Start: 2014-03-03 17:35:11 UTC Package: gromacs Priority: extra Section: science Installed-Size: 15844 Maintainer: Debichem Team Architecture: amd64 Version: 4.0.7-3 Depends: gromacs-data (= 4.0.7-3), libc6 (>= 2.7), libfftw3-3, libgsl0ldbl (>= 1.9), libice6 (>= 1:1.0.0), libsm6, libx11-6 (>= 0) Recommends: cpp Conflicts: radiance (<= 3R8+20070924.dfsg-1) Filename: pool/main/g/gromacs/gromacs_4.0.7-3_amd64.deb Size: 4539814 MD5sum: e7cae0743a4323efd007c9aa4d08c3a3 SHA1: 769969e42937ac91d84443e99fb0e7c9043965c0 SHA256: 21be5ab3ac9060f4b0d306c8dad4267f8cda0a86827c6d9c91ef8d7e9fb59989 Description: Molecular dynamics simulator, with building and analysis tools GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. . It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non- biological systems, e.g. polymers. . GROMACS offers entirely too many features for a brief description to do it justice. A more complete listing is available at . Homepage: http://www.gromacs.org/ Tag: field::{biology,biology:structural,chemistry}, implemented-in::c, interface::commandline, interface::x11, role::program, uitoolkit::xlib, x11::application 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 gromacs=4.0.7-3 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 0.57.1~201403012113~0.57-23-gfd8571c 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 gromacs=4.0.7-3 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/tmpxbrv_k 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpxbrv_k 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz'] 0m1.8s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'mount', '-t', 'proc', 'proc', '/proc'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'mount', '-t', 'proc', 'proc', '/proc'] 0m1.8s 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/tmpxbrv_k', '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 0s (9039 kB/s) Reading package lists... 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'apt-get', 'update'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'apt-get', '-yf', 'dist-upgrade'] 0m4.8s 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 (49.2 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 Mar 3 17:35:16 UTC 2014. Universal Time is now: Mon Mar 3 17:35:16 UTC 2014. Run 'dpkg-reconfigure tzdata' if you wish to change it. 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'apt-get', '-yf', 'dist-upgrade'] 0m4.8s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpxbrv_k/tmp/scripts/ 0m4.8s DEBUG: Copying scriptsdir /etc/piuparts/scripts-squeeze to /srv/piuparts.debian.org/tmp/tmpxbrv_k/tmp/scripts/ 0m4.8s INFO: Running scripts post_setup 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/post_setup_experimental'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/post_setup_experimental'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/post_setup_forbid_home'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/post_setup_forbid_home'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.8s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' `/bin/sync' -> `true' 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/post_setup_squeeze-fake-essential'] 0m5.6s 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 (12.2 MB/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) ... 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/post_setup_squeeze-fake-essential'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'apt-get', 'clean'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'apt-get', 'clean'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg', '--get-selections', '*'] 0m6.2s 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 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 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg', '--get-selections', '*'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg-divert', '--list'] 0m6.2s DUMP: diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /bin/sync to /bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg-divert', '--list'] 0m6.2s INFO: apt-cache does not know about any of the requested packages 0m6.2s INFO: Running scripts pre_test 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/pre_test_root_password'] 0m6.2s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/pre_test_root_password'] 0m6.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxbrv_k'] 0m6.