Start: 2014-03-12 15:38:16 UTC Package: bioperl-run Priority: optional Section: science Installed-Size: 2136 Maintainer: Debian Med Packaging Team Architecture: all Version: 1.6.1-1 Depends: bioperl (>= 1.6.0) Recommends: libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl Suggests: amap-align, emboss, hmmer, wise, molphy, phylip, clustalw, sim4, t-coffee, blast2, exonerate Filename: pool/main/b/bioperl-run/bioperl-run_1.6.1-1_all.deb Size: 694910 MD5sum: 4c2a83ba5734c8141dc4cdab9e5449ff SHA1: 7498f217e2ef6e8c8afde89a7c1ddd91a286c9f5 SHA256: 41ce19fd12dd74cabfe5a05d68e500592fd2c667b5f10c7bd186ac3ab8ca27e0 Description: Wrapper modules for BioPerl Contains modules that provide a Perl interface to various bioinformatics applications to allow them to be used with common BioPerl objects. . Not all the wrappable applications are packaged in Debian. The ones that are are "Suggested" by this package. Homepage: http://www.bioperl.org/wiki/Run_package Tag: field::biology, field::biology:bioinformatics, implemented-in::perl, interface::commandline, role::program 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 bioperl-run=1.6.1-1 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 0.57.1~201403012113~0.57-23-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 bioperl-run=1.6.1-1 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/tmpZRn4Rv 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpZRn4Rv 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz'] 0m1.8s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'mount', '-t', 'proc', 'proc', '/proc'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', '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/tmpZRn4Rv', 'apt-get', 'update'] 0m4.0s 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 (5745 kB/s) Reading package lists... 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'apt-get', 'update'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'apt-get', '-yf', 'dist-upgrade'] 0m5.5s 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 (8347 kB/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: Wed Mar 12 15:38:21 UTC 2014. Universal Time is now: Wed Mar 12 15:38:21 UTC 2014. Run 'dpkg-reconfigure tzdata' if you wish to change it. 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'apt-get', '-yf', 'dist-upgrade'] 0m5.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpZRn4Rv/tmp/scripts/ 0m5.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts-squeeze to /srv/piuparts.debian.org/tmp/tmpZRn4Rv/tmp/scripts/ 0m5.5s INFO: Running scripts post_setup 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/post_setup_experimental'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/post_setup_experimental'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/post_setup_forbid_home'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/post_setup_forbid_home'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.5s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' `/bin/sync' -> `true' 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/post_setup_squeeze-fake-essential'] 0m6.5s 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 (6063 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) ... 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/post_setup_squeeze-fake-essential'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'apt-get', 'clean'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'apt-get', 'clean'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg', '--get-selections', '*'] 0m7.0s 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 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg', '--get-selections', '*'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg-divert', '--list'] 0m7.0s 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 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg-divert', '--list'] 0m7.0s INFO: apt-cache does not know about any of the requested packages 0m7.0s INFO: Running scripts pre_test 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/pre_test_root_password'] 0m7.0s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/pre_test_root_password'] 0m7.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv'] 0m7.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv'] 0m8.0s DEBUG: No broken symlinks as far as we can find. 0m8.0s INFO: Running scripts pre_install 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/pre_install_database-server'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/pre_install_database-server'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/pre_install_exceptions'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/pre_install_exceptions'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/pre_install_extras'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/pre_install_extras'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'apt-cache', 'show', 'bioperl-run=1.6.1-1'] 0m8.1s DUMP: Package: bioperl-run Priority: optional Section: science Installed-Size: 2136 Maintainer: Debian Med Packaging Team Architecture: all Version: 1.6.1-1 Depends: bioperl (>= 1.6.0) Recommends: libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl Suggests: amap-align, emboss, hmmer, wise, molphy, phylip, clustalw, sim4, t-coffee, blast2, exonerate Filename: pool/main/b/bioperl-run/bioperl-run_1.6.1-1_all.deb Size: 694910 MD5sum: 4c2a83ba5734c8141dc4cdab9e5449ff SHA1: 7498f217e2ef6e8c8afde89a7c1ddd91a286c9f5 SHA256: 41ce19fd12dd74cabfe5a05d68e500592fd2c667b5f10c7bd186ac3ab8ca27e0 Description: Wrapper modules for BioPerl Contains modules that provide a Perl interface to various bioinformatics applications to allow them to be used with common BioPerl objects. . Not all the wrappable applications are packaged in Debian. The ones that are are "Suggested" by this package. Homepage: http://www.bioperl.org/wiki/Run_package Tag: field::biology, field::biology:bioinformatics, implemented-in::perl, interface::commandline, role::program 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'apt-cache', 'show', 'bioperl-run=1.6.1-1'] 0m8.1s 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: bioperl (>= 1.6.0) 0m8.1s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpfms7aZ/piuparts-depends-dummy'] 0m8.2s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmpfms7aZ/piuparts-depends-dummy.deb'. 