Start: 2018-08-11 00:10:23 UTC Package: python-biopython Version: 1.59-1 Installed-Size: 5786 Maintainer: Debian Med Packaging Team Architecture: amd64 Replaces: python2.3-biopython (<< 1.42-1), python2.4-biopython (<< 1.42-1) Provides: python2.6-biopython, python2.7-biopython Depends: python (<< 2.8), python (>= 2.6), python-numpy (>= 1:1.4.1), python-numpy-abi9, python-support (>= 0.90.0), libc6 (>= 2.2.5), python-reportlab Recommends: python-biopython-doc (= 1.59-1) Suggests: python-tk, wise, muscle, clustalw, mafft, emboss, blast2 Conflicts: python2.3-biopython (<< 1.42-1), python2.4-biopython (<< 1.42-1) Description: Python library for bioinformatics Homepage: http://biopython.org Description-md5: bacfe9ff423c05fc8056742f7e6c80cd Python-Version: 2.6, 2.7 Tag: devel::lang:python, devel::library, field::biology, field::biology:bioinformatics, implemented-in::python, role::devel-lib, role::shared-lib Section: python Priority: optional Filename: pool/main/p/python-biopython/python-biopython_1.59-1_amd64.deb Size: 1317216 MD5sum: 1b04d312cb0c32d7040bde9cc2a37c21 SHA1: 0376312a63bced640b7c1cac6eb1c9c90322fb13 SHA256: e5dc5516760be996e5ea55e56f91cfb088d69a40359133fac77d9fd2923a226a Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python2.7/dist-packages timeout -s INT -k 5m 80m /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 --scriptsdir /etc/piuparts/scripts-wheezy --warn-on-debsums-errors --warn-on-install-over-symlink --mirror 'http://mirror.bm.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz -d wheezy --no-upgrade-test --apt python-biopython=1.59-1 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 0.90~201808101311~0.89-6-ge00d965a 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 --scriptsdir /etc/piuparts/scripts-wheezy --warn-on-debsums-errors --warn-on-install-over-symlink --mirror 'http://mirror.bm.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz -d wheezy --no-upgrade-test --apt python-biopython=1.59-1 0m0.0s INFO: Running on: Linux piu-slave-bm-a 4.9.0-7-amd64 #1 SMP Debian 4.9.110-3+deb9u1 (2018-08-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpbJZl5Y 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpbJZl5Y 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz'] 0m2.0s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz'] 0m2.0s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/proc'] 0m2.0s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/proc'] 0m2.0s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/dev/pts'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/dev/pts'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/dev/ptmx'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/dev/ptmx'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/dev/console'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/dev/console'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/run/shm'] 0m2.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/run/shm'] 0m2.2s DEBUG: sources.list: deb http://mirror.bm.debian.org/debian/ wheezy main 0m2.2s DEBUG: Created policy-rc.d and chmodded it. 0m2.2s DEBUG: Created resolv.conf. 0m2.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpbJZl5Y/tmp/scripts/ 0m2.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts-wheezy to /srv/piuparts.debian.org/tmp/tmpbJZl5Y/tmp/scripts/ 0m2.2s INFO: Running scripts post_chroot_unpack 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-get', 'update'] 0m5.1s DUMP: Hit http://mirror.bm.debian.org wheezy Release.gpg Hit http://mirror.bm.debian.org wheezy Release Hit http://mirror.bm.debian.org wheezy/main amd64 Packages Hit http://mirror.bm.debian.org wheezy/main Translation-en Reading package lists... 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-get', 'update'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-get', '-yf', 'dist-upgrade'] 0m5.7s DUMP: Reading package lists... Building dependency tree... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-get', '-yf', 'dist-upgrade'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.2s DUMP: 0c96df6df725ee7ec7aebd2b6a77fb72 - 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.2s INFO: Running scripts post_setup 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_setup_dummy_users'] 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_setup_dummy_users'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_setup_experimental'] 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_setup_experimental'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_setup_forbid_home'] 0m7.7s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_setup_forbid_home'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.7s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' `/bin/sync' -> `true' 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_setup_minimize'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_setup_minimize'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_setup_wheezy-fake-essential'] 0m9.3s 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 335 kB of archives. After this operation, 1327 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ wheezy/main adduser all 3.113+nmu3 [264 kB] Get:2 http://mirror.bm.debian.org/debian/ wheezy/main ucf all 3.0025+nmu3 [70.