcc1:amd64 libgcc1 1:4.7.2-5 install ok installed libgsl0ldbl libgsl0ldbl 1.15+dfsg.2-2 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+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 muscle muscle 1:3.8.31-1 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+deb7u5 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 theseus theseus 1.6.2-2 install ok installed tzdata tzdata 2017c-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 0m28.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m30.1s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp3rsGak', '-ac', '--ignore-obsolete'] 0m31.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp3rsGak', '-ac', '--ignore-obsolete'] 0m31.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m31.3s DUMP: 0.15.1 0m31.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m31.3s INFO: Running adequate version 0.15.1 now. 0m31.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'theseus'] 0m31.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'theseus'] 0m31.5s INFO: Running scripts pre_remove 0m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m31.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m31.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m31.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m31.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m32.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m32.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_remove_exceptions'] 0m33.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/pre_remove_exceptions'] 0m33.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-get', 'remove', 'libgsl0ldbl', 'muscle', 'theseus'] 0m34.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libgsl0ldbl muscle theseus 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. After this operation, 5780 kB disk space will be freed. (Reading database ... 6829 files and directories currently installed.) Removing theseus ... Removing libgsl0ldbl ... Removing muscle ... 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-get', 'remove', 'libgsl0ldbl', 'muscle', 'theseus'] 0m34.0s INFO: Running scripts post_remove 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_remove_exceptions'] 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_remove_exceptions'] 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_remove_extras'] 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_remove_extras'] 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'dpkg', '--purge', 'libgsl0ldbl', 'muscle'] 0m34.1s DUMP: (Reading database ... 6780 files and directories currently installed.) Removing libgsl0ldbl ... Purging configuration files for libgsl0ldbl ... dpkg: warning: ignoring request to remove muscle which isn't installed 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'dpkg', '--purge', 'libgsl0ldbl', 'muscle'] 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'dpkg', '--purge', 'theseus'] 0m34.1s DUMP: dpkg: warning: ignoring request to remove theseus which isn't installed 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'dpkg', '--purge', 'theseus'] 0m34.1s INFO: Running scripts post_purge 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_purge_exceptions'] 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_purge_exceptions'] 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'dpkg', '--purge', '--pending'] 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'dpkg', '--purge', '--pending'] 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'dpkg', '--remove', '--pending'] 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'dpkg', '--remove', '--pending'] 0m34.2s INFO: Running scripts post_test 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_test_exceptions'] 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'tmp/scripts/post_test_exceptions'] 0m34.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3rsGak'] 0m35.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3rsGak'] 0m35.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'dpkg-divert', '--list'] 0m35.4s 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 local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m35.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'dpkg-divert', '--list'] 0m35.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-get', 'clean'] 0m35.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3rsGak', 'apt-get', 'clean'] 0m35.5s DEBUG: Recording chroot state 0m39.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3rsGak/run/shm'] 0m39.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3rsGak/run/shm'] 0m39.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3rsGak/dev/console'] 0m39.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3rsGak/dev/console'] 0m39.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3rsGak/dev/ptmx'] 0m39.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3rsGak/dev/ptmx'] 0m39.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3rsGak/dev/pts'] 0m39.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3rsGak/dev/pts'] 0m39.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3rsGak/proc'] 0m39.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3rsGak/proc'] 0m39.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp3rsGak'] 0m39.5s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp3rsGak'] 0m39.5s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp3rsGak 0m39.5s INFO: PASS: Upgrading between Debian distributions. 0m39.5s INFO: PASS: All tests. 0m39.5s INFO: piuparts run ends. ret=0 End: 2018-02-03 07:53:47 UTC