Start: 2018-02-12 20:44:53 UTC Package: mira-assembler Source: mira Version: 3.4.0.1-3 Installed-Size: 8087 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libboost-regex1.49.0 (>= 1.49.0-1), libboost-thread1.49.0 (>= 1.49.0-1), libc6 (>= 2.3.2), libexpat1 (>= 2.0.1), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.6), libtcmalloc-minimal4, zlib1g (>= 1:1.1.4) Suggests: mira-examples, mira-doc Description: Whole Genome Shotgun and EST Sequence Assembler Homepage: http://chevreux.org/projects_mira.html Description-md5: dc1bc48d28cd89e7841bc54ff8d3b7b2 Tag: role::program Section: science Priority: optional Filename: pool/main/m/mira/mira-assembler_3.4.0.1-3_amd64.deb Size: 3666718 MD5sum: 7be62d6df83a4e0c50fbee387a03f3a7 SHA1: 2c99ee707859c0bb4278a906c4c95b4faaf01cfc SHA256: 23aa4e58d59bb6c2ee1cf080daea4d24a0ad75b6aebb6382f6f3dc98b711a990 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 mira-assembler=3.4.0.1-3 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 0.84~201801121530~0.83-4-g6e16ed9a 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 mira-assembler=3.4.0.1-3 0m0.0s INFO: Running on: Linux piu-slave-bm-a 4.9.0-5-amd64 #1 SMP Debian 4.9.65-3+deb9u2 (2018-01-04) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpfRUL4E 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpfRUL4E 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz'] 0m1.9s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/proc'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/proc'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/dev/pts'] 0m2.0s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/dev/pts'] 0m2.0s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/dev/ptmx'] 0m2.0s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/dev/ptmx'] 0m2.0s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/dev/console'] 0m2.0s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/dev/console'] 0m2.0s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/run/shm'] 0m2.0s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/run/shm'] 0m2.0s DEBUG: sources.list: deb http://mirror.bm.debian.org/debian/ wheezy main 0m2.0s DEBUG: Created policy-rc.d and chmodded it. 0m2.0s DEBUG: Created resolv.conf. 0m2.0s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpfRUL4E/tmp/scripts/ 0m2.0s DEBUG: Copying scriptsdir /etc/piuparts/scripts-wheezy to /srv/piuparts.debian.org/tmp/tmpfRUL4E/tmp/scripts/ 0m2.0s INFO: Running scripts post_chroot_unpack 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-get', 'update'] 0m4.8s 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... 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-get', 'update'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-get', '-yf', 'dist-upgrade'] 0m5.3s DUMP: Reading package lists... Building dependency tree... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-get', '-yf', 'dist-upgrade'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.7s DUMP: 0c96df6df725ee7ec7aebd2b6a77fb72 - 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.7s INFO: Running scripts post_setup 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_setup_dummy_users'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_setup_dummy_users'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_setup_experimental'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_setup_experimental'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_setup_forbid_home'] 0m7.2s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_setup_forbid_home'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.3s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' `/bin/sync' -> `true' 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_setup_minimize'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_setup_minimize'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_setup_wheezy-fake-essential'] 0m8.6s DUMP: *** Adding fake essential packages *** Reading package lists... Building dependency tree... Suggested packages: perl-modules The following NEW packages will be installed: adduser ucf 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 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 (11.7 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) ... 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_setup_wheezy-fake-essential'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_setup_zz_backports'] 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_setup_zz_backports'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-get', 'clean'] 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-get', 'clean'] 0m8.7s DEBUG: Recording chroot state 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m10.6s 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 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg-divert', '--list'] 0m10.6s 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 local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg-divert', '--list'] 0m10.6s INFO: Running scripts is_testable 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/is_testable_uninstallable'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/is_testable_uninstallable'] 0m10.6s INFO: apt-cache does not know about any of the requested packages 0m10.6s INFO: Running scripts pre_test 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_test_exceptions'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_test_exceptions'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_test_root_password'] 0m10.7s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_test_root_password'] 0m10.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfRUL4E'] 0m11.