Start: 2014-02-24 03:19:56 UTC Package: apbs Priority: optional Section: science Installed-Size: 900 Maintainer: Debichem Team Architecture: amd64 Version: 1.2.1b-1 Depends: libblas3gf | libblas.so.3gf | libatlas3gf-base, libc6 (>= 2.7), libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.3), libmaloc1 (>= 0.2-1), libopenmpi1.3 Filename: pool/main/a/apbs/apbs_1.2.1b-1_amd64.deb Size: 338166 MD5sum: c80d7abc62e1886a2535b92c859507df SHA1: 8ac999f9394c099d4a0a820eae804712541e09d4 SHA256: 78ade03a9e743aedc69a65bd55aa46e786d0af2e3d68a414c1a60c1ced00a88f Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including: . * simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, * implicit solvent molecular dynamics of biomolecules , * solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, * and biomolecular titration studies. . APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms. Homepage: http://apbs.sourceforge.net Tag: field::chemistry, implemented-in::c, interface::commandline, role::program, scope::utility 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 apbs=1.2.1b-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at http://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 0.57.1~201402172317~0.57-12-g4a108e2 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 apbs=1.2.1b-1 0m0.0s INFO: Running on: Linux piu-slave-bm-a 3.2.0-4-amd64 #1 SMP Debian 3.2.54-2 x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp0nqrAp 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp0nqrAp 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz'] 0m1.7s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz'] 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'mount', '-t', 'proc', 'proc', '/proc'] 0m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'mount', '-t', 'proc', 'proc', '/proc'] 0m1.7s DEBUG: sources.list: deb http://mirror.bm.debian.org/debian/ squeeze main 0m1.8s DEBUG: Created policy-rc.d and chmodded it. 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-get', 'update'] 0m3.6s DUMP: Get:1 http://mirror.bm.debian.org squeeze Release.gpg [1672 B] Ign http://mirror.bm.debian.org/debian/ squeeze/main Translation-en Get:2 http://mirror.bm.debian.org squeeze Release [96.0 kB] Get:3 http://mirror.bm.debian.org squeeze/main amd64 Packages [8388 kB] Fetched 8486 kB in 1s (7979 kB/s) Reading package lists... 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-get', 'update'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-get', '-yf', 'dist-upgrade'] 0m4.7s DUMP: Reading package lists... Building dependency tree... The following packages will be upgraded: base-files gnupg gpgv tzdata 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3067 kB of archives. After this operation, 52.2 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ squeeze/main base-files amd64 6.0squeeze9 [76.1 kB] Get:2 http://mirror.bm.debian.org/debian/ squeeze/main gpgv amd64 1.4.10-4+squeeze4 [222 kB] Get:3 http://mirror.bm.debian.org/debian/ squeeze/main gnupg amd64 1.4.10-4+squeeze4 [2148 kB] Get:4 http://mirror.bm.debian.org/debian/ squeeze/main tzdata all 2013i-0squeeze1 [621 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3067 kB in 0s (15.8 MB/s) (Reading database ... 6155 files and directories currently installed.) Preparing to replace base-files 6.0squeeze8 (using .../base-files_6.0squeeze9_amd64.deb) ... Unpacking replacement base-files ... Setting up base-files (6.0squeeze9) ... Installing new version of config file /etc/debian_version ... (Reading database ... 6155 files and directories currently installed.) Preparing to replace gpgv 1.4.10-4+squeeze3 (using .../gpgv_1.4.10-4+squeeze4_amd64.deb) ... Unpacking replacement gpgv ... Setting up gpgv (1.4.10-4+squeeze4) ... (Reading database ... 6155 files and directories currently installed.) Preparing to replace gnupg 1.4.10-4+squeeze3 (using .../gnupg_1.4.10-4+squeeze4_amd64.deb) ... Unpacking replacement gnupg ... Setting up gnupg (1.4.10-4+squeeze4) ... (Reading database ... 6155 files and directories currently installed.) Preparing to replace tzdata 2013d-0squeeze1 (using .../tzdata_2013i-0squeeze1_all.deb) ... Unpacking replacement tzdata ... Setting up tzdata (2013i-0squeeze1) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Feb 24 03:20:01 UTC 2014. Universal Time is now: Mon Feb 24 03:20:01 UTC 2014. Run 'dpkg-reconfigure tzdata' if you wish to change it. 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-get', '-yf', 'dist-upgrade'] 0m4.7s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp0nqrAp/tmp/scripts/ 0m4.7s DEBUG: Copying scriptsdir /etc/piuparts/scripts-squeeze to /srv/piuparts.debian.org/tmp/tmp0nqrAp/tmp/scripts/ 0m4.7s INFO: Running scripts post_setup 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/post_setup_experimental'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/post_setup_experimental'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/post_setup_forbid_home'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/post_setup_forbid_home'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.7s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' `/bin/sync' -> `true' 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/post_setup_squeeze-fake-essential'] 0m6.0s DUMP: *** Adding fake essential packages *** Reading package lists... Building dependency tree... Reading state information... 