0m8.2s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpfms7aZ/piuparts-depends-dummy'] 0m8.2s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmpfms7aZ/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmpZRn4Rv/tmp 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m8.2s 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 bioperl (>= 1.6.0); however: Package bioperl is not installed. dpkg: error processing piuparts-depends-dummy (--install): dependency problems - leaving unconfigured Errors were encountered while processing: piuparts-depends-dummy 0m8.2s DEBUG: Command failed (status=1), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'apt-get', '-yf', 'install'] 0m12.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Correcting dependencies... Done The following extra packages will be installed: bioperl libdata-stag-perl libdb4.7 libgdbm3 libio-string-perl perl perl-modules Suggested packages: libmath-random-perl libxml-sax-expatxs-perl perl-doc libterm-readline-gnu-perl libterm-readline-perl-perl make Recommended packages: bioperl-run libace-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl libdbd-pg-perl libgraph-perl libgraphviz-perl libhtml-parser-perl liblist-moreutils-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libstorable-perl libsvg-perl libsvg-graph-perl liburi-perl libxml-dom-xpath-perl libxml-parser-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libxml-libxml-perl libwww-perl perl-tk libgd-gd2-perl libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl netbase The following NEW packages will be installed: bioperl libdata-stag-perl libdb4.7 libgdbm3 libio-string-perl perl perl-modules 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 1 not fully installed or removed. Need to get 15.5 MB of archives. After this operation, 57.7 MB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ squeeze/main perl-modules all 5.10.1-17squeeze6 [3482 kB] Get:2 http://mirror.bm.debian.org/debian/ squeeze/main libdb4.7 amd64 4.7.25-9 [662 kB] Get:3 http://mirror.bm.debian.org/debian/ squeeze/main libgdbm3 amd64 1.8.3-9 [46.2 kB] Get:4 http://mirror.bm.debian.org/debian/ squeeze/main perl amd64 5.10.1-17squeeze6 [4462 kB] Get:5 http://mirror.bm.debian.org/debian/ squeeze/main libio-string-perl all 1.08-2 [12.0 kB] Get:6 http://mirror.bm.debian.org/debian/ squeeze/main libdata-stag-perl all 0.11-2 [509 kB] Get:7 http://mirror.bm.debian.org/debian/ squeeze/main bioperl all 1.6.1-2 [6367 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 15.5 MB in 2s (5983 kB/s) Selecting previously deselected package perl-modules. (Reading database ... 6258 files and directories currently installed.) Unpacking perl-modules (from .../perl-modules_5.10.1-17squeeze6_all.deb) ... Selecting previously deselected package libdb4.7. Unpacking libdb4.7 (from .../libdb4.7_4.7.25-9_amd64.deb) ... Selecting previously deselected package libgdbm3. Unpacking libgdbm3 (from .../libgdbm3_1.8.3-9_amd64.deb) ... Selecting previously deselected package perl. Unpacking perl (from .../perl_5.10.1-17squeeze6_amd64.deb) ... Selecting previously deselected package libio-string-perl. Unpacking libio-string-perl (from .../libio-string-perl_1.08-2_all.deb) ... Selecting previously deselected package libdata-stag-perl. Unpacking libdata-stag-perl (from .../libdata-stag-perl_0.11-2_all.deb) ... Selecting previously deselected package bioperl. Unpacking bioperl (from .../bioperl_1.6.1-2_all.deb) ... Setting up libdb4.7 (4.7.25-9) ... Setting up libgdbm3 (1.8.3-9) ... Setting up perl-modules (5.10.1-17squeeze6) ... Setting up perl (5.10.1-17squeeze6) ... update-alternatives: using /usr/bin/prename to provide /usr/bin/rename (rename) in auto mode. Setting up libio-string-perl (1.08-2) ... Setting up libdata-stag-perl (0.11-2) ... Setting up bioperl (1.6.1-2) ... Setting up piuparts-depends-dummy (0.invalid.0) ... 0m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'apt-get', '-yf', 'install'] 0m12.2s INFO: Installation of ['tmp/piuparts-depends-dummy.deb'] ok 0m12.2s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmpZRn4Rv/tmp/piuparts-depends-dummy.deb 0m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m12.2s DUMP: piuparts-depends-dummy install ok installed 0m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m12.3s DUMP: (Reading database ... 9827 files and directories currently installed.) Removing piuparts-depends-dummy ... 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'apt-get', 'clean'] 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'apt-get', 'clean'] 0m12.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv'] 0m13.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv'] 0m14.3s DEBUG: No broken symlinks as far as we can find. 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'apt-cache', 'policy'] 0m14.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror.bm.debian.org/debian/ squeeze/main amd64 Packages release v=6.0.9,o=Debian,a=oldstable,n=squeeze,l=Debian,c=main origin mirror.bm.debian.org Pinned packages: 0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'apt-cache', 'policy'] 0m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'apt-cache', 'policy', 'bioperl-run'] 0m14.4s DUMP: bioperl-run: Installed: (none) Candidate: 1.6.1-1 Version table: 1.6.1-1 0 500 http://mirror.bm.debian.org/debian/ squeeze/main amd64 Packages 0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'apt-cache', 'policy', 'bioperl-run'] 0m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'apt-get', '-y', 'install', 'bioperl-run=1.6.1-1'] 0m15.1s DUMP: Reading package lists... Building dependency tree... Reading state information... Suggested packages: amap-align emboss hmmer wise molphy phylip clustalw sim4 t-coffee blast2 exonerate Recommended packages: libalgorithm-diff-perl libipc-run-perl libxml-twig-perl The following NEW packages will be installed: bioperl-run 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 695 kB of archives. After this operation, 2187 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ squeeze/main bioperl-run all 1.6.1-1 [695 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 695 kB in 0s (6954 kB/s) Selecting previously deselected package bioperl-run. (Reading database ... 