Start: 2014-10-28 09:10:21 UTC Package: theseus Priority: optional Section: science Installed-Size: 2176 Maintainer: Debian Med Packaging Team Architecture: amd64 Version: 1.4.3-2 Depends: libc6 (>= 2.7), libgsl0ldbl (>= 1.9), liblapack3gf | liblapack.so.3gf | libatlas3gf-base Suggests: muscle, clustlaw, mafft, t-coffee, kalign, dialign Filename: pool/main/t/theseus/theseus_1.4.3-2_amd64.deb Size: 1349238 MD5sum: 62554e8e0db19d779f91130bca6caf14 SHA1: b927b76d4157c05a6c41de7a980086e056cb1df1 SHA256: 28cb9c5091d7ebcfcac927eb06279a1ea0492d9ac0f63a81786dbb527dd064b2 Description: 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 Tag: biology::peptidic, field::{biology,biology:bioinformatics,biology:structural}, implemented-in::c, interface::commandline, role::program, use::analysing, use::comparing, works-with-format::plaintext Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python2.7/dist-packages timeout -s INT -k 5m 35m /srv/piuparts.debian.org/sbin/piuparts --skip-logrotatefiles-test --warn-on-others --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge -i /etc/shells --scriptsdir /etc/piuparts/scripts-squeeze --warn-on-debsums-errors --mirror 'http://mirror.bm.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz -d squeeze --no-upgrade-test --apt theseus=1.4.3-2 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 0.61~201410261922~0.59-22-g69325c0 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --skip-logrotatefiles-test --warn-on-others --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge -i /etc/shells --scriptsdir /etc/piuparts/scripts-squeeze --warn-on-debsums-errors --mirror 'http://mirror.bm.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz -d squeeze --no-upgrade-test --apt theseus=1.4.3-2 0m0.0s INFO: Running on: Linux piu-slave-bm-a 3.2.0-4-amd64 #1 SMP Debian 3.2.63-2 x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpNEy5Xj 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpNEy5Xj 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz'] 0m1.7s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz'] 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'mount', '-t', 'proc', 'proc', '/proc'] 0m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'mount', '-t', 'proc', 'proc', '/proc'] 0m1.7s DEBUG: sources.list: deb http://mirror.bm.debian.org/debian/ squeeze main 0m1.7s DEBUG: Created policy-rc.d and chmodded it. 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-get', 'update'] 0m1.8s DUMP: Hit http://mirror.bm.debian.org squeeze Release.gpg Ign http://mirror.bm.debian.org/debian/ squeeze/main Translation-en Hit http://mirror.bm.debian.org squeeze Release Hit http://mirror.bm.debian.org squeeze/main amd64 Packages Reading package lists... 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-get', 'update'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DUMP: Reading package lists... Building dependency tree... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpNEy5Xj/tmp/scripts/ 0m2.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts-squeeze to /srv/piuparts.debian.org/tmp/tmpNEy5Xj/tmp/scripts/ 0m2.1s INFO: Running scripts post_setup 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/post_setup_experimental'] 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/post_setup_experimental'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/post_setup_forbid_home'] 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/post_setup_forbid_home'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/post_setup_squeeze-fake-essential'] 0m2.9s DUMP: *** Adding fake essential packages *** Reading package lists... Building dependency tree... Suggested packages: perl-modules The following NEW packages will be installed: adduser ucf 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 320 kB of archives. After this operation, 1532 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ squeeze/main adduser all 3.112+nmu2 [250 kB] Get:2 http://mirror.bm.debian.org/debian/ squeeze/main ucf all 3.0025+nmu1 [69.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 320 kB in 0s (5912 kB/s) Selecting previously deselected package adduser. (Reading database ... 6138 files and directories currently installed.) Unpacking adduser (from .../adduser_3.112+nmu2_all.deb) ... Selecting previously deselected package ucf. Unpacking ucf (from .../ucf_3.0025+nmu1_all.deb) ... Moving old data out of the way Setting up adduser (3.112+nmu2) ... Setting up ucf (3.0025+nmu1) ... 