Start: 2014-03-16 11:22:18 UTC Package: libbio-samtools-perl Priority: optional Section: perl Installed-Size: 576 Maintainer: Debian Perl Group Architecture: amd64 Version: 1.20-1 Depends: perl (>= 5.10.1-13), perlapi-5.10.1, libc6 (>= 2.7), zlib1g (>= 1:1.2.3.3.dfsg), bioperl (>= 1.6) Filename: pool/main/libb/libbio-samtools-perl/libbio-samtools-perl_1.20-1_amd64.deb Size: 205940 MD5sum: 80114cf439407f96a3b69e0b7fdf4bb2 SHA1: bd76b819430e372aed4e961ba83396562b4be706 SHA256: cf618e96cbaf88865cbecc5c595b36c41230ed81a1f785025d1eead7cd22b054 Description: read SAM/BAM nucleotide sequence aligment database files Bio::SamTools provides a Perl interface to the libbam library for indexed and unindexed SAM/BAM sequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information across large regions. It also provides callback functionality for calling SNPs and performing other base-by-base functions. Most operations are compatible with the BioPerl Bio::SeqFeatureI interface, allowing BAM files to be used as a backend to the GBrowse genome browser application. Enhances: gbrowse, samtools Homepage: http://search.cpan.org/dist/Bio-SamTools/ Tag: devel::lang:perl, devel::library, implemented-in::c, implemented-in::perl, role::shared-lib 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 libbio-samtools-perl=1.20-1 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 libbio-samtools-perl=1.20-1 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/tmp6Pd30j 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp6Pd30j 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz'] 0m1.8s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'mount', '-t', 'proc', 'proc', '/proc'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'mount', '-t', 'proc', 'proc', '/proc'] 0m1.8s DEBUG: sources.list: deb http://mirror.bm.debian.org/debian/ squeeze main 0m1.9s DEBUG: Created policy-rc.d and chmodded it. 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-get', 'update'] 0m1.9s DUMP: Hit http://mirror.bm.debian.org squeeze Release.gpg Ign http://mirror.bm.debian.org/debian/ squeeze/main Translation-en Hit http://mirror.bm.debian.org squeeze Release Hit http://mirror.bm.debian.org squeeze/main amd64 Packages Reading package lists... 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-get', 'update'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DUMP: Reading package lists... Building dependency tree... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp6Pd30j/tmp/scripts/ 0m2.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts-squeeze to /srv/piuparts.debian.org/tmp/tmp6Pd30j/tmp/scripts/ 0m2.3s INFO: Running scripts post_setup 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/post_setup_experimental'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/post_setup_experimental'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/post_setup_forbid_home'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/post_setup_forbid_home'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/post_setup_squeeze-fake-essential'] 0m3.6s DUMP: *** Adding fake essential packages *** Reading package lists... Building dependency tree... Suggested packages: perl-modules The following NEW packages will be installed: adduser ucf 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 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 (2233 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) ... 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/post_setup_squeeze-fake-essential'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-get', 'clean'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-get', 'clean'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg', '--get-selections', '*'] 0m4.1s 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 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg', '--get-selections', '*'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg-divert', '--list'] 0m4.1s 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 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg-divert', '--list'] 0m4.1s INFO: apt-cache does not know about any of the requested packages 0m4.1s INFO: Running scripts pre_test 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/pre_test_root_password'] 0m4.1s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/pre_test_root_password'] 0m4.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6Pd30j'] 0m4.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6Pd30j'] 0m5.1s DEBUG: No broken symlinks as far as we can find. 0m5.1s INFO: Running scripts pre_install 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/pre_install_database-server'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/pre_install_database-server'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/pre_install_exceptions'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/pre_install_exceptions'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/pre_install_extras'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/pre_install_extras'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-cache', 'show', 'libbio-samtools-perl=1.20-1'] 0m5.2s DUMP: Package: libbio-samtools-perl Priority: optional Section: perl Installed-Size: 576 Maintainer: Debian Perl Group Architecture: amd64 Version: 1.20-1 Depends: perl (>= 5.10.1-13), perlapi-5.10.1, libc6 (>= 2.7), zlib1g (>= 1:1.2.3.3.dfsg), bioperl (>= 1.6) Filename: pool/main/libb/libbio-samtools-perl/libbio-samtools-perl_1.20-1_amd64.deb Size: 205940 MD5sum: 80114cf439407f96a3b69e0b7fdf4bb2 SHA1: bd76b819430e372aed4e961ba83396562b4be706 SHA256: cf618e96cbaf88865cbecc5c595b36c41230ed81a1f785025d1eead7cd22b054 Description: read SAM/BAM nucleotide sequence aligment database files Bio::SamTools provides a Perl interface to the libbam library for indexed and unindexed SAM/BAM sequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information across large regions. It also provides callback functionality for calling SNPs and performing other base-by-base functions. Most operations are compatible with the BioPerl Bio::SeqFeatureI interface, allowing BAM files to be used as a backend to the GBrowse genome browser application. Enhances: gbrowse, samtools Homepage: http://search.cpan.org/dist/Bio-SamTools/ Tag: devel::lang:perl, devel::library, implemented-in::c, implemented-in::perl, role::shared-lib 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-cache', 'show', 'libbio-samtools-perl=1.20-1'] 0m5.3s 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: perl (>= 5.10.1-13), perlapi-5.10.1, libc6 (>= 2.7), zlib1g (>= 1:1.2.3.3.dfsg), bioperl (>= 1.6) 0m5.3s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpAj8z3Q/piuparts-depends-dummy'] 0m5.3s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmpAj8z3Q/piuparts-depends-dummy.deb'. 0m5.3s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpAj8z3Q/piuparts-depends-dummy'] 0m5.3s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmpAj8z3Q/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmp6Pd30j/tmp 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m5.3s 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 perl (>= 5.10.1-13); however: Package perl is not installed. piuparts-depends-dummy depends on bioperl (>= 1.6); 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 0m5.3s DEBUG: Command failed (status=1), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-get', '-yf', 'install'] 0m7.8s 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 0s (17.4 MB/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) ... 