Start: 2014-10-19 02:36:09 UTC Package: gff2aplot Priority: optional Section: science Installed-Size: 784 Maintainer: Debian-Med Packaging Team Architecture: amd64 Version: 2.0-5 Depends: libc6 (>= 2.7-1), perl Suggests: gff2ps, postscript-viewer Filename: pool/main/g/gff2aplot/gff2aplot_2.0-5_amd64.deb Size: 326390 MD5sum: 137de3931a4f6a9ee7a137742e111705 SHA1: f73f66a1e071cc4b50c999a2d6303682d424fa00 SHA256: f86f47c746741d4ccc9bd60822193b25b4f53ee538de23601cfbf32050fc7a97 Description: pair-wise alignment-plots for genomic sequences in PostScript A program to visualize the alignment of two genomic sequences together with their annotations. From GFF-format input files it produces PostScript figures for that alignment. The following menu lists many features of gff2aplot: * Comprehensive alignment plots for any GFF-feature. Attributes are defined separately so you can modify only whatsoever attributes for a given file or share same customization across different data-sets. * All parameters are set by default within the program, but it can be also fully configured via gff2ps-like flexible customization files. Program can handle several of such files, summarizing all the settings before producing the corresponding figure. Moreover, all customization parameters can be set via command-line switches, which allows users to play with those parameters before adding any to a customization file. * Source order is taken from input files, if you swap file order you can visualize alignment and its annotation with the new input arrangement. * All alignment scores can be visualized in a PiP box below gff2aplot area, using grey-color scale, user-defined color scale or score-dependent gradients. * Scalable fonts, which can also be chosen among the basic PostScript default fonts. Feature and group labels can be rotated to improve readability in both annotation axes. * The program is still defined as a Unix filter so it can handle data from files, redirections and pipes, writing output to standard-output and warnings to standard error. * gff2aplot is able to manage many physical page formats (from A0 to A10, and more -see available page sizes in its manual-), including user-defined ones. This allows, for instance, the generation of poster size genomic maps, or the use of a continuous-paper supporting plotting device, either in portrait or landscape. * You can draw different alignments on same alignment plot and distinguish them by using different colors for each. * Shape dictionary has been expanded, so that further feature shapes are now available (see manual). * Annotation projections through alignment plots (so called ribbons) emulate transparencies via complementary color fill patterns. This feature allows to show color pseudo-blending when horizontal and vertical ribbons overlap. Homepage: http://genome.imim.es/software/gfftools/GFF2APLOT.html Tag: field::biology, field::biology:bioinformatics, implemented-in::c, implemented-in::perl, interface::commandline, interface::shell, role::program, scope::utility, use::converting, use::viewing, works-with::image:vector, works-with-format::plaintext, works-with-format::postscript 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 gff2aplot=2.0-5 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 0.59 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 gff2aplot=2.0-5 0m0.0s INFO: Running on: Linux piu-slave-bm-a 3.2.0-4-amd64 #1 SMP Debian 3.2.63-2 x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpkN6loz 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpkN6loz 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpkN6loz', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz'] 0m1.8s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpkN6loz', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'mount', '-t', 'proc', 'proc', '/proc'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', '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/tmpkN6loz', 'apt-get', 'update'] 0m1.8s DUMP: Hit http://mirror.bm.debian.org squeeze Release.gpg Ign http://mirror.bm.debian.org/debian/ squeeze/main Translation-en Hit http://mirror.bm.debian.org squeeze Release Hit http://mirror.bm.debian.org squeeze/main amd64 Packages Reading package lists... 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'apt-get', 'update'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DUMP: Reading package lists... Building dependency tree... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpkN6loz/tmp/scripts/ 0m2.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts-squeeze to /srv/piuparts.debian.org/tmp/tmpkN6loz/tmp/scripts/ 0m2.1s INFO: Running scripts post_setup 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/post_setup_experimental'] 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/post_setup_experimental'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/post_setup_forbid_home'] 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/post_setup_forbid_home'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/post_setup_squeeze-fake-essential'] 0m2.9s DUMP: *** Adding fake essential packages *** Reading package lists... Building dependency tree... Suggested packages: perl-modules The following NEW packages will be installed: adduser ucf 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 320 kB of archives. After this operation, 1532 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ squeeze/main adduser all 3.112+nmu2 [250 kB] Get:2 http://mirror.bm.debian.org/debian/ squeeze/main ucf all 3.0025+nmu1 [69.