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 (3645 kB/s) Selecting previously deselected package adduser. (Reading database ... 6135 files and directories currently installed.) Unpacking adduser (from .../adduser_3.112+nmu2_all.deb) ... Selecting previously deselected package ucf. Unpacking ucf (from .../ucf_3.0025+nmu1_all.deb) ... Moving old data out of the way Setting up adduser (3.112+nmu2) ... Setting up ucf (3.0025+nmu1) ... 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/post_setup_squeeze-fake-essential'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-get', 'clean'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-get', 'clean'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg', '--get-selections', '*'] 0m6.6s 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 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg', '--get-selections', '*'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg-divert', '--list'] 0m6.6s DUMP: diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /bin/sync to /bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg-divert', '--list'] 0m6.6s INFO: apt-cache does not know about any of the requested packages 0m6.6s INFO: Running scripts pre_test 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/pre_test_root_password'] 0m6.6s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/pre_test_root_password'] 0m6.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp0nqrAp'] 0m6.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp0nqrAp'] 0m7.6s DEBUG: No broken symlinks as far as we can find. 0m7.6s INFO: Running scripts pre_install 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/pre_install_database-server'] 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/pre_install_database-server'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/pre_install_exceptions'] 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/pre_install_exceptions'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/pre_install_extras'] 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/pre_install_extras'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-cache', 'show', 'apbs=1.2.1b-1'] 0m7.7s DUMP: Package: apbs Priority: optional Section: science Installed-Size: 900 Maintainer: Debichem Team Architecture: amd64 Version: 1.2.1b-1 Depends: libblas3gf | libblas.so.3gf | libatlas3gf-base, libc6 (>= 2.7), libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.3), libmaloc1 (>= 0.2-1), libopenmpi1.3 Filename: pool/main/a/apbs/apbs_1.2.1b-1_amd64.deb Size: 338166 MD5sum: c80d7abc62e1886a2535b92c859507df SHA1: 8ac999f9394c099d4a0a820eae804712541e09d4 SHA256: 78ade03a9e743aedc69a65bd55aa46e786d0af2e3d68a414c1a60c1ced00a88f Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including: . * simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, * implicit solvent molecular dynamics of biomolecules , * solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, * and biomolecular titration studies. . APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms. Homepage: http://apbs.sourceforge.net Tag: field::chemistry, implemented-in::c, interface::commandline, role::program, scope::utility 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-cache', 'show', 'apbs=1.2.1b-1'] 0m7.7s 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: libblas3gf | libblas.so.3gf | libatlas3gf-base, libc6 (>= 2.7), libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.3), libmaloc1 (>= 0.2-1), libopenmpi1.3 0m7.7s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpyjGJiG/piuparts-depends-dummy'] 0m7.7s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmpyjGJiG/piuparts-depends-dummy.deb'. 0m7.7s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpyjGJiG/piuparts-depends-dummy'] 0m7.7s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmpyjGJiG/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmp0nqrAp/tmp 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m7.7s DUMP: Selecting previously deselected package piuparts-depends-dummy. (Reading database ... 6258 files and directories currently installed.) Unpacking piuparts-depends-dummy (from tmp/piuparts-depends-dummy.deb) ... dpkg: dependency problems prevent configuration of piuparts-depends-dummy: piuparts-depends-dummy depends on libblas3gf | libblas.so.3gf | libatlas3gf-base; however: Package libblas3gf is not installed. Package libblas.so.3gf is not installed. Package libatlas3gf-base is not installed. piuparts-depends-dummy depends on libgfortran3 (>= 4.3); however: Package libgfortran3 is not installed. piuparts-depends-dummy depends on libmaloc1 (>= 0.2-1); however: Package libmaloc1 is not installed. piuparts-depends-dummy depends on libopenmpi1.3; however: Package libopenmpi1.3 is not installed. dpkg: error processing piuparts-depends-dummy (--install): dependency problems - leaving unconfigured Errors were encountered while processing: piuparts-depends-dummy 0m7.7s DEBUG: Command failed (status=1), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-get', '-yf', 'install'] 0m9.