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfRUL4E'] 0m13.5s DEBUG: No broken symlinks as far as we can find. 0m13.5s INFO: Running scripts pre_install 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_install_database-server'] 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_install_database-server'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_install_exceptions'] 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_install_exceptions'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_install_extras'] 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_install_extras'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_install_foreign_architecture'] 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_install_foreign_architecture'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-cache', 'show', 'mira-assembler=3.4.0.1-3'] 0m15.1s DUMP: Package: mira-assembler Source: mira Version: 3.4.0.1-3 Installed-Size: 8087 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libboost-regex1.49.0 (>= 1.49.0-1), libboost-thread1.49.0 (>= 1.49.0-1), libc6 (>= 2.3.2), libexpat1 (>= 2.0.1), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.6), libtcmalloc-minimal4, zlib1g (>= 1:1.1.4) Suggests: mira-examples, mira-doc Description-en: Whole Genome Shotgun and EST Sequence Assembler The mira genome fragment assembler is a specialised assembler for sequencing projects classified as 'hard' due to high number of similar repeats. For expressed sequence tags (ESTs) transcripts, miraEST is specialised on reconstructing pristine mRNA transcripts while detecting and classifying single nucleotide polymorphisms (SNP) occuring in different variations thereof. . The assembler is routinely used for such various tasks as mutation detection in different cell types, similarity analysis of transcripts between organisms, and pristine assembly of sequences from various sources for oligo design in clinical microarray experiments. . The package provides the following executables: Binaries provided: * mira: for assembly of genome sequences * miramem: estimating memory needed to assemble projects. Realised through link to mira. * convert_project: for converting project file types into other types * caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some frequently used file converters (realised through links to convert_project) * scftool: set of tools useful when working with SCF trace files * fastatool: set of tools useful when working with FASTA trace files . Scripts provided: * fasta2frag.tcl: fragmenting sequences into smaller, overlapping subsequences. Useful for simulating shotgun sequences. Can create subsequences in both directions (/default) and also paired-end sequences. * fastaselect.tcl: given a FASTA file (and possibly a FASTA quality file) and a file with names of reads, select the sequences from the input FASTA (and quality file) and writes them to an output FASTA * fastqselect.tcl: like fastaselect.tcl, only for FASTQ * fixACE4consed.tcl: Consed has a bug which incapacitates it from reading consensus tags in ACE files written by the MIRA assembler (and possibly other programs). This script massages an ACE file so that consed can read the consensus tags. Homepage: http://chevreux.org/projects_mira.html Description-md5: dc1bc48d28cd89e7841bc54ff8d3b7b2 Tag: role::program Section: science Priority: optional Filename: pool/main/m/mira/mira-assembler_3.4.0.1-3_amd64.deb Size: 3666718 MD5sum: 7be62d6df83a4e0c50fbee387a03f3a7 SHA1: 2c99ee707859c0bb4278a906c4c95b4faaf01cfc SHA256: 23aa4e58d59bb6c2ee1cf080daea4d24a0ad75b6aebb6382f6f3dc98b711a990 0m15.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-cache', 'show', 'mira-assembler=3.4.0.1-3'] 0m15.1s 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: libboost-regex1.49.0 (>= 1.49.0-1), libboost-thread1.49.0 (>= 1.49.0-1), libc6 (>= 2.3.2), libexpat1 (>= 2.0.1), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.6), libtcmalloc-minimal4, zlib1g (>= 1:1.1.4) 0m15.1s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpy7L7oC/piuparts-depends-dummy'] 0m15.1s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmpy7L7oC/piuparts-depends-dummy.deb'. 0m15.1s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpy7L7oC/piuparts-depends-dummy'] 0m15.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m15.2s DUMP: 0.9.7.9+deb7u7 0m15.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m15.2s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmpy7L7oC/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmpfRUL4E/tmp 0m15.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg', '-i', './tmp/piuparts-depends-dummy.deb'] 0m15.2s 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 libboost-regex1.49.0 (>= 1.49.0-1); however: Package libboost-regex1.49.0 is not installed. piuparts-depends-dummy depends on libboost-thread1.49.0 (>= 1.49.0-1); however: Package libboost-thread1.49.0 is not installed. piuparts-depends-dummy depends on libexpat1 (>= 2.0.1); however: Package libexpat1 is not installed. piuparts-depends-dummy depends on libtcmalloc-minimal4; however: Package libtcmalloc-minimal4 is not installed. dpkg: error processing piuparts-depends-dummy (--install): dependency problems - leaving unconfigured Errors were encountered while processing: piuparts-depends-dummy 0m15.2s DEBUG: Command failed (status=1), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg', '-i', './tmp/piuparts-depends-dummy.deb'] 0m15.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-get', '-yf', 'install'] 0m17.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Correcting dependencies... Done The following extra packages will be installed: libboost-regex1.49.0 libboost-thread1.49.0 libexpat1 libicu48 libtcmalloc-minimal4 The following NEW packages will be installed: libboost-regex1.49.0 libboost-thread1.49.0 libexpat1 libicu48 libtcmalloc-minimal4 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 1 not fully installed or removed. Need to get 5601 kB of archives. After this operation, 24.5 MB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ wheezy/main libicu48 amd64 4.8.1.1-12+deb7u3 [4761 kB] Get:2 http://mirror.bm.debian.org/debian/ wheezy/main libboost-regex1.49.0 amd64 1.49.0-3.2 [459 kB] Get:3 http://mirror.bm.debian.org/debian/ wheezy/main libboost-thread1.49.0 amd64 1.49.0-3.2 [64.0 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 libtcmalloc-minimal4 amd64 2.0-2 [177 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 5601 kB in 0s (25.7 MB/s) Selecting previously unselected package libicu48:amd64. (Reading database ... 