Start: 2014-09-28 20:36:51 UTC Package: phyml Priority: optional Section: science Installed-Size: 1148 Maintainer: Debian Med Packaging Team Architecture: amd64 Version: 2:20100123-1 Depends: libc6 (>= 2.7) Filename: pool/main/p/phyml/phyml_20100123-1_amd64.deb Size: 652072 MD5sum: da0a83957f1d9ffc621def0ade0718f6 SHA1: 60835c3d14be7162060adeb4da8262cb70ef132f SHA256: 74a7881b96b6394acdb12176b774ed5aae1f664431709cd25c73ebc86605c0a2 Description: Phylogenetic estimation using Maximum Likelihood PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test). . PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the “comfort zone” for PhyML generally lies around 3 to 500 sequences less than 2,000 character long. Homepage: http://www.atgc-montpellier.fr/phyml Tag: biology::peptidic, field::biology, field::biology:bioinformatics, implemented-in::c, interface::commandline, role::program, use::analysing, use::comparing 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 phyml=2:20100123-1 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 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 phyml=2:20100123-1 0m0.0s INFO: Running on: Linux piu-slave-bm-a 3.2.0-4-amd64 #1 SMP Debian 3.2.60-1+deb7u3 x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp_IHGaI 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp_IHGaI 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz'] 0m1.8s DUMP: tar: ./proc: time stamp 2014-10-15 13:49:47 is 1444374.9059571 s in the future 0m1.8s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/squeeze_amd64.tar.gz'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'mount', '-t', 'proc', 'proc', '/proc'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', '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/tmp_IHGaI', '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/tmp_IHGaI', 'apt-get', 'update'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DUMP: Reading package lists... Building dependency tree... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp_IHGaI/tmp/scripts/ 0m2.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts-squeeze to /srv/piuparts.debian.org/tmp/tmp_IHGaI/tmp/scripts/ 0m2.2s INFO: Running scripts post_setup 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/post_setup_experimental'] 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/post_setup_experimental'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/post_setup_forbid_home'] 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/post_setup_forbid_home'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/post_setup_squeeze-fake-essential'] 0m3.0s 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 (27.0 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) ... 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/post_setup_squeeze-fake-essential'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'apt-get', 'clean'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'apt-get', 'clean'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'dpkg', '--get-selections', '*'] 0m3.6s DUMP: adduser install apt install base-files install base-passwd install bash install bsdutils install coreutils install dash install debconf install debconf-i18n install debian-archive-keyring install debianutils install diffutils install dpkg install e2fslibs install e2fsprogs install findutils install gcc-4.4-base install gnupg install gpgv install grep install gzip install hostname install initscripts install insserv install libacl1 install libattr1 install libblkid1 install libbz2-1.0 install libc-bin install libc6 install libcomerr2 install libdb4.8 install libgcc1 install liblocale-gettext-perl install liblzma2 install libncurses5 install libpam-modules install libpam-runtime install libpam0g install libreadline6 install libselinux1 install libsepol1 install libslang2 install libss2 install libstdc++6 install libtext-charwidth-perl install libtext-iconv-perl install libtext-wrapi18n-perl install libusb-0.1-4 install libuuid1 install login install lsb-base install mawk install mount install ncurses-base install ncurses-bin install passwd install perl-base install readline-common install sed install sensible-utils install sysv-rc install sysvinit install sysvinit-utils install tar install tzdata install ucf install util-linux install xz-utils install zlib1g install 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'dpkg', '--get-selections', '*'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'dpkg-divert', '--list'] 0m3.6s DUMP: diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /bin/sync to /bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'dpkg-divert', '--list'] 0m3.6s INFO: apt-cache does not know about any of the requested packages 0m3.6s INFO: Running scripts pre_test 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/pre_test_root_password'] 0m3.6s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/pre_test_root_password'] 0m3.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_IHGaI'] 0m3.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_IHGaI'] 0m4.7s DEBUG: No broken symlinks as far as we can find. 0m4.7s INFO: Running scripts pre_install 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/pre_install_database-server'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/pre_install_database-server'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/pre_install_exceptions'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/pre_install_exceptions'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/pre_install_extras'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/pre_install_extras'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'apt-cache', 'show', 'phyml=2:20100123-1'] 0m4.8s DUMP: Package: phyml Priority: optional Section: science Installed-Size: 1148 Maintainer: Debian Med Packaging Team Architecture: amd64 Version: 2:20100123-1 Depends: libc6 (>= 2.7) Filename: pool/main/p/phyml/phyml_20100123-1_amd64.deb Size: 652072 MD5sum: da0a83957f1d9ffc621def0ade0718f6 SHA1: 60835c3d14be7162060adeb4da8262cb70ef132f SHA256: 74a7881b96b6394acdb12176b774ed5aae1f664431709cd25c73ebc86605c0a2 Description: Phylogenetic estimation using Maximum Likelihood PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test). . PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the ??comfort zone?? for PhyML generally lies around 3 to 500 sequences less than 2,000 character long. Homepage: http://www.atgc-montpellier.fr/phyml Tag: biology::peptidic, field::biology, field::biology:bioinformatics, implemented-in::c, interface::commandline, role::program, use::analysing, use::comparing 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'apt-cache', 'show', 'phyml=2:20100123-1'] 0m4.8s 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) 0m4.8s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmp2qBUiZ/piuparts-depends-dummy'] 0m4.8s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmp2qBUiZ/piuparts-depends-dummy.deb'. 0m4.8s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmp2qBUiZ/piuparts-depends-dummy'] 0m4.8s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmp2qBUiZ/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmp_IHGaI/tmp 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m4.8s 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) ... Setting up piuparts-depends-dummy (0.invalid.0) ... 