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 320 kB in 0s (25.9 MB/s) Selecting previously deselected package adduser. (Reading database ... 6138 files and directories currently installed.) Unpacking adduser (from .../adduser_3.112+nmu2_all.deb) ... Selecting previously deselected package ucf. Unpacking ucf (from .../ucf_3.0025+nmu1_all.deb) ... Moving old data out of the way Setting up adduser (3.112+nmu2) ... Setting up ucf (3.0025+nmu1) ... 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/post_setup_squeeze-fake-essential'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'apt-get', 'clean'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'apt-get', 'clean'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg', '--get-selections', '*'] 0m3.4s DUMP: adduser install apt install base-files install base-passwd install bash install bsdutils install coreutils install dash install debconf install debconf-i18n install debian-archive-keyring install debianutils install diffutils install dpkg install e2fslibs install e2fsprogs install findutils install gcc-4.4-base install gnupg install gpgv install grep install gzip install hostname install initscripts install insserv install libacl1 install libattr1 install libblkid1 install libbz2-1.0 install libc-bin install libc6 install libcomerr2 install libdb4.8 install libgcc1 install liblocale-gettext-perl install liblzma2 install libncurses5 install libpam-modules install libpam-runtime install libpam0g install libreadline6 install libselinux1 install libsepol1 install libslang2 install libss2 install libstdc++6 install libtext-charwidth-perl install libtext-iconv-perl install libtext-wrapi18n-perl install libusb-0.1-4 install libuuid1 install login install lsb-base install mawk install mount install ncurses-base install ncurses-bin install passwd install perl-base install readline-common install sed install sensible-utils install sysv-rc install sysvinit install sysvinit-utils install tar install tzdata install ucf install util-linux install xz-utils install zlib1g install 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg', '--get-selections', '*'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg-divert', '--list'] 0m3.5s 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 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg-divert', '--list'] 0m3.5s INFO: apt-cache does not know about any of the requested packages 0m3.5s INFO: Running scripts pre_test 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/pre_test_root_password'] 0m3.5s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/pre_test_root_password'] 0m3.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkN6loz'] 0m3.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkN6loz'] 0m4.5s DEBUG: No broken symlinks as far as we can find. 0m4.5s INFO: Running scripts pre_install 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/pre_install_database-server'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/pre_install_database-server'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/pre_install_exceptions'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/pre_install_exceptions'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/pre_install_extras'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/pre_install_extras'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'apt-cache', 'show', 'gff2aplot=2.0-5'] 0m4.6s DUMP: Package: gff2aplot Priority: optional Section: science Installed-Size: 784 Maintainer: Debian-Med Packaging Team Architecture: amd64 Version: 2.0-5 Depends: libc6 (>= 2.7-1), perl Suggests: gff2ps, postscript-viewer Filename: pool/main/g/gff2aplot/gff2aplot_2.0-5_amd64.deb Size: 326390 MD5sum: 137de3931a4f6a9ee7a137742e111705 SHA1: f73f66a1e071cc4b50c999a2d6303682d424fa00 SHA256: f86f47c746741d4ccc9bd60822193b25b4f53ee538de23601cfbf32050fc7a97 Description: pair-wise alignment-plots for genomic sequences in PostScript A program to visualize the alignment of two genomic sequences together with their annotations. From GFF-format input files it produces PostScript figures for that alignment. The following menu lists many features of gff2aplot: * Comprehensive alignment plots for any GFF-feature. Attributes are defined separately so you can modify only whatsoever attributes for a given file or share same customization across different data-sets. * All parameters are set by default within the program, but it can be also fully configured via gff2ps-like flexible customization files. Program can handle several of such files, summarizing all the settings before producing the corresponding figure. Moreover, all customization parameters can be set via command-line switches, which allows users to play with those parameters before adding any to a customization file. * Source order is taken from input files, if you swap file order you can visualize alignment and its annotation with the new input arrangement. * All alignment scores can be visualized in a PiP box below gff2aplot area, using grey-color scale, user-defined color scale or score-dependent gradients. * Scalable fonts, which can also be chosen among the basic PostScript default fonts. Feature and group labels can be rotated to improve readability in both annotation axes. * The program is still defined as a Unix filter so it can handle data from files, redirections and pipes, writing output to standard-output and