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Correcting dependencies... Done The following extra packages will be installed: libblas3gf libgfortran3 libibverbs1 libmaloc1 libnuma1 libopenmpi1.3 libtorque2 The following NEW packages will be installed: libblas3gf libgfortran3 libibverbs1 libmaloc1 libnuma1 libopenmpi1.3 libtorque2 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 1 not fully installed or removed. Need to get 2156 kB of archives. After this operation, 6394 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ squeeze/main libgfortran3 amd64 4.4.5-8 [291 kB] Get:2 http://mirror.bm.debian.org/debian/ squeeze/main libblas3gf amd64 1.2-8 [229 kB] Get:3 http://mirror.bm.debian.org/debian/ squeeze/main libmaloc1 amd64 0.2-2.1 [60.5 kB] Get:4 http://mirror.bm.debian.org/debian/ squeeze/main libibverbs1 amd64 1.1.3-2 [33.7 kB] Get:5 http://mirror.bm.debian.org/debian/ squeeze/main libnuma1 amd64 2.0.5-1 [26.7 kB] Get:6 http://mirror.bm.debian.org/debian/ squeeze/main libtorque2 amd64 2.4.8+dfsg-9squeeze3 [115 kB] Get:7 http://mirror.bm.debian.org/debian/ squeeze/main libopenmpi1.3 amd64 1.4.2-4 [1400 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 2156 kB in 0s (4039 kB/s) Selecting previously deselected package libgfortran3. (Reading database ... 6258 files and directories currently installed.) 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 libmaloc1. Unpacking libmaloc1 (from .../libmaloc1_0.2-2.1_amd64.deb) ... Selecting previously deselected package libibverbs1. Unpacking libibverbs1 (from .../libibverbs1_1.1.3-2_amd64.deb) ... Selecting previously deselected package libnuma1. Unpacking libnuma1 (from .../libnuma1_2.0.5-1_amd64.deb) ... Selecting previously deselected package libtorque2. Unpacking libtorque2 (from .../libtorque2_2.4.8+dfsg-9squeeze3_amd64.deb) ... Selecting previously deselected package libopenmpi1.3. Unpacking libopenmpi1.3 (from .../libopenmpi1.3_1.4.2-4_amd64.deb) ... 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 libmaloc1 (0.2-2.1) ... Setting up libibverbs1 (1.1.3-2) ... Setting up libnuma1 (2.0.5-1) ... Setting up libtorque2 (2.4.8+dfsg-9squeeze3) ... Setting up libopenmpi1.3 (1.4.2-4) ... Setting up piuparts-depends-dummy (0.invalid.0) ... 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-get', '-yf', 'install'] 0m9.6s INFO: Installation of ['tmp/piuparts-depends-dummy.deb'] ok 0m9.6s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmp0nqrAp/tmp/piuparts-depends-dummy.deb 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m9.6s DUMP: piuparts-depends-dummy install ok installed 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m9.6s DUMP: (Reading database ... 6398 files and directories currently installed.) Removing piuparts-depends-dummy ... 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-get', 'clean'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-get', 'clean'] 0m10.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp0nqrAp'] 0m10.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp0nqrAp'] 0m11.2s DEBUG: No broken symlinks as far as we can find. 0m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-cache', 'policy'] 0m11.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror.bm.debian.org/debian/ squeeze/main amd64 Packages release v=6.0.9,o=Debian,a=oldstable,n=squeeze,l=Debian,c=main origin mirror.bm.debian.org Pinned packages: 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-cache', 'policy'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-cache', 'policy', 'apbs'] 0m11.3s DUMP: apbs: Installed: (none) Candidate: 1.2.1b-1 Version table: 1.2.1b-1 0 500 http://mirror.bm.debian.org/debian/ squeeze/main amd64 Packages 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-cache', 'policy', 'apbs'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-get', '-y', 'install', 'apbs=1.2.1b-1'] 0m11.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: apbs 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 338 kB of archives. After this operation, 922 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ squeeze/main apbs amd64 1.2.1b-1 [338 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 338 kB in 0s (2778 kB/s) Selecting previously deselected package apbs. (Reading database ... 6398 files and directories currently installed.) Unpacking apbs (from .../apbs_1.2.1b-1_amd64.deb) ... Setting up apbs (1.2.1b-1) ... 0m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-get', '-y', 'install', 'apbs=1.2.1b-1'] 0m11.9s INFO: Running scripts post_install 0m11.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp0nqrAp'] 0m12.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp0nqrAp'] 0m12.9s DEBUG: No broken symlinks as far as we can find. 