9827 files and directories currently installed.) Unpacking bioperl-run (from .../bioperl-run_1.6.1-1_all.deb) ... Setting up bioperl-run (1.6.1-1) ... 0m15.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'apt-get', '-y', 'install', 'bioperl-run=1.6.1-1'] 0m15.1s INFO: Running scripts post_install 0m15.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv'] 0m15.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv'] 0m16.6s DEBUG: No broken symlinks as far as we can find. 0m16.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg', '--get-selections', '*'] 0m16.7s DUMP: adduser install apt install base-files install base-passwd install bash install bioperl install bioperl-run 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 libdata-stag-perl install libdb4.7 install libdb4.8 install libgcc1 install libgdbm3 install libio-string-perl 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 install perl-base install perl-modules 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 0m16.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg', '--get-selections', '*'] 0m17.5s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', '-ac'] 0m18.3s DUMP: debsums: no md5sums for mawk 0m18.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', '-ac'] 0m18.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m18.4s DUMP: 0.11.3~bpo70+1 0m18.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m18.4s INFO: Running adequate version 0.11.3~bpo70+1 now. 0m18.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'bioperl-run'] 0m18.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'bioperl-run'] 0m18.5s INFO: Running scripts pre_remove 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/pre_remove_exceptions'] 0m18.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/pre_remove_exceptions'] 0m18.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'apt-get', 'remove', 'perl-modules', 'libdata-stag-perl', 'perl', 'libdb4.7', 'libgdbm3', 'libio-string-perl', 'bioperl', 'bioperl-run'] 0m19.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bioperl bioperl-run libdata-stag-perl libdb4.7 libgdbm3 libio-string-perl perl perl-modules 0 upgraded, 0 newly installed, 8 to remove and 0 not upgraded. After this operation, 59.9 MB disk space will be freed. (Reading database ... 10045 files and directories currently installed.) Removing bioperl-run ... Removing bioperl ... Removing libdata-stag-perl ... Removing libio-string-perl ... Removing perl ... Removing perl-modules ... Removing libdb4.7 ... Removing libgdbm3 ... 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'apt-get', 'remove', 'perl-modules', 'libdata-stag-perl', 'perl', 'libdb4.7', 'libgdbm3', 'libio-string-perl', 'bioperl', 'bioperl-run'] 0m19.4s INFO: Running scripts post_remove 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/post_remove_exceptions_lenny'] 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/post_remove_exceptions_lenny'] 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/post_remove_extras'] 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/post_remove_extras'] 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg', '--purge', 'perl-modules', 'libdata-stag-perl', 'perl', 'libdb4.7', 'libgdbm3', 'libio-string-perl', 'bioperl'] 0m19.4s DUMP: (Reading database ... 6261 files and directories currently installed.) Removing perl-modules ... Purging configuration files for perl-modules ... dpkg: warning: ignoring request to remove libdata-stag-perl which isn't installed. dpkg: warning: ignoring request to remove perl which isn't installed. dpkg: warning: ignoring request to remove libdb4.7 which isn't installed. Removing libgdbm3 ... Purging configuration files for libgdbm3 ... dpkg: warning: ignoring request to remove libio-string-perl which isn't installed. dpkg: warning: ignoring request to remove bioperl which isn't installed. 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg', '--purge', 'perl-modules', 'libdata-stag-perl', 'perl', 'libdb4.7', 'libgdbm3', 'libio-string-perl', 'bioperl'] 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg', '--purge', 'bioperl-run'] 0m19.4s DUMP: dpkg: warning: ignoring request to remove bioperl-run which isn't installed. 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg', '--purge', 'bioperl-run'] 0m19.4s INFO: Running scripts post_purge 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/post_purge_exceptions'] 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'tmp/scripts/post_purge_exceptions'] 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg', '--purge', '--pending'] 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg', '--purge', '--pending'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg', '--remove', '--pending'] 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg', '--remove', '--pending'] 0m19.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv'] 0m19.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv'] 0m20.5s DEBUG: No broken symlinks as far as we can find. 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg-divert', '--list'] 0m20.5s 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 0m20.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'dpkg-divert', '--list'] 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'apt-get', 'clean'] 0m20.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'apt-get', 'clean'] 0m21.5s INFO: PASS: Installation and purging test. 0m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'umount', '/proc'] 0m21.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv', 'umount', '/proc'] 0m21.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv'] 0m21.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpZRn4Rv'] 0m21.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpZRn4Rv 0m21.8s INFO: PASS: All tests. 0m21.8s INFO: piuparts run ends. ret=0 End: 2014-03-12 15:38:38 UTC