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxbrv_k'] 0m7.3s DEBUG: No broken symlinks as far as we can find. 0m7.3s INFO: Running scripts pre_install 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/pre_install_database-server'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/pre_install_database-server'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/pre_install_exceptions'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/pre_install_exceptions'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/pre_install_extras'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/pre_install_extras'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'apt-cache', 'show', 'gromacs=4.0.7-3'] 0m7.4s DUMP: Package: gromacs Priority: extra Section: science Installed-Size: 15844 Maintainer: Debichem Team Architecture: amd64 Version: 4.0.7-3 Depends: gromacs-data (= 4.0.7-3), libc6 (>= 2.7), libfftw3-3, libgsl0ldbl (>= 1.9), libice6 (>= 1:1.0.0), libsm6, libx11-6 (>= 0) Recommends: cpp Conflicts: radiance (<= 3R8+20070924.dfsg-1) Filename: pool/main/g/gromacs/gromacs_4.0.7-3_amd64.deb Size: 4539814 MD5sum: e7cae0743a4323efd007c9aa4d08c3a3 SHA1: 769969e42937ac91d84443e99fb0e7c9043965c0 SHA256: 21be5ab3ac9060f4b0d306c8dad4267f8cda0a86827c6d9c91ef8d7e9fb59989 Description: Molecular dynamics simulator, with building and analysis tools GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. . It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non- biological systems, e.g. polymers. . GROMACS offers entirely too many features for a brief description to do it justice. A more complete listing is available at . Homepage: http://www.gromacs.org/ Tag: field::{biology,biology:structural,chemistry}, implemented-in::c, interface::commandline, interface::x11, role::program, uitoolkit::xlib, x11::application 0m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'apt-cache', 'show', 'gromacs=4.0.7-3'] 0m7.4s 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: gromacs-data (= 4.0.7-3), libc6 (>= 2.7), libfftw3-3, libgsl0ldbl (>= 1.9), libice6 (>= 1:1.0.0), libsm6, libx11-6 (>= 0) Conflicts: radiance (<= 3R8+20070924.dfsg-1) 0m7.4s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpxFqN9H/piuparts-depends-dummy'] 0m7.4s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmpxFqN9H/piuparts-depends-dummy.deb'. 0m7.4s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpxFqN9H/piuparts-depends-dummy'] 0m7.4s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmpxFqN9H/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmpxbrv_k/tmp 0m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m7.4s 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 gromacs-data (= 4.0.7-3); however: Package gromacs-data is not installed. piuparts-depends-dummy depends on libfftw3-3; however: Package libfftw3-3 is not installed. piuparts-depends-dummy depends on libgsl0ldbl (>= 1.9); however: Package libgsl0ldbl is not installed. piuparts-depends-dummy depends on libice6 (>= 1:1.0.0); however: Package libice6 is not installed. piuparts-depends-dummy depends on libsm6; however: Package libsm6 is not installed. piuparts-depends-dummy depends on libx11-6 (>= 0); however: Package libx11-6 is not installed. dpkg: error processing piuparts-depends-dummy (--install): dependency problems - leaving unconfigured Errors were encountered while processing: piuparts-depends-dummy 0m7.4s DEBUG: Command failed (status=1), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'apt-get', '-yf', 'install'] 0m9.4s DUMP: Reading package lists... Building dependency tree... Reading state information... Correcting dependencies... Done The following extra packages will be installed: gromacs-data libfftw3-3 libgsl0ldbl libice6 libsm6 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 x11-common Suggested packages: tcsh c-shell libfftw3-dev gsl-ref-psdoc gsl-doc-pdf gsl-doc-info gsl-ref-html Recommended packages: gromacs The following NEW packages will be installed: gromacs-data libfftw3-3 libgsl0ldbl libice6 libsm6 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 x11-common 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 1 not fully installed or removed. Need to get 5458 kB of archives. After this operation, 18.3 MB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ squeeze/main gromacs-data all 4.0.7-3 [1565 kB] Get:2 http://mirror.bm.debian.org/debian/ squeeze/main libfftw3-3 amd64 3.2.2-1 [1399 kB] Get:3 http://mirror.bm.debian.org/debian/ squeeze/main libgsl0ldbl amd64 1.14+dfsg-1 [1024 kB] Get:4 http://mirror.bm.debian.org/debian/ squeeze/main x11-common all 1:7.5+8+squeeze1 [279 kB] Get:5 http://mirror.bm.debian.org/debian/ squeeze/main libice6 amd64 2:1.0.6-2 [53.8 kB] Get:6 http://mirror.bm.debian.org/debian/ squeeze/main libsm6 amd64 2:1.1.1-1 [25.0 kB] Get:7 http://mirror.bm.debian.org/debian/ squeeze/main libxau6 amd64 1:1.0.6-1 [16.8 kB] Get:8 http://mirror.bm.debian.org/debian/ squeeze/main libxdmcp6 amd64 1:1.0.3-2 [19.3 kB] Get:9 http://mirror.bm.debian.org/debian/ squeeze/main libxcb1 amd64 1.6-1+squeeze1 [44.3 kB] Get:10 http://mirror.bm.debian.org/debian/ squeeze/main libx11-data all 2:1.3.3-4+squeeze1 [184 kB] Get:11 http://mirror.bm.debian.org/debian/ squeeze/main libx11-6 amd64 2:1.3.3-4+squeeze1 [847 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 5458 kB in 0s (9837 kB/s) Selecting previously deselected package gromacs-data. (Reading database ... 