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg', '--get-selections', '*'] 0m13.0s DUMP: adduser install apbs 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 libibverbs1 install liblocale-gettext-perl install liblzma2 install libmaloc1 install libncurses5 install libnuma1 install libopenmpi1.3 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 libtorque2 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 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg', '--get-selections', '*'] 0m13.5s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', '-ac'] 0m14.1s DUMP: debsums: no md5sums for mawk 0m14.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', '-ac'] 0m14.1s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m14.1s DUMP: 0.11.3~bpo70+1 0m14.1s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m14.1s INFO: Running adequate version 0.11.3~bpo70+1 now. 0m14.1s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apbs'] 0m14.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apbs'] 0m14.2s INFO: Running scripts pre_remove 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/pre_remove_exceptions'] 0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/pre_remove_exceptions'] 0m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-get', 'remove', 'libblas3gf', 'libopenmpi1.3', 'libibverbs1', 'libgfortran3', 'libnuma1', 'libtorque2', 'libmaloc1', 'apbs'] 0m15.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: apbs libblas3gf libgfortran3 libibverbs1 libmaloc1 libnuma1 libopenmpi1.3 libtorque2 0 upgraded, 0 newly installed, 8 to remove and 0 not upgraded. After this operation, 7315 kB disk space will be freed. (Reading database ... 6407 files and directories currently installed.) Removing apbs ... Removing libblas3gf ... Removing libopenmpi1.3 ... Removing libgfortran3 ... Removing libibverbs1 ... Removing libmaloc1 ... Removing libnuma1 ... Removing libtorque2 ... 0m15.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-get', 'remove', 'libblas3gf', 'libopenmpi1.3', 'libibverbs1', 'libgfortran3', 'libnuma1', 'libtorque2', 'libmaloc1', 'apbs'] 0m15.0s INFO: Running scripts post_remove 0m15.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/post_remove_exceptions_lenny'] 0m15.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/post_remove_exceptions_lenny'] 0m15.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/post_remove_extras'] 0m15.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/post_remove_extras'] 0m15.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg', '--purge', 'libblas3gf', 'libopenmpi1.3', 'libibverbs1', 'libgfortran3', 'libnuma1', 'libtorque2', 'libmaloc1'] 0m15.0s DUMP: (Reading database ... 6258 files and directories currently installed.) Removing libblas3gf ... Purging configuration files for libblas3gf ... Removing libopenmpi1.3 ... Purging configuration files for libopenmpi1.3 ... Removing libibverbs1 ... Purging configuration files for libibverbs1 ... Removing libgfortran3 ... Purging configuration files for libgfortran3 ... Removing libnuma1 ... Purging configuration files for libnuma1 ... Removing libtorque2 ... Purging configuration files for libtorque2 ... Removing libmaloc1 ... Purging configuration files for libmaloc1 ... 0m15.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg', '--purge', 'libblas3gf', 'libopenmpi1.3', 'libibverbs1', 'libgfortran3', 'libnuma1', 'libtorque2', 'libmaloc1'] 0m15.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg', '--purge', 'apbs'] 0m15.0s DUMP: dpkg: warning: ignoring request to remove apbs which isn't installed. 0m15.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg', '--purge', 'apbs'] 0m15.0s INFO: Running scripts post_purge 0m15.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/post_purge_exceptions'] 0m15.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'tmp/scripts/post_purge_exceptions'] 0m15.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg', '--purge', '--pending'] 0m15.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg', '--purge', '--pending'] 0m15.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg', '--remove', '--pending'] 0m15.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg', '--remove', '--pending'] 0m15.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp0nqrAp'] 0m15.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp0nqrAp'] 0m16.1s DEBUG: No broken symlinks as far as we can find. 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg-divert', '--list'] 0m16.1s 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 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'dpkg-divert', '--list'] 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-get', 'clean'] 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'apt-get', 'clean'] 0m17.1s INFO: PASS: Installation and purging test. 0m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'umount', '/proc'] 0m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp0nqrAp', 'umount', '/proc'] 0m17.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp0nqrAp'] 0m17.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp0nqrAp'] 0m17.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp0nqrAp 0m17.4s INFO: PASS: All tests. 0m17.4s INFO: piuparts run ends. ret=0 End: 2014-02-24 03:20:14 UTC