warnings to standard error. * gff2aplot is able to manage many physical page formats (from A0 to A10, and more -see available page sizes in its manual-), including user-defined ones. This allows, for instance, the generation of poster size genomic maps, or the use of a continuous-paper supporting plotting device, either in portrait or landscape. * You can draw different alignments on same alignment plot and distinguish them by using different colors for each. * Shape dictionary has been expanded, so that further feature shapes are now available (see manual). * Annotation projections through alignment plots (so called ribbons) emulate transparencies via complementary color fill patterns. This feature allows to show color pseudo-blending when horizontal and vertical ribbons overlap. Homepage: http://genome.imim.es/software/gfftools/GFF2APLOT.html Tag: field::biology, field::biology:bioinformatics, implemented-in::c, implemented-in::perl, interface::commandline, interface::shell, role::program, scope::utility, use::converting, use::viewing, works-with::image:vector, works-with-format::plaintext, works-with-format::postscript 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'apt-cache', 'show', 'gff2aplot=2.0-5'] 0m4.6s DEBUG: metapackage: Package: piuparts-depends-dummy Version: 0.invalid.0 Architecture: all Maintainer: piuparts developers team Description: Dummy package to satisfy dependencies - created by piuparts This package was created automatically by piuparts and can safely be removed Depends: libc6 (>= 2.7-1), perl 0m4.6s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpm89nLI/piuparts-depends-dummy'] 0m4.6s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmpm89nLI/piuparts-depends-dummy.deb'. 0m4.6s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpm89nLI/piuparts-depends-dummy'] 0m4.6s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmpm89nLI/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmpkN6loz/tmp 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m4.6s DUMP: Selecting previously deselected package piuparts-depends-dummy. (Reading database ... 6261 files and directories currently installed.) Unpacking piuparts-depends-dummy (from tmp/piuparts-depends-dummy.deb) ... dpkg: dependency problems prevent configuration of piuparts-depends-dummy: piuparts-depends-dummy depends on perl; however: Package perl is not installed. dpkg: error processing piuparts-depends-dummy (--install): dependency problems - leaving unconfigured Errors were encountered while processing: piuparts-depends-dummy 0m4.6s DEBUG: Command failed (status=1), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'apt-get', '-yf', 'install'] 0m6.0s DUMP: Reading package lists... Building dependency tree... Reading state information... Correcting dependencies... Done The following extra packages will be installed: libdb4.7 libgdbm3 perl perl-modules Suggested packages: perl-doc libterm-readline-gnu-perl libterm-readline-perl-perl make Recommended packages: netbase The following NEW packages will be installed: libdb4.7 libgdbm3 perl perl-modules 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 1 not fully installed or removed. Need to get 8653 kB of archives. After this operation, 36.8 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] debconf: delaying package configuration, since apt-utils is not installed Fetched 8653 kB in 0s (35.5 MB/s) Selecting previously deselected package perl-modules. (Reading database ... 6261 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) ... 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 piuparts-depends-dummy (0.invalid.0) ... 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'apt-get', '-yf', 'install'] 0m6.0s INFO: Installation of ['tmp/piuparts-depends-dummy.deb'] ok 0m6.0s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmpkN6loz/tmp/piuparts-depends-dummy.deb 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m6.0s DUMP: piuparts-depends-dummy install ok installed 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m6.0s DUMP: (Reading database ... 7606 files and directories currently installed.) Removing piuparts-depends-dummy ... 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'apt-get', 'clean'] 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'apt-get', 'clean'] 0m6.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkN6loz'] 0m6.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkN6loz'] 0m7.7s DEBUG: No broken symlinks as far as we can find. 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'apt-cache', 'policy'] 0m7.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror.bm.debian.org/debian/ squeeze/main amd64 Packages release v=6.0.10,o=Debian,a=oldstable,n=squeeze,l=Debian,c=main origin mirror.bm.debian.org Pinned packages: 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'apt-cache', 'policy'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'apt-cache', 'policy', 'gff2aplot'] 0m7.8s DUMP: gff2aplot: Installed: (none) Candidate: 2.0-5 Version table: 2.0-5 0 500 http://mirror.bm.debian.org/debian/ squeeze/main amd64 Packages 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'apt-cache', 'policy', 'gff2aplot'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'apt-get', '-y', 'install', 'gff2aplot=2.0-5'] 0m8.4s DUMP: Reading package lists... Building dependency tree... Reading state information... Suggested packages: gff2ps postscript-viewer The following NEW packages will be installed: gff2aplot 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 326 kB of archives. After this operation, 803 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ squeeze/main gff2aplot amd64 2.0-5 [326 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 326 kB in 0s (4458 kB/s) Selecting previously deselected package gff2aplot. (Reading database ... 