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 335 kB in 0s (16.2 MB/s) Selecting previously unselected package adduser. (Reading database ... 6639 files and directories currently installed.) Unpacking adduser (from .../adduser_3.113+nmu3_all.deb) ... Selecting previously unselected package ucf. Unpacking ucf (from .../ucf_3.0025+nmu3_all.deb) ... Moving old data out of the way Setting up adduser (3.113+nmu3) ... Setting up ucf (3.0025+nmu3) ... 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_setup_wheezy-fake-essential'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_setup_zz_backports'] 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_setup_zz_backports'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-get', 'clean'] 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-get', 'clean'] 0m9.3s DEBUG: Recording chroot state 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m11.4s DUMP: install ok installed adduser adduser 3.113+nmu3 install ok installed apt apt 0.9.7.9+deb7u7 install ok installed base-files base-files 7.1wheezy11 install ok installed base-passwd base-passwd 3.5.26 install ok installed bash bash 4.2+dfsg-0.1+deb7u3 install ok installed bsdutils bsdutils 1:2.20.1-5.3 install ok installed coreutils coreutils 8.13-3.5 install ok installed dash dash 0.5.7-3 install ok installed debconf debconf 1.5.49 install ok installed debconf-i18n debconf-i18n 1.5.49 install ok installed debian-archive-keyring debian-archive-keyring 2014.3~deb7u1 install ok installed debianutils debianutils 4.3.2 install ok installed diffutils diffutils 1:3.2-6 install ok installed dpkg dpkg 1.16.18 install ok installed e2fslibs:amd64 e2fslibs 1.42.5-1.1+deb7u1 install ok installed e2fsprogs e2fsprogs 1.42.5-1.1+deb7u1 install ok installed findutils findutils 4.4.2-4 install ok installed gcc-4.7-base:amd64 gcc-4.7-base 4.7.2-5 install ok installed gnupg gnupg 1.4.12-7+deb7u7 install ok installed gpgv gpgv 1.4.12-7+deb7u7 install ok installed grep grep 2.12-2 install ok installed gzip gzip 1.5-1.1 install ok installed hostname hostname 3.11 install ok installed initscripts initscripts 2.88dsf-41+deb7u1 install ok installed insserv insserv 1.14.0-5 install ok installed libacl1:amd64 libacl1 2.2.51-8 install ok installed libapt-pkg4.12:amd64 libapt-pkg4.12 0.9.7.9+deb7u7 install ok installed libattr1:amd64 libattr1 1:2.4.46-8 install ok installed libblkid1:amd64 libblkid1 2.20.1-5.3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-4 install ok installed libc-bin libc-bin 2.13-38+deb7u10 install ok installed libc6:amd64 libc6 2.13-38+deb7u10 install ok installed libcomerr2:amd64 libcomerr2 1.42.5-1.1+deb7u1 install ok installed libdb5.1:amd64 libdb5.1 5.1.29-5 install ok installed libgcc1:amd64 libgcc1 1:4.7.2-5 install ok installed liblocale-gettext-perl liblocale-gettext-perl 1.05-7+b1 install ok installed liblzma5:amd64 liblzma5 5.1.1alpha+20120614-2 install ok installed libmount1 libmount1 2.20.1-5.3 install ok installed libncurses5:amd64 libncurses5 5.9-10 install ok installed libpam-modules:amd64 libpam-modules 1.1.3-7.1 install ok installed libpam-modules-bin libpam-modules-bin 1.1.3-7.1 install ok installed libpam-runtime libpam-runtime 1.1.3-7.1 install ok installed libpam0g:amd64 libpam0g 1.1.3-7.1 install ok installed libreadline6:amd64 libreadline6 6.2+dfsg-0.1 install ok installed libselinux1:amd64 libselinux1 2.1.9-5 install ok installed libsemanage-common libsemanage-common 2.1.6-6 install ok installed libsemanage1:amd64 libsemanage1 2.1.6-6 install ok installed libsepol1:amd64 libsepol1 2.1.4-3 install ok installed libslang2:amd64 libslang2 2.2.4-15 install ok installed libss2:amd64 libss2 1.42.5-1.1+deb7u1 install ok installed libstdc++6:amd64 libstdc++6 4.7.2-5 install ok installed libtext-charwidth-perl libtext-charwidth-perl 0.04-7+b1 install ok installed libtext-iconv-perl libtext-iconv-perl 1.7-5 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-7 install ok installed libtinfo5:amd64 libtinfo5 5.9-10 install ok installed libusb-0.1-4:amd64 libusb-0.1-4 2:0.1.12-20+nmu1 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-3 install ok installed libuuid1:amd64 libuuid1 2.20.1-5.3 install ok installed login login 1:4.1.5.1-1 install ok installed lsb-base lsb-base 4.1+Debian8+deb7u1 install ok installed mawk mawk 1.3.3-17 install ok installed mount mount 2.20.1-5.3 install ok installed multiarch-support multiarch-support 2.13-38+deb7u10 install ok installed