6768 files and directories currently installed.) Unpacking libicu48:amd64 (from .../libicu48_4.8.1.1-12+deb7u3_amd64.deb) ... Selecting previously unselected package libboost-regex1.49.0. Unpacking libboost-regex1.49.0 (from .../libboost-regex1.49.0_1.49.0-3.2_amd64.deb) ... Selecting previously unselected package libboost-thread1.49.0. Unpacking libboost-thread1.49.0 (from .../libboost-thread1.49.0_1.49.0-3.2_amd64.deb) ... Selecting previously unselected package libexpat1:amd64. Unpacking libexpat1:amd64 (from .../libexpat1_2.1.0-1+deb7u2_amd64.deb) ... Selecting previously unselected package libtcmalloc-minimal4. Unpacking libtcmalloc-minimal4 (from .../libtcmalloc-minimal4_2.0-2_amd64.deb) ... Setting up libicu48:amd64 (4.8.1.1-12+deb7u3) ... Setting up libboost-regex1.49.0 (1.49.0-3.2) ... Setting up libboost-thread1.49.0 (1.49.0-3.2) ... Setting up libexpat1:amd64 (2.1.0-1+deb7u2) ... Setting up libtcmalloc-minimal4 (2.0-2) ... Setting up piuparts-depends-dummy (0.invalid.0) ... 0m17.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-get', '-yf', 'install'] 0m17.5s INFO: Installation of ['./tmp/piuparts-depends-dummy.deb'] ok 0m17.5s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmpfRUL4E/./tmp/piuparts-depends-dummy.deb 0m17.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m17.5s DUMP: piuparts-depends-dummy install ok installed 0m17.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m17.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m17.6s DUMP: (Reading database ... 6823 files and directories currently installed.) Removing piuparts-depends-dummy ... 0m17.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m17.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-get', 'clean'] 0m17.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-get', 'clean'] 0m17.6s DEBUG: Recording chroot state 0m19.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfRUL4E'] 0m20.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfRUL4E'] 0m22.2s DEBUG: No broken symlinks as far as we can find. 0m22.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-cache', 'policy'] 0m23.7s 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: 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-cache', 'policy'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-cache', 'policy', 'mira-assembler'] 0m23.7s DUMP: mira-assembler: Installed: (none) Candidate: 3.4.0.1-3 Version table: 3.4.0.1-3 0 500 http://mirror.bm.debian.org/debian/ wheezy/main amd64 Packages 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-cache', 'policy', 'mira-assembler'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-get', '-y', 'install', 'mira-assembler=3.4.0.1-3'] 0m24.9s DUMP: Reading package lists... Building dependency tree... Reading state information... Suggested packages: mira-examples mira-doc The following NEW packages will be installed: mira-assembler 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 3667 kB of archives. After this operation, 8281 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ wheezy/main mira-assembler amd64 3.4.0.1-3 [3667 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3667 kB in 0s (22.0 MB/s) Selecting previously unselected package mira-assembler. (Reading database ... 6823 files and directories currently installed.) Unpacking mira-assembler (from .../mira-assembler_3.4.0.1-3_amd64.deb) ... Setting up mira-assembler (3.4.0.1-3) ... 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-get', '-y', 'install', 'mira-assembler=3.4.0.1-3'] 0m24.9s INFO: Running scripts post_install 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_install_exceptions'] 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_install_exceptions'] 0m24.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfRUL4E'] 0m25.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfRUL4E'] 0m27.6s DEBUG: No broken symlinks as far as we can find. 0m27.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m27.7s 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 libboost-regex1.49.0 libboost-regex1.49.0 1.49.0-3.2 install ok installed libboost-thread1.49.0 libboost-thread1.49.0 1.49.0-3.2 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 libicu48:amd64 libicu48 4.8.1.1-12+deb7u3 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 libtcmalloc-minimal4 libtcmalloc-minimal4 2.0-2 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 mira-assembler mira-assembler 3.4.0.1-3 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 0m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m28.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', '-ac', '--ignore-obsolete'] 0m29.9s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', '-ac', '--ignore-obsolete'] 0m29.9s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m29.9s DUMP: 0.15.1 0m29.9s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m29.9s INFO: Running adequate version 0.15.1 now. 0m29.9s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'mira-assembler'] 0m30.3s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'mira-assembler'] 0m30.3s INFO: Running scripts pre_remove 0m30.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m30.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m30.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m31.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m31.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m31.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m31.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m31.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m31.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_remove_exceptions'] 0m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/pre_remove_exceptions'] 0m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-get', 'remove', 'libboost-thread1.49.0', 'libtcmalloc-minimal4', 'libicu48:amd64', 'libexpat1:amd64', 'libboost-regex