6258 files and directories currently installed.) Unpacking gromacs-data (from .../gromacs-data_4.0.7-3_all.deb) ... Selecting previously deselected package libfftw3-3. Unpacking libfftw3-3 (from .../libfftw3-3_3.2.2-1_amd64.deb) ... Selecting previously deselected package libgsl0ldbl. Unpacking libgsl0ldbl (from .../libgsl0ldbl_1.14+dfsg-1_amd64.deb) ... Selecting previously deselected package x11-common. Unpacking x11-common (from .../x11-common_1%3a7.5+8+squeeze1_all.deb) ... Selecting previously deselected package libice6. Unpacking libice6 (from .../libice6_2%3a1.0.6-2_amd64.deb) ... Selecting previously deselected package libsm6. Unpacking libsm6 (from .../libsm6_2%3a1.1.1-1_amd64.deb) ... Selecting previously deselected package libxau6. Unpacking libxau6 (from .../libxau6_1%3a1.0.6-1_amd64.deb) ... Selecting previously deselected package libxdmcp6. Unpacking libxdmcp6 (from .../libxdmcp6_1%3a1.0.3-2_amd64.deb) ... Selecting previously deselected package libxcb1. Unpacking libxcb1 (from .../libxcb1_1.6-1+squeeze1_amd64.deb) ... Selecting previously deselected package libx11-data. Unpacking libx11-data (from .../libx11-data_2%3a1.3.3-4+squeeze1_all.deb) ... Selecting previously deselected package libx11-6. Unpacking libx11-6 (from .../libx11-6_2%3a1.3.3-4+squeeze1_amd64.deb) ... Setting up gromacs-data (4.0.7-3) ... Setting up libfftw3-3 (3.2.2-1) ... Setting up libgsl0ldbl (1.14+dfsg-1) ... Setting up x11-common (1:7.5+8+squeeze1) ... invoke-rc.d: policy-rc.d denied execution of start. Setting up libice6 (2:1.0.6-2) ... Setting up libsm6 (2:1.1.1-1) ... Setting up libxau6 (1:1.0.6-1) ... Setting up libxdmcp6 (1:1.0.3-2) ... Setting up libxcb1 (1.6-1+squeeze1) ... Setting up libx11-data (2:1.3.3-4+squeeze1) ... Setting up libx11-6 (2:1.3.3-4+squeeze1) ... Setting up piuparts-depends-dummy (0.invalid.0) ... 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'apt-get', '-yf', 'install'] 0m9.4s INFO: Installation of ['tmp/piuparts-depends-dummy.deb'] ok 0m9.4s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmpxbrv_k/tmp/piuparts-depends-dummy.deb 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m9.4s DUMP: piuparts-depends-dummy install ok installed 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m9.4s DUMP: (Reading database ... 7167 files and directories currently installed.) Removing piuparts-depends-dummy ... 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'apt-get', 'clean'] 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'apt-get', 'clean'] 0m10.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxbrv_k'] 0m10.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxbrv_k'] 0m11.1s DEBUG: No broken symlinks as far as we can find. 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'apt-cache', 'policy'] 0m11.2s 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: 0m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'apt-cache', 'policy'] 0m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'apt-cache', 'policy', 'gromacs'] 0m11.2s DUMP: gromacs: Installed: (none) Candidate: 4.0.7-3 Version table: 4.0.7-3 0 500 http://mirror.bm.debian.org/debian/ squeeze/main amd64 Packages 0m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'apt-cache', 'policy', 'gromacs'] 0m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'apt-get', '-y', 'install', 'gromacs=4.0.7-3'] 0m12.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Recommended packages: cpp The following NEW packages will be installed: gromacs 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 4540 kB of archives. After this operation, 16.2 MB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ squeeze/main gromacs amd64 4.0.7-3 [4540 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 4540 kB in 0s (13.4 MB/s) Selecting previously deselected package gromacs. (Reading database ... 7167 files and directories currently installed.) Unpacking gromacs (from .../gromacs_4.0.7-3_amd64.deb) ... Setting up gromacs (4.0.7-3) ... 0m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'apt-get', '-y', 'install', 'gromacs=4.0.7-3'] 0m12.2s INFO: Running scripts post_install 0m12.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxbrv_k'] 0m12.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxbrv_k'] 0m13.4s DEBUG: No broken symlinks as far as we can find. 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg', '--get-selections', '*'] 0m13.5s 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 gromacs install gromacs-data 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 libfftw3-3 install libgcc1 install libgsl0ldbl install libice6 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 libsm6 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 libx11-6 install libx11-data install libxau6 install libxcb1 install libxdmcp6 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 x11-common install xz-utils install zlib1g install 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg', '--get-selections', '*'] 0m14.1s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', '-ac'] 0m14.8s DUMP: debsums: no md5sums for mawk 0m14.8s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', '-ac'] 0m14.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m14.8s DUMP: 0.11.3~bpo70+1 0m14.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m14.8s INFO: Running adequate version 0.11.3~bpo70+1 now. 0m14.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'gromacs'] 0m16.