ncurses-base ncurses-base 5.9-10 install ok installed ncurses-bin ncurses-bin 5.9-10 install ok installed passwd passwd 1:4.1.5.1-1 install ok installed perl-base perl-base 5.14.2-21+deb7u3 install ok installed readline-common readline-common 6.2+dfsg-0.1 install ok installed sed sed 4.2.1-10 install ok installed sensible-utils sensible-utils 0.0.7 install ok installed sysv-rc sysv-rc 2.88dsf-41+deb7u1 install ok installed sysvinit sysvinit 2.88dsf-41+deb7u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-41+deb7u1 install ok installed tar tar 1.26+dfsg-0.1 install ok installed tzdata tzdata 2016d-0+deb7u1 install ok installed ucf ucf 3.0025+nmu3 install ok installed util-linux util-linux 2.20.1-5.3 install ok installed xz-utils xz-utils 5.1.1alpha+20120614-2 install ok installed zlib1g:amd64 zlib1g 1:1.2.7.dfsg-13 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg-divert', '--list'] 0m11.4s 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 local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg-divert', '--list'] 0m11.4s INFO: Running scripts is_testable 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/is_testable_uninstallable'] 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/is_testable_uninstallable'] 0m11.4s INFO: apt-cache does not know about any of the requested packages 0m11.4s INFO: Running scripts pre_test 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_test_exceptions'] 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_test_exceptions'] 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_test_root_password'] 0m11.4s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_test_root_password'] 0m11.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y'] 0m12.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y'] 0m14.5s DEBUG: No broken symlinks as far as we can find. 0m14.5s INFO: Running scripts pre_install 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_install_database-server'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_install_database-server'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_install_exceptions'] 0m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_install_exceptions'] 0m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_install_extras'] 0m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_install_extras'] 0m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_install_foreign_architecture'] 0m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_install_foreign_architecture'] 0m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-cache', 'show', '--no-all-versions', 'python-biopython=1.59-1'] 0m16.1s DUMP: Package: python-biopython Version: 1.59-1 Installed-Size: 5786 Maintainer: Debian Med Packaging Team Architecture: amd64 Replaces: python2.3-biopython (<< 1.42-1), python2.4-biopython (<< 1.42-1) Provides: python2.6-biopython, python2.7-biopython Depends: python (<< 2.8), python (>= 2.6), python-numpy (>= 1:1.4.1), python-numpy-abi9, python-support (>= 0.90.0), libc6 (>= 2.2.5), python-reportlab Recommends: python-biopython-doc (= 1.59-1) Suggests: python-tk, wise, muscle, clustalw, mafft, emboss, blast2 Conflicts: python2.3-biopython (<< 1.42-1), python2.4-biopython (<< 1.42-1) Description-en: Python library for bioinformatics The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology. . It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world. We work along with the Open Bioinformatics Foundation, who generously provide web and CVS space for the project. Homepage: http://biopython.org Description-md5: bacfe9ff423c05fc8056742f7e6c80cd Python-Version: 2.6, 2.7 Tag: devel::lang:python, devel::library, field::biology, field::biology:bioinformatics, implemented-in::python, role::devel-lib, role::shared-lib Section: python Priority: optional Filename: pool/main/p/python-biopython/python-biopython_1.59-1_amd64.deb Size: 1317216 MD5sum: 1b04d312cb0c32d7040bde9cc2a37c21 SHA1: 0376312a63bced640b7c1cac6eb1c9c90322fb13 SHA256: e5dc5516760be996e5ea55e56f91cfb088d69a40359133fac77d9fd2923a226a 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-cache', 'show', '--no-all-versions', 'python-biopython=1.59-1'] 0m16.1s DEBUG: metapackage: Package: piuparts-depends-dummy Version: 0.invalid.0 Architecture: amd64 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: python (<< 2.8), python (>= 2.6), python-numpy (>= 1:1.4.1), python-numpy-abi9, python-support (>= 0.90.0), libc6 (>= 2.2.5), python-reportlab Conflicts: python2.3-biopython (<< 1.42-1), python2.4-biopython (<< 1.42-1) 0m16.1s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpxRsXFi/piuparts-depends-dummy'] 0m16.1s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmpxRsXFi/piuparts-depends-dummy.deb'. 