7606 files and directories currently installed.) Unpacking gff2aplot (from .../gff2aplot_2.0-5_amd64.deb) ... Setting up gff2aplot (2.0-5) ... 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'apt-get', '-y', 'install', 'gff2aplot=2.0-5'] 0m8.4s INFO: Running scripts post_install 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/post_install_exceptions'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/post_install_exceptions'] 0m8.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkN6loz'] 0m8.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkN6loz'] 0m9.6s DEBUG: No broken symlinks as far as we can find. 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg', '--get-selections', '*'] 0m9.7s 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 gff2aplot 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 libdb4.7 install libdb4.8 install libgcc1 install libgdbm3 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 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg', '--get-selections', '*'] 0m10.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpkN6loz', '-ac'] 0m11.0s DUMP: debsums: no md5sums for mawk 0m11.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpkN6loz', '-ac'] 0m11.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m11.0s DUMP: 0.12~bpo70+1 0m11.0s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m11.0s INFO: Running adequate version 0.12~bpo70+1 now. 0m11.0s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'gff2aplot'] 0m11.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'gff2aplot'] 0m11.1s INFO: Running scripts pre_remove 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/pre_remove_exceptions'] 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/pre_remove_exceptions'] 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'apt-get', 'remove', 'perl-modules', 'libdb4.7', 'libgdbm3', 'perl', 'gff2aplot'] 0m12.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: gff2aplot libdb4.7 libgdbm3 perl perl-modules 0 upgraded, 0 newly installed, 5 to remove and 0 not upgraded. After this operation, 37.6 MB disk space will be freed. (Reading database ... 7669 files and directories currently installed.) Removing gff2aplot ... Removing perl ... Removing perl-modules ... Removing libdb4.7 ... Removing libgdbm3 ... 0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'apt-get', 'remove', 'perl-modules', 'libdb4.7', 'libgdbm3', 'perl', 'gff2aplot'] 0m12.0s INFO: Running scripts post_remove 0m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/post_remove_exceptions_lenny'] 0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/post_remove_exceptions_lenny'] 0m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/post_remove_extras'] 0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/post_remove_extras'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg', '--purge', 'perl-modules', 'libdb4.7', 'libgdbm3', 'perl'] 0m12.1s DUMP: (Reading database ... 6264 files and directories currently installed.) Removing perl-modules ... Purging configuration files for perl-modules ... 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 perl which isn't installed. 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg', '--purge', 'perl-modules', 'libdb4.7', 'libgdbm3', 'perl'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg', '--purge', 'gff2aplot'] 0m12.1s DUMP: dpkg: warning: ignoring request to remove gff2aplot which isn't installed. 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg', '--purge', 'gff2aplot'] 0m12.1s INFO: Running scripts post_purge 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/post_purge_exceptions'] 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'tmp/scripts/post_purge_exceptions'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg', '--purge', '--pending'] 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg', '--purge', '--pending'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg', '--remove', '--pending'] 0m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg', '--remove', '--pending'] 0m12.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkN6loz'] 0m12.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkN6loz'] 0m13.2s DEBUG: No broken symlinks as far as we can find. 0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg-divert', '--list'] 0m13.2s 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 0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'dpkg-divert', '--list'] 0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'apt-get', 'clean'] 0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'apt-get', 'clean'] 0m14.1s INFO: PASS: Installation and purging test. 0m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'umount', '/proc'] 0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkN6loz', 'umount', '/proc'] 0m14.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpkN6loz'] 0m14.5s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpkN6loz'] 0m14.5s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpkN6loz 0m14.5s INFO: PASS: All tests. 0m14.5s INFO: piuparts run ends. ret=0 End: 2014-10-19 02:36:23 UTC