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'apt-get', '-yf', 'install'] 0m5.2s DUMP: Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'apt-get', '-yf', 'install'] 0m5.2s INFO: Installation of ['tmp/piuparts-depends-dummy.deb'] ok 0m5.2s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmp_IHGaI/tmp/piuparts-depends-dummy.deb 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m5.3s DUMP: piuparts-depends-dummy install ok installed 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m5.3s DUMP: (Reading database ... 6261 files and directories currently installed.) Removing piuparts-depends-dummy ... 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'apt-get', 'clean'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'apt-get', 'clean'] 0m5.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_IHGaI'] 0m6.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_IHGaI'] 0m6.8s DEBUG: No broken symlinks as far as we can find. 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'apt-cache', 'policy'] 0m6.9s 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: 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'apt-cache', 'policy'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'apt-cache', 'policy', 'phyml'] 0m6.9s DUMP: phyml: Installed: (none) Candidate: 2:20100123-1 Version table: 2:20100123-1 0 500 http://mirror.bm.debian.org/debian/ squeeze/main amd64 Packages 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'apt-cache', 'policy', 'phyml'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'apt-get', '-y', 'install', 'phyml=2:20100123-1'] 0m7.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: phyml 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 652 kB of archives. After this operation, 1176 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ squeeze/main phyml amd64 2:20100123-1 [652 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 652 kB in 0s (7074 kB/s) Selecting previously deselected package phyml. (Reading database ... 6261 files and directories currently installed.) Unpacking phyml (from .../phyml_2%3a20100123-1_amd64.deb) ... Setting up phyml (2:20100123-1) ... 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'apt-get', '-y', 'install', 'phyml=2:20100123-1'] 0m7.5s INFO: Running scripts post_install 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/post_install_exceptions'] 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/post_install_exceptions'] 0m7.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_IHGaI'] 0m7.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_IHGaI'] 0m8.5s DEBUG: No broken symlinks as far as we can find. 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'dpkg', '--get-selections', '*'] 0m8.6s DUMP: adduser install apt install base-files install base-passwd install bash install bsdutils install coreutils install dash install debconf install debconf-i18n install debian-archive-keyring install debianutils install diffutils install dpkg install e2fslibs install e2fsprogs install findutils install gcc-4.4-base install gnupg install gpgv install grep install gzip install hostname install initscripts install insserv install libacl1 install libattr1 install libblkid1 install libbz2-1.0 install libc-bin install libc6 install libcomerr2 install libdb4.8 install libgcc1 install liblocale-gettext-perl install liblzma2 install libncurses5 install libpam-modules install libpam-runtime install libpam0g install libreadline6 install libselinux1 install libsepol1 install libslang2 install libss2 install libstdc++6 install libtext-charwidth-perl install libtext-iconv-perl install libtext-wrapi18n-perl install libusb-0.1-4 install libuuid1 install login install lsb-base install mawk install mount install ncurses-base install ncurses-bin install passwd install perl-base install phyml 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 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'dpkg', '--get-selections', '*'] 0m9.1s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', '-ac'] 0m9.7s DUMP: debsums: no md5sums for mawk 0m9.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', '-ac'] 0m9.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m9.7s DUMP: 0.12~bpo70+1 0m9.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m9.7s INFO: Running adequate version 0.12~bpo70+1 now. 0m9.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'phyml'] 0m9.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'phyml'] 0m9.8s INFO: Running scripts pre_remove 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/pre_remove_exceptions'] 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/pre_remove_exceptions'] 0m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'apt-get', 'remove', 'phyml'] 0m10.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: phyml 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. After this operation, 1176 kB disk space will be freed. (Reading database ... 6268 files and directories currently installed.) Removing phyml ... 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'apt-get', 'remove', 'phyml'] 0m10.7s INFO: Running scripts post_remove 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/post_remove_exceptions_lenny'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/post_remove_exceptions_lenny'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/post_remove_extras'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/post_remove_extras'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'dpkg', '--purge', 'phyml'] 0m10.7s DUMP: dpkg: warning: ignoring request to remove phyml which isn't installed. 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'dpkg', '--purge', 'phyml'] 0m10.7s INFO: Running scripts post_purge 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/post_purge_exceptions'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'tmp/scripts/post_purge_exceptions'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'dpkg', '--purge', '--pending'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'dpkg', '--purge', '--pending'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'dpkg', '--remove', '--pending'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'dpkg', '--remove', '--pending'] 0m10.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_IHGaI'] 0m11.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_IHGaI'] 0m11.8s DEBUG: No broken symlinks as far as we can find. 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'dpkg-divert', '--list'] 0m11.8s DUMP: diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /bin/sync to /bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'dpkg-divert', '--list'] 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'apt-get', 'clean'] 0m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'apt-get', 'clean'] 0m12.8s INFO: PASS: Installation and purging test. 0m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'umount', '/proc'] 0m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_IHGaI', 'umount', '/proc'] 0m13.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp_IHGaI'] 0m13.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp_IHGaI'] 0m13.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp_IHGaI 0m13.2s INFO: PASS: All tests. 0m13.2s INFO: piuparts run ends. ret=0 End: 2014-09-28 20:37:05 UTC