0m16.1s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpxRsXFi/piuparts-depends-dummy'] 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m16.2s DUMP: 0.9.7.9+deb7u7 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m16.2s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmpxRsXFi/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmpbJZl5Y/tmp 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg', '-i', './tmp/piuparts-depends-dummy.deb'] 0m16.2s DUMP: Selecting previously unselected package piuparts-depends-dummy. (Reading database ... 6768 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 python (<< 2.8); however: Package python is not installed. piuparts-depends-dummy depends on python (>= 2.6); however: Package python is not installed. piuparts-depends-dummy depends on python-numpy (>= 1:1.4.1); however: Package python-numpy is not installed. piuparts-depends-dummy depends on python-numpy-abi9; however: Package python-numpy-abi9 is not installed. piuparts-depends-dummy depends on python-support (>= 0.90.0); however: Package python-support is not installed. piuparts-depends-dummy depends on python-reportlab; however: Package python-reportlab is not installed. dpkg: error processing piuparts-depends-dummy (--install): dependency problems - leaving unconfigured Errors were encountered while processing: piuparts-depends-dummy 0m16.2s DEBUG: Command failed (status=1), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg', '-i', './tmp/piuparts-depends-dummy.deb'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-get', '-yf', 'install'] 0m25.7s DUMP: Reading package lists... Building dependency tree... Reading state information... Correcting dependencies... Done The following extra packages will be installed: libblas3 libexpat1 libgfortran3 liblapack3 libncursesw5 libquadmath0 libsqlite3-0 libssl1.0.0 mime-support python python-minimal python-numpy python-reportlab python-support python2.7 python2.7-minimal Suggested packages: python-doc python-tk python-numpy-doc python-numpy-dbg python-nose python-dev gfortran gcc pdf-viewer python-egenix-mxtexttools python-reportlab-doc python2.7-doc binutils binfmt-support Recommended packages: libgpm2 file python-reportlab-accel python-renderpm python-imaging The following NEW packages will be installed: libblas3 libexpat1 libgfortran3 liblapack3 libncursesw5 libquadmath0 libsqlite3-0 libssl1.0.0 mime-support python python-minimal python-numpy python-reportlab python-support python2.7 python2.7-minimal 0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. 1 not fully installed or removed. Need to get 15.8 MB of archives. After this operation, 46.5 MB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ wheezy/main libssl1.0.0 amd64 1.0.1e-2+deb7u20 [1263 kB] Get:2 http://mirror.bm.debian.org/debian/ wheezy/main python2.7-minimal amd64 2.7.3-6+deb7u2 [1785 kB] Get:3 http://mirror.bm.debian.org/debian/ wheezy/main mime-support all 3.52-1+deb7u1 [35.5 kB] Get:4 http://mirror.bm.debian.org/debian/ wheezy/main libexpat1 amd64 2.1.0-1+deb7u2 [139 kB] Get:5 http://mirror.bm.debian.org/debian/ wheezy/main libncursesw5 amd64 5.9-10 [141 kB] Get:6 http://mirror.bm.debian.org/debian/ wheezy/main libsqlite3-0 amd64 3.7.13-1+deb7u2 [454 kB] Get:7 http://mirror.bm.debian.org/debian/ wheezy/main python2.7 amd64 2.7.3-6+deb7u2 [2728 kB] Get:8 http://mirror.bm.debian.org/debian/ wheezy/main python-minimal all 2.7.3-4+deb7u1 [42.8 kB] Get:9 http://mirror.bm.debian.org/debian/ wheezy/main python all 2.7.3-4+deb7u1 [181 kB] Get:10 http://mirror.bm.debian.org/debian/ wheezy/main python-support all 1.0.15 [33.6 kB] Get:11 http://mirror.bm.debian.org/debian/ wheezy/main libquadmath0 amd64 4.7.2-5 [125 kB] Get:12 http://mirror.bm.debian.org/debian/ wheezy/main libgfortran3 amd64 4.7.2-5 [351 kB] Get:13 http://mirror.bm.debian.org/debian/ wheezy/main libblas3 amd64 1.2.20110419-5 [293 kB] Get:14 http://mirror.bm.debian.org/debian/ wheezy/main liblapack3 amd64 3.4.1+dfsg-1+deb70u1 [5036 kB] Get:15 http://mirror.bm.debian.org/debian/ wheezy/main python-numpy amd64 1:1.6.2-1.2 [2632 kB] Get:16 http://mirror.bm.debian.org/debian/ wheezy/main python-reportlab all 2.5-1.1 [572 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 15.8 MB in 0s (21.1 MB/s) Selecting previously unselected package libssl1.0.0:amd64. (Reading database ... 6768 files and directories currently installed.) Unpacking libssl1.0.0:amd64 (from .../libssl1.0.0_1.0.1e-2+deb7u20_amd64.deb) ... Selecting previously unselected package python2.7-minimal. Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3-6+deb7u2_amd64.deb) ... Selecting previously unselected package mime-support. Unpacking mime-support (from .../mime-support_3.52-1+deb7u1_all.deb) ... Selecting previously unselected package libexpat1:amd64. Unpacking libexpat1:amd64 (from .../libexpat1_2.1.0-1+deb7u2_amd64.deb) ... Selecting previously unselected package libncursesw5:amd64. Unpacking libncursesw5:amd64 (from .../libncursesw5_5.9-10_amd64.deb) ... Selecting previously unselected package libsqlite3-0:amd64. Unpacking libsqlite3-0:amd64 (from .../libsqlite3-0_3.7.13-1+deb7u2_amd64.deb) ... Selecting previously unselected package python2.7. Unpacking python2.7 (from .../python2.7_2.7.3-6+deb7u2_amd64.deb) ... Selecting previously unselected package python-minimal. Unpacking python-minimal (from .../python-minimal_2.7.3-4+deb7u1_all.deb) ... Selecting previously unselected package python. Unpacking python (from .../python_2.7.3-4+deb7u1_all.deb) ... Selecting previously unselected package python-support. Unpacking python-support (from .../python-support_1.0.15_all.deb) ... Selecting previously unselected package libquadmath0:amd64. Unpacking libquadmath0:amd64 (from .../libquadmath0_4.7.2-5_amd64.deb) ... Selecting previously unselected package libgfortran3:amd64. Unpacking libgfortran3:amd64 (from .../libgfortran3_4.7.2-5_amd64.deb) ... Selecting previously unselected package libblas3. Unpacking libblas3 (from .../libblas3_1.2.20110419-5_amd64.deb) ... Selecting previously unselected package liblapack3. Unpacking liblapack3 (from .../liblapack3_3.4.1+dfsg-1+deb70u1_amd64.deb) ... Selecting previously unselected package python-numpy. Unpacking python-numpy (from .../python-numpy_1%3a1.6.2-1.2_amd64.deb) ... Selecting previously unselected package python-reportlab. Unpacking python-reportlab (from .../python-reportlab_2.5-1.1_all.deb) ... Setting up libssl1.0.0:amd64 (1.0.1e-2+deb7u20) ... Setting up python2.7-minimal (2.7.3-6+deb7u2) ... Setting up mime-support (3.52-1+deb7u1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode Setting up libexpat1:amd64 (2.1.0-1+deb7u2) ... Setting up libncursesw5:amd64 (5.9-10) ... Setting up libsqlite3-0:amd64 (3.7.13-1+deb7u2) ... Setting up python2.7 (2.7.3-6+deb7u2) ... Setting up python-minimal (2.7.3-4+deb7u1) ... Setting up python (2.7.3-4+deb7u1) ... Setting up python-support (1.0.15) ... Setting up libquadmath0:amd64 (4.7.2-5) ... Setting up libgfortran3:amd64 (4.7.2-5) ... Setting up libblas3 (1.2.20110419-5) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up liblapack3 (3.4.1+dfsg-1+deb70u1) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up python-numpy (1:1.6.2-1.2) ... Setting up python-reportlab (2.5-1.1) ... Setting up piuparts-depends-dummy (0.invalid.0) ... Processing triggers for python-support ... 0m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-get', '-yf', 'install'] 0m25.7s INFO: Installation of ['./tmp/piuparts-depends-dummy.deb'] ok 0m25.7s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmpbJZl5Y/./tmp/piuparts-depends-dummy.deb 0m25.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m25.7s DUMP: piuparts-depends-dummy install ok installed 0m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m25.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m25.7s DUMP: (Reading database ... 8683 files and directories currently installed.) Removing piuparts-depends-dummy ... 0m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m25.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-get', 'clean'] 0m25.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-get', 'clean'] 0m25.8s DEBUG: Recording chroot state 0m27.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y'] 0m29.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y'] 0m31.8s ERROR: WARN: Broken symlinks: /usr/include/python2.6_d/numpy -> ../../lib/pymodules/python2.6/numpy/core/include/numpy /usr/include/python2.6/numpy -> ../../lib/pymodules/python2.6/numpy/core/include/numpy 0m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-cache', 'policy'] 0m33.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror.bm.debian.org/debian/ wheezy/main Translation-en 500 http://mirror.bm.debian.org/debian/ wheezy/main amd64 Packages release v=7.11,o=Debian,a=oldoldstable,n=wheezy,l=Debian,c=main origin mirror.bm.debian.org Pinned packages: 0m33.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-cache', 'policy'] 0m33.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-cache', 'policy', 'python-biopython'] 0m33.4s DUMP: python-biopython: Installed: (none) Candidate: 1.59-1 Version table: 1.59-1 0 500 http://mirror.bm.debian.org/debian/ wheezy/main amd64 Packages 0m33.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-cache', 'policy', 'python-biopython'] 0m33.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-get', '-y', 'install', 'python-biopython=1.59-1'] 0m36.1s DUMP: Reading package lists... Building dependency tree... Reading state information... Suggested packages: python-tk wise muscle clustalw mafft emboss blast2 Recommended packages: python-biopython-doc The following NEW packages will be installed: python-biopython 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 1317 kB of archives. After this operation, 5925 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ wheezy/main python-biopython amd64 1.59-1 [1317 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1317 kB in 0s (10.9 MB/s) Selecting previously unselected package python-biopython. (Reading database ... 