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/post_setup_squeeze-fake-essential'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-get', 'clean'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-get', 'clean'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg', '--get-selections', '*'] 0m3.4s DUMP: adduser install apt install base-files install base-passwd install bash install bsdutils install coreutils install dash install debconf install debconf-i18n install debian-archive-keyring install debianutils install diffutils install dpkg install e2fslibs install e2fsprogs install findutils install gcc-4.4-base install gnupg install gpgv install grep install gzip install hostname install initscripts install insserv install libacl1 install libattr1 install libblkid1 install libbz2-1.0 install libc-bin install libc6 install libcomerr2 install libdb4.8 install libgcc1 install liblocale-gettext-perl install liblzma2 install libncurses5 install libpam-modules install libpam-runtime install libpam0g install libreadline6 install libselinux1 install libsepol1 install libslang2 install libss2 install libstdc++6 install libtext-charwidth-perl install libtext-iconv-perl install libtext-wrapi18n-perl install libusb-0.1-4 install libuuid1 install login install lsb-base install mawk install mount install ncurses-base install ncurses-bin install passwd install perl-base install readline-common install sed install sensible-utils install sysv-rc install sysvinit install sysvinit-utils install tar install tzdata install ucf install util-linux install xz-utils install zlib1g install 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg', '--get-selections', '*'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg-divert', '--list'] 0m3.4s DUMP: diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /bin/sync to /bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg-divert', '--list'] 0m3.4s INFO: apt-cache does not know about any of the requested packages 0m3.4s INFO: Running scripts pre_test 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/pre_test_root_password'] 0m3.4s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/pre_test_root_password'] 0m3.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj'] 0m3.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj'] 0m4.5s DEBUG: No broken symlinks as far as we can find. 0m4.5s INFO: Running scripts pre_install 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/pre_install_database-server'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/pre_install_database-server'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/pre_install_exceptions'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/pre_install_exceptions'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/pre_install_extras'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/pre_install_extras'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-cache', 'show', 'theseus=1.4.3-2'] 0m4.6s DUMP: Package: theseus Priority: optional Section: science Installed-Size: 2176 Maintainer: Debian Med Packaging Team Architecture: amd64 Version: 1.4.3-2 Depends: libc6 (>= 2.7), libgsl0ldbl (>= 1.9), liblapack3gf | liblapack.so.3gf | libatlas3gf-base Suggests: muscle, clustlaw, mafft, t-coffee, kalign, dialign Filename: pool/main/t/theseus/theseus_1.4.3-2_amd64.deb Size: 1349238 MD5sum: 62554e8e0db19d779f91130bca6caf14 SHA1: b927b76d4157c05a6c41de7a980086e056cb1df1 SHA256: 28cb9c5091d7ebcfcac927eb06279a1ea0492d9ac0f63a81786dbb527dd064b2 Description: 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 Tag: biology::peptidic, field::{biology,biology:bioinformatics,biology:structural}, implemented-in::c, interface::commandline, role::program, use::analysing, use::comparing, works-with-format::plaintext 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-cache', 'show', 'theseus=1.4.3-2'] 0m4.6s DEBUG: metapackage: Package: piuparts-depends-dummy Version: 0.invalid.0 Architecture: all Maintainer: piuparts developers team Description: Dummy package to satisfy dependencies - created by piuparts This package was created automatically by piuparts and can safely be removed Depends: libc6 (>= 2.7), libgsl0ldbl (>= 1.9), liblapack3gf | liblapack.so.3gf | libatlas3gf-base 0m4.6s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpxEVYx3/piuparts-depends-dummy'] 0m4.6s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmpxEVYx3/piuparts-depends-dummy.deb'. 0m4.6s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpxEVYx3/piuparts-depends-dummy'] 0m4.6s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmpxEVYx3/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmpNEy5Xj/tmp 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m4.6s DUMP: Selecting previously deselected package piuparts-depends-dummy. (Reading database ... 6261 files and directories currently installed.) Unpacking piuparts-depends-dummy (from tmp/piuparts-depends-dummy.deb) ... dpkg: dependency problems prevent configuration of piuparts-depends-dummy: piuparts-depends-dummy depends on libgsl0ldbl (>= 1.9); however: Package libgsl0ldbl is not installed. piuparts-depends-dummy depends on liblapack3gf | liblapack.so.3gf | libatlas3gf-base; however: Package liblapack3gf is not installed. Package liblapack.so.3gf is not installed. Package libatlas3gf-base is not installed. dpkg: error processing piuparts-depends-dummy (--install): dependency problems - leaving unconfigured Errors were encountered while processing: piuparts-depends-dummy 0m4.6s DEBUG: Command failed (status=1), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-get', '-yf', 'install'] 0m5.8s DUMP: Reading package lists... Building dependency tree... Reading state information... Correcting dependencies... Done The following extra packages will be installed: libblas3gf libgfortran3 libgsl0ldbl liblapack3gf Suggested packages: gsl-ref-psdoc gsl-doc-pdf gsl-doc-info gsl-ref-html The following NEW packages will be installed: libblas3gf libgfortran3 libgsl0ldbl liblapack3gf 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 1 not fully installed or removed. Need to get 5978 kB of archives. After this operation, 13.6 MB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ squeeze/main libgsl0ldbl amd64 1.14+dfsg-1 [1024 kB] Get:2 http://mirror.bm.debian.org/debian/ squeeze/main libgfortran3 amd64 4.4.5-8 [291 kB] Get:3 http://mirror.bm.debian.org/debian/ squeeze/main libblas3gf amd64 1.2-8 [229 kB] Get:4 http://mirror.bm.debian.org/debian/ squeeze/main liblapack3gf amd64 3.2.1-8 [4434 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 5978 kB in 0s (18.5 MB/s) Selecting previously deselected package libgsl0ldbl. (Reading database ... 