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-get', '-yf', 'install'] 0m7.8s INFO: Installation of ['tmp/piuparts-depends-dummy.deb'] ok 0m7.8s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmp6Pd30j/tmp/piuparts-depends-dummy.deb 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m7.8s DUMP: piuparts-depends-dummy install ok installed 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m7.8s DUMP: (Reading database ... 9827 files and directories currently installed.) Removing piuparts-depends-dummy ... 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-get', 'clean'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-get', 'clean'] 0m8.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6Pd30j'] 0m8.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6Pd30j'] 0m9.9s DEBUG: No broken symlinks as far as we can find. 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-cache', 'policy'] 0m10.0s 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: 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-cache', 'policy'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-cache', 'policy', 'libbio-samtools-perl'] 0m10.0s DUMP: libbio-samtools-perl: Installed: (none) Candidate: 1.20-1 Version table: 1.20-1 0 500 http://mirror.bm.debian.org/debian/ squeeze/main amd64 Packages 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-cache', 'policy', 'libbio-samtools-perl'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-get', '-y', 'install', 'libbio-samtools-perl=1.20-1'] 0m10.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: libbio-samtools-perl 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 206 kB of archives. After this operation, 590 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ squeeze/main libbio-samtools-perl amd64 1.20-1 [206 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 206 kB in 0s (7540 kB/s) Selecting previously deselected package libbio-samtools-perl. (Reading database ... 9827 files and directories currently installed.) Unpacking libbio-samtools-perl (from .../libbio-samtools-perl_1.20-1_amd64.deb) ... Setting up libbio-samtools-perl (1.20-1) ... 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-get', '-y', 'install', 'libbio-samtools-perl=1.20-1'] 0m10.7s INFO: Running scripts post_install 0m10.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6Pd30j'] 0m11.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6Pd30j'] 0m12.2s DEBUG: No broken symlinks as far as we can find. 0m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg', '--get-selections', '*'] 0m12.2s DUMP: adduser install apt install base-files install base-passwd install bash install bioperl 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 libbio-samtools-perl 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 0m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg', '--get-selections', '*'] 0m13.1s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', '-ac'] 0m13.9s DUMP: debsums: no md5sums for mawk 0m13.9s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', '-ac'] 0m13.9s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m13.9s DUMP: 0.11.3~bpo70+1 0m13.9s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m13.9s INFO: Running adequate version 0.11.3~bpo70+1 now. 0m13.9s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'libbio-samtools-perl'] 0m14.0s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'libbio-samtools-perl'] 0m14.0s INFO: Running scripts pre_remove 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/pre_remove_exceptions'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/pre_remove_exceptions'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-get', 'remove', 'perl-modules', 'libdata-stag-perl', 'perl', 'libdb4.7', 'libgdbm3', 'libio-string-perl', 'bioperl', 'libbio-samtools-perl'] 0m14.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bioperl libbio-samtools-perl 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, 58.3 MB disk space will be freed. (Reading database ... 9863 files and directories currently installed.) Removing libbio-samtools-perl ... Removing bioperl ... Removing libdata-stag-perl ... Removing libio-string-perl ... Removing perl ... Removing perl-modules ... Removing libdb4.7 ... Removing libgdbm3 ... 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-get', 'remove', 'perl-modules', 'libdata-stag-perl', 'perl', 'libdb4.7', 'libgdbm3', 'libio-string-perl', 'bioperl', 'libbio-samtools-perl'] 0m14.8s INFO: Running scripts post_remove 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/post_remove_exceptions_lenny'] 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/post_remove_exceptions_lenny'] 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/post_remove_extras'] 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/post_remove_extras'] 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg', '--purge', 'perl-modules', 'libdata-stag-perl', 'perl', 'libdb4.7', 'libgdbm3', 'libio-string-perl', 'bioperl'] 0m14.9s 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. 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg', '--purge', 'perl-modules', 'libdata-stag-perl', 'perl', 'libdb4.7', 'libgdbm3', 'libio-string-perl', 'bioperl'] 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg', '--purge', 'libbio-samtools-perl'] 0m14.9s DUMP: dpkg: warning: ignoring request to remove libbio-samtools-perl which isn't installed. 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg', '--purge', 'libbio-samtools-perl'] 0m14.9s INFO: Running scripts post_purge 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/post_purge_exceptions'] 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'tmp/scripts/post_purge_exceptions'] 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg', '--purge', '--pending'] 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg', '--purge', '--pending'] 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg', '--remove', '--pending'] 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg', '--remove', '--pending'] 0m14.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6Pd30j'] 0m15.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6Pd30j'] 0m15.9s DEBUG: No broken symlinks as far as we can find. 0m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg-divert', '--list'] 0m16.0s 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 0m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'dpkg-divert', '--list'] 0m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-get', 'clean'] 0m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'apt-get', 'clean'] 0m17.2s INFO: PASS: Installation and purging test. 0m17.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'umount', '/proc'] 0m17.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6Pd30j', 'umount', '/proc'] 0m17.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp6Pd30j'] 0m17.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp6Pd30j'] 0m17.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp6Pd30j 0m17.6s INFO: PASS: All tests. 0m17.6s INFO: piuparts run ends. ret=0 End: 2014-03-16 11:22:36 UTC