8683 files and directories currently installed.) Unpacking python-biopython (from .../python-biopython_1.59-1_amd64.deb) ... Setting up python-biopython (1.59-1) ... Processing triggers for python-support ... 0m36.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-get', '-y', 'install', 'python-biopython=1.59-1'] 0m36.1s INFO: Running scripts post_install 0m36.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_install_exceptions'] 0m36.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_install_exceptions'] 0m36.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y'] 0m37.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y'] 0m40.7s ERROR: WARN: Broken symlinks: /usr/include/python2.6_d/numpy -> ../../lib/pymodules/python2.6/numpy/core/include/numpy /usr/include/python2.6/numpy -> ../../lib/pymodules/python2.6/numpy/core/include/numpy 0m40.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m40.8s DUMP: install ok installed adduser adduser 3.113+nmu3 install ok installed apt apt 0.9.7.9+deb7u7 install ok installed base-files base-files 7.1wheezy11 install ok installed base-passwd base-passwd 3.5.26 install ok installed bash bash 4.2+dfsg-0.1+deb7u3 install ok installed bsdutils bsdutils 1:2.20.1-5.3 install ok installed coreutils coreutils 8.13-3.5 install ok installed dash dash 0.5.7-3 install ok installed debconf debconf 1.5.49 install ok installed debconf-i18n debconf-i18n 1.5.49 install ok installed debian-archive-keyring debian-archive-keyring 2014.3~deb7u1 install ok installed debianutils debianutils 4.3.2 install ok installed diffutils diffutils 1:3.2-6 install ok installed dpkg dpkg 1.16.18 install ok installed e2fslibs:amd64 e2fslibs 1.42.5-1.1+deb7u1 install ok installed e2fsprogs e2fsprogs 1.42.5-1.1+deb7u1 install ok installed findutils findutils 4.4.2-4 install ok installed gcc-4.7-base:amd64 gcc-4.7-base 4.7.2-5 install ok installed gnupg gnupg 1.4.12-7+deb7u7 install ok installed gpgv gpgv 1.4.12-7+deb7u7 install ok installed grep grep 2.12-2 install ok installed gzip gzip 1.5-1.1 install ok installed hostname hostname 3.11 install ok installed initscripts initscripts 2.88dsf-41+deb7u1 install ok installed insserv insserv 1.14.0-5 install ok installed libacl1:amd64 libacl1 2.2.51-8 install ok installed libapt-pkg4.12:amd64 libapt-pkg4.12 0.9.7.9+deb7u7 install ok installed libattr1:amd64 libattr1 1:2.4.46-8 install ok installed libblas3 libblas3 1.2.20110419-5 install ok installed libblkid1:amd64 libblkid1 2.20.1-5.3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-4 install ok installed libc-bin libc-bin 2.13-38+deb7u10 install ok installed libc6:amd64 libc6 2.13-38+deb7u10 install ok installed libcomerr2:amd64 libcomerr2 1.42.5-1.1+deb7u1 install ok installed libdb5.1:amd64 libdb5.1 5.1.29-5 install ok installed libexpat1:amd64 libexpat1 2.1.0-1+deb7u2 install ok installed libgcc1:amd64 libgcc1 1:4.7.2-5 install ok installed libgfortran3:amd64 libgfortran3 4.7.2-5 install ok installed liblapack3 liblapack3 3.4.1+dfsg-1+deb70u1 install ok installed liblocale-gettext-perl liblocale-gettext-perl 1.05-7+b1 install ok installed liblzma5:amd64 liblzma5 5.1.1alpha+20120614-2 install ok installed libmount1 libmount1 2.20.1-5.3 install ok installed libncurses5:amd64 libncurses5 5.9-10 install ok installed libncursesw5:amd64 libncursesw5 5.9-10 install ok installed libpam-modules:amd64 libpam-modules 1.1.3-7.1 install ok installed libpam-modules-bin libpam-modules-bin 1.1.3-7.1 install ok installed libpam-runtime libpam-runtime 1.1.3-7.1 install ok installed libpam0g:amd64 libpam0g 1.1.3-7.1 install ok installed libquadmath0:amd64 libquadmath0 4.7.2-5 install ok installed libreadline6:amd64 libreadline6 6.2+dfsg-0.1 install ok installed libselinux1:amd64 libselinux1 2.1.9-5 install ok installed libsemanage-common libsemanage-common 2.1.6-6 install ok installed libsemanage1:amd64 libsemanage1 2.1.6-6 install ok installed libsepol1:amd64 libsepol1 2.1.4-3 install ok installed libslang2:amd64 libslang2 2.2.4-15 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.7.13-1+deb7u2 install ok installed libss2:amd64 libss2 1.42.5-1.1+deb7u1 install ok installed libssl1.0.0:amd64 libssl1.0.0 1.0.1e-2+deb7u20 install ok installed libstdc++6:amd64 libstdc++6 4.7.2-5 install ok installed libtext-charwidth-perl libtext-charwidth-perl 0.04-7+b1 install ok installed libtext-iconv-perl libtext-iconv-perl 1.7-5 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-7 install ok installed libtinfo5:amd64 libtinfo5 5.9-10 install ok installed libusb-0.1-4:amd64 libusb-0.1-4 2:0.1.12-20+nmu1 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-3 install ok installed