6261 files and directories currently installed.) Unpacking libgsl0ldbl (from .../libgsl0ldbl_1.14+dfsg-1_amd64.deb) ... Selecting previously deselected package libgfortran3. Unpacking libgfortran3 (from .../libgfortran3_4.4.5-8_amd64.deb) ... Selecting previously deselected package libblas3gf. Unpacking libblas3gf (from .../libblas3gf_1.2-8_amd64.deb) ... Selecting previously deselected package liblapack3gf. Unpacking liblapack3gf (from .../liblapack3gf_3.2.1-8_amd64.deb) ... Setting up libgsl0ldbl (1.14+dfsg-1) ... Setting up libgfortran3 (4.4.5-8) ... Setting up libblas3gf (1.2-8) ... update-alternatives: using /usr/lib/libblas/libblas.so.3gf to provide /usr/lib/libblas.so.3gf (libblas.so.3gf) in auto mode. Setting up liblapack3gf (3.2.1-8) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3gf to provide /usr/lib/liblapack.so.3gf (liblapack.so.3gf) in auto mode. Setting up piuparts-depends-dummy (0.invalid.0) ... 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-get', '-yf', 'install'] 0m5.8s INFO: Installation of ['tmp/piuparts-depends-dummy.deb'] ok 0m5.8s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmpNEy5Xj/tmp/piuparts-depends-dummy.deb 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m5.8s DUMP: piuparts-depends-dummy install ok installed 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m5.9s DUMP: (Reading database ... 6298 files and directories currently installed.) Removing piuparts-depends-dummy ... 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-get', 'clean'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-get', 'clean'] 0m6.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj'] 0m6.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj'] 0m7.4s DEBUG: No broken symlinks as far as we can find. 0m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-cache', 'policy'] 0m7.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror.bm.debian.org/debian/ squeeze/main amd64 Packages release v=6.0.10,o=Debian,a=oldstable,n=squeeze,l=Debian,c=main origin mirror.bm.debian.org Pinned packages: 0m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-cache', 'policy'] 0m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-cache', 'policy', 'theseus'] 0m7.5s DUMP: theseus: Installed: (none) Candidate: 1.4.3-2 Version table: 1.4.3-2 0 500 http://mirror.bm.debian.org/debian/ squeeze/main amd64 Packages 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-cache', 'policy', 'theseus'] 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-get', '-y', 'install', 'theseus=1.4.3-2'] 0m8.1s DUMP: Reading package lists... Building dependency tree... Reading state information... Suggested packages: muscle clustlaw mafft t-coffee kalign dialign The following NEW packages will be installed: theseus 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 1349 kB of archives. After this operation, 2228 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ squeeze/main theseus amd64 1.4.3-2 [1349 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1349 kB in 0s (15.4 MB/s) Selecting previously deselected package theseus. (Reading database ... 6298 files and directories currently installed.) Unpacking theseus (from .../theseus_1.4.3-2_amd64.deb) ... Setting up theseus (1.4.3-2) ... 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-get', '-y', 'install', 'theseus=1.4.3-2'] 0m8.1s INFO: Running scripts post_install 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/post_install_exceptions'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/post_install_exceptions'] 0m8.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj'] 0m8.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj'] 0m9.2s DEBUG: No broken symlinks as far as we can find. 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg', '--get-selections', '*'] 0m9.2s DUMP: adduser install apt install base-files install base-passwd install bash install bsdutils install coreutils install dash install debconf install debconf-i18n install debian-archive-keyring install debianutils install diffutils install dpkg install e2fslibs install e2fsprogs install findutils install gcc-4.4-base install gnupg install gpgv install grep install gzip install hostname install initscripts install insserv install libacl1 install libattr1 install libblas3gf install libblkid1 install libbz2-1.0 install libc-bin install libc6 install libcomerr2 install libdb4.8 install libgcc1 install libgfortran3 install libgsl0ldbl install liblapack3gf install liblocale-gettext-perl install liblzma2 install libncurses5 install libpam-modules install libpam-runtime install libpam0g install libreadline6 install libselinux1 install libsepol1 install libslang2 install libss2 install libstdc++6 install libtext-charwidth-perl install libtext-iconv-perl install libtext-wrapi18n-perl install libusb-0.1-4 install libuuid1 install login install lsb-base install mawk install mount install ncurses-base install ncurses-bin install passwd install perl-base install readline-common install sed install sensible-utils install sysv-rc install sysvinit install sysvinit-utils install tar install theseus install tzdata install ucf install util-linux install xz-utils install zlib1g install 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg', '--get-selections', '*'] 0m9.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', '-ac'] 0m10.5s DUMP: debsums: no md5sums for mawk 0m10.5s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', '-ac'] 0m10.5s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m10.5s DUMP: 0.12~bpo70+1 0m10.5s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m10.5s INFO: Running adequate version 0.12~bpo70+1 now. 0m10.5s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'theseus'] 0m10.7s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'theseus'] 0m10.7s INFO: Running scripts pre_remove 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/pre_remove_exceptions'] 0m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/pre_remove_exceptions'] 0m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-get', 'remove', 'liblapack3gf', 'libgsl0ldbl', 'libgfortran3', 'libblas3gf', 'theseus'] 0m11.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libblas3gf libgfortran3 libgsl0ldbl liblapack3gf theseus 0 upgraded, 0 newly installed, 5 to remove and 0 not upgraded. After this operation, 15.8 MB disk space will be freed. (Reading database ... 6333 files and directories currently installed.) Removing theseus ... Removing liblapack3gf ... Removing libblas3gf ... Removing libgfortran3 ... Removing libgsl0ldbl ... 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-get', 'remove', 'liblapack3gf', 'libgsl0ldbl', 'libgfortran3', 'libblas3gf', 'theseus'] 0m11.7s INFO: Running scripts post_remove 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/post_remove_exceptions_lenny'] 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/post_remove_exceptions_lenny'] 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/post_remove_extras'] 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/post_remove_extras'] 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg', '--purge', 'liblapack3gf', 'libgsl0ldbl', 'libgfortran3', 'libblas3gf'] 0m11.8s DUMP: (Reading database ... 6261 files and directories currently installed.) Removing liblapack3gf ... Purging configuration files for liblapack3gf ... Removing libgsl0ldbl ... Purging configuration files for libgsl0ldbl ... Removing libgfortran3 ... Purging configuration files for libgfortran3 ... Removing libblas3gf ... Purging configuration files for libblas3gf ... 0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg', '--purge', 'liblapack3gf', 'libgsl0ldbl', 'libgfortran3', 'libblas3gf'] 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg', '--purge', 'theseus'] 0m11.8s DUMP: dpkg: warning: ignoring request to remove theseus which isn't installed. 0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg', '--purge', 'theseus'] 0m11.8s INFO: Running scripts post_purge 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/post_purge_exceptions'] 0m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'tmp/scripts/post_purge_exceptions'] 0m11.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg', '--purge', '--pending'] 0m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg', '--purge', '--pending'] 0m11.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg', '--remove', '--pending'] 0m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg', '--remove', '--pending'] 0m11.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj'] 0m12.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj'] 0m12.9s ERROR: WARN: Broken symlinks: /etc/alternatives/liblapack.so.3gf -> /usr/lib/lapack/liblapack.so.3gf 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg-divert', '--list'] 0m13.0s DUMP: diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /bin/sync to /bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'dpkg-divert', '--list'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-get', 'clean'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'apt-get', 'clean'] 0m13.9s INFO: Warning: Package purging left files on system: /etc/alternatives/liblapack.so.3gf -> /usr/lib/lapack/liblapack.so.3gf not owned These files seem to have been left by dependencies rather than by packages being explicitly tested. 0m13.9s INFO: PASS: Installation and purging test. 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'umount', '/proc'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj', 'umount', '/proc'] 0m14.2s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj'] 0m14.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpNEy5Xj'] 0m14.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpNEy5Xj 0m14.3s INFO: PASS: All tests. 0m14.3s INFO: piuparts run ends. ret=0 End: 2014-10-28 09:10:36 UTC