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'gromacs'] 0m16.2s INFO: Running scripts pre_remove 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m16.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m16.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/pre_remove_exceptions'] 0m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/pre_remove_exceptions'] 0m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'apt-get', 'remove', 'libx11-6', 'libx11-data', 'libsm6', 'libxcb1', 'x11-common', 'libice6', 'gromacs-data', 'libxau6', 'libfftw3-3', 'libgsl0ldbl', 'libxdmcp6', 'gromacs'] 0m17.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: gromacs gromacs-data libfftw3-3 libgsl0ldbl libice6 libsm6 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 x11-common 0 upgraded, 0 newly installed, 12 to remove and 0 not upgraded. After this operation, 34.5 MB disk space will be freed. (Reading database ... 7363 files and directories currently installed.) Removing gromacs ... Removing gromacs-data ... Removing libfftw3-3 ... Removing libgsl0ldbl ... Removing libsm6 ... Removing libice6 ... Removing libx11-6 ... Removing libx11-data ... Removing libxcb1 ... Removing libxau6 ... Removing libxdmcp6 ... Removing x11-common ... invoke-rc.d: policy-rc.d denied execution of stop. 0m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'apt-get', 'remove', 'libx11-6', 'libx11-data', 'libsm6', 'libxcb1', 'x11-common', 'libice6', 'gromacs-data', 'libxau6', 'libfftw3-3', 'libgsl0ldbl', 'libxdmcp6', 'gromacs'] 0m17.3s INFO: Running scripts post_remove 0m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/post_remove_exceptions_lenny'] 0m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/post_remove_exceptions_lenny'] 0m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/post_remove_extras'] 0m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/post_remove_extras'] 0m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg', '--purge', 'libx11-6', 'libx11-data', 'libsm6', 'libxcb1', 'x11-common', 'libice6', 'gromacs-data', 'libxau6', 'libfftw3-3', 'libgsl0ldbl', 'libxdmcp6'] 0m17.6s DUMP: (Reading database ... 6275 files and directories currently installed.) Removing libx11-6 ... Purging configuration files for libx11-6 ... dpkg: warning: ignoring request to remove libx11-data which isn't installed. Removing libsm6 ... Purging configuration files for libsm6 ... Removing libxcb1 ... Purging configuration files for libxcb1 ... Removing x11-common ... Purging configuration files for x11-common ... Removing libice6 ... Purging configuration files for libice6 ... dpkg: warning: ignoring request to remove gromacs-data which isn't installed. Removing libxau6 ... Purging configuration files for libxau6 ... Removing libfftw3-3 ... Purging configuration files for libfftw3-3 ... Removing libgsl0ldbl ... Purging configuration files for libgsl0ldbl ... Removing libxdmcp6 ... Purging configuration files for libxdmcp6 ... 0m17.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg', '--purge', 'libx11-6', 'libx11-data', 'libsm6', 'libxcb1', 'x11-common', 'libice6', 'gromacs-data', 'libxau6', 'libfftw3-3', 'libgsl0ldbl', 'libxdmcp6'] 0m17.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg', '--purge', 'gromacs'] 0m17.7s DUMP: (Reading database ... 6258 files and directories currently installed.) Removing gromacs ... Purging configuration files for gromacs ... 0m17.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg', '--purge', 'gromacs'] 0m17.7s INFO: Running scripts post_purge 0m17.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/post_purge_exceptions'] 0m17.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'tmp/scripts/post_purge_exceptions'] 0m17.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg', '--purge', '--pending'] 0m17.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg', '--purge', '--pending'] 0m17.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg', '--remove', '--pending'] 0m17.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg', '--remove', '--pending'] 0m17.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxbrv_k'] 0m18.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxbrv_k'] 0m18.8s DEBUG: No broken symlinks as far as we can find. 0m18.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg-divert', '--list'] 0m18.8s 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 0m18.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'dpkg-divert', '--list'] 0m18.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'apt-get', 'clean'] 0m18.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'apt-get', 'clean'] 0m19.9s INFO: PASS: Installation and purging test. 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'umount', '/proc'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxbrv_k', 'umount', '/proc'] 0m20.2s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpxbrv_k'] 0m20.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpxbrv_k'] 0m20.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpxbrv_k 0m20.2s INFO: PASS: All tests. 0m20.2s INFO: piuparts run ends. ret=0 End: 2014-03-03 17:35:32 UTC