libuuid1:amd64 libuuid1 2.20.1-5.3 install ok installed login login 1:4.1.5.1-1 install ok installed lsb-base lsb-base 4.1+Debian8+deb7u1 install ok installed mawk mawk 1.3.3-17 install ok installed mime-support mime-support 3.52-1+deb7u1 install ok installed mount mount 2.20.1-5.3 install ok installed multiarch-support multiarch-support 2.13-38+deb7u10 install ok installed ncurses-base ncurses-base 5.9-10 install ok installed ncurses-bin ncurses-bin 5.9-10 install ok installed passwd passwd 1:4.1.5.1-1 install ok installed perl-base perl-base 5.14.2-21+deb7u3 install ok installed python python 2.7.3-4+deb7u1 install ok installed python-biopython python-biopython 1.59-1 install ok installed python-minimal python-minimal 2.7.3-4+deb7u1 install ok installed python-numpy python-numpy 1:1.6.2-1.2 install ok installed python-reportlab python-reportlab 2.5-1.1 install ok installed python-support python-support 1.0.15 install ok installed python2.7 python2.7 2.7.3-6+deb7u2 install ok installed python2.7-minimal python2.7-minimal 2.7.3-6+deb7u2 install ok installed readline-common readline-common 6.2+dfsg-0.1 install ok installed sed sed 4.2.1-10 install ok installed sensible-utils sensible-utils 0.0.7 install ok installed sysv-rc sysv-rc 2.88dsf-41+deb7u1 install ok installed sysvinit sysvinit 2.88dsf-41+deb7u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-41+deb7u1 install ok installed tar tar 1.26+dfsg-0.1 install ok installed tzdata tzdata 2016d-0+deb7u1 install ok installed ucf ucf 3.0025+nmu3 install ok installed util-linux util-linux 2.20.1-5.3 install ok installed xz-utils xz-utils 5.1.1alpha+20120614-2 install ok installed zlib1g:amd64 zlib1g 1:1.2.7.dfsg-13 0m40.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m42.2s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', '-ac', '--ignore-obsolete'] 0m43.8s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', '-ac', '--ignore-obsolete'] 0m43.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m43.9s DUMP: 0.15.1 0m43.9s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m43.9s INFO: Running adequate version 0.15.1 now. 0m43.9s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'python-biopython'] 0m44.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'python-biopython'] 0m44.1s INFO: Running scripts pre_remove 0m44.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m44.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m44.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m44.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m44.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m45.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m45.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m45.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m45.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_remove_exceptions'] 0m45.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/pre_remove_exceptions'] 0m45.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-get', 'remove', 'liblapack3', 'libblas3', 'python', 'python2.7', 'libexpat1:amd64', 'python-numpy', 'libssl1.0.0:amd64', 'libncursesw5:amd64', 'python2.7-minimal', 'python-reportlab', 'python-support', 'libquadmath0:amd64', 'mime-support', 'libgfortran3:amd64', 'python-minimal', 'libsqlite3-0:amd64', 'python-biopython'] 0m47.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libblas3 libexpat1 libgfortran3 liblapack3 libncursesw5 libquadmath0 libsqlite3-0 libssl1.0.0 mime-support python python-biopython python-minimal python-numpy python-reportlab python-support python2.7 python2.7-minimal 0 upgraded, 0 newly installed, 17 to remove and 0 not upgraded. After this operation, 52.5 MB disk space will be freed. (Reading database ... 9213 files and directories currently installed.) Removing python-biopython ... Removing python-numpy ... Removing liblapack3 ... Removing libblas3 ... Removing python-reportlab ... Removing python-support ... Removing python ... Removing python2.7 ... Removing libexpat1:amd64 ... Removing libgfortran3:amd64 ... Removing libncursesw5:amd64 ... Removing libquadmath0:amd64 ... Removing libsqlite3-0:amd64 ... Removing python-minimal ... Removing python2.7-minimal ... Removing libssl1.0.0:amd64 ... Removing mime-support ... 0m47.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-get', 'remove', 'liblapack3', 'libblas3', 'python', 'python2.7', 'libexpat1:amd64', 'python-numpy', 'libssl1.0.0:amd64', 'libncursesw5:amd64', 'python2.7-minimal', 'python-reportlab', 'python-support', 'libquadmath0:amd64', 'mime-support', 'libgfortran3:amd64', 'python-minimal', 'libsqlite3-0:amd64', 'python-biopython'] 0m47.5s INFO: Running scripts post_remove 0m47.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_remove_exceptions'] 0m47.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_remove_exceptions'] 0m47.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_remove_extras'] 0m47.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_remove_extras'] 0m47.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg', '--purge', 'liblapack3', 'libblas3', 'python', 'python2.7', 'libexpat1:amd64', 'python-numpy', 'libssl1.0.0:amd64', 'libncursesw5:amd64', 'python2.7-minimal', 'python-reportlab', 'python-support', 'libquadmath0:amd64', 'mime-support', 'libgfortran3:amd64', 'python-minimal', 'libsqlite3-0:amd64'] 0m48.0s DUMP: (Reading database ... 6773 files and directories currently installed.) Removing liblapack3 ... Purging configuration files for liblapack3 ... dpkg: warning: ignoring request to remove libblas3 which isn't installed Removing python ... Purging configuration files for python ... Removing python2.7 ... Purging configuration files for python2.7 ... Removing libexpat1:amd64 ... Purging configuration files for libexpat1:amd64 ... dpkg: warning: ignoring request to remove python-numpy which isn't installed Removing libssl1.0.0:amd64 ... Purging configuration files for libssl1.0.0:amd64 ... Removing libncursesw5:amd64 ... Purging configuration files for libncursesw5:amd64 ... Removing python2.7-minimal ... Purging configuration files for python2.7-minimal ... dpkg: warning: ignoring request to remove python-reportlab which isn't installed Removing python-support ... Purging configuration files for python-support ... Removing libquadmath0:amd64 ... Purging configuration files for libquadmath0:amd64 ... Removing mime-support ... Purging configuration files for mime-support ... Removing libgfortran3:amd64 ... Purging configuration files for libgfortran3:amd64 ... dpkg: warning: ignoring request to remove python-minimal which isn't installed Removing libsqlite3-0:amd64 ... Purging configuration files for libsqlite3-0:amd64 ... 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg', '--purge', 'liblapack3', 'libblas3', 'python', 'python2.7', 'libexpat1:amd64', 'python-numpy', 'libssl1.0.0:amd64', 'libncursesw5:amd64', 'python2.7-minimal', 'python-reportlab', 'python-support', 'libquadmath0:amd64', 'mime-support', 'libgfortran3:amd64', 'python-minimal', 'libsqlite3-0:amd64'] 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg', '--purge', 'python-biopython'] 0m48.0s DUMP: dpkg: warning: ignoring request to remove python-biopython which isn't installed 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg', '--purge', 'python-biopython'] 0m48.0s INFO: Running scripts post_purge 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_purge_exceptions'] 0m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_purge_exceptions'] 0m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg', '--purge', '--pending'] 0m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg', '--purge', '--pending'] 0m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg', '--remove', '--pending'] 0m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg', '--remove', '--pending'] 0m48.1s INFO: Running scripts post_test 0m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_test_exceptions'] 0m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'tmp/scripts/post_test_exceptions'] 0m48.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y'] 0m49.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y'] 0m51.0s DEBUG: No broken symlinks as far as we can find. 0m51.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg-divert', '--list'] 0m51.0s 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 local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m51.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'dpkg-divert', '--list'] 0m51.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-get', 'clean'] 0m51.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y', 'apt-get', 'clean'] 0m51.0s DEBUG: Recording chroot state 0m53.8s INFO: PASS: Installation and purging test. 0m54.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/run/shm'] 0m55.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/run/shm'] 0m55.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/dev/console'] 0m55.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/dev/console'] 0m55.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/dev/ptmx'] 0m55.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/dev/ptmx'] 0m55.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/dev/pts'] 0m55.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/dev/pts'] 0m55.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/proc'] 0m55.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y/proc'] 0m55.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y'] 0m55.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpbJZl5Y'] 0m55.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpbJZl5Y 0m55.3s INFO: PASS: All tests. 0m55.3s INFO: piuparts run ends. ret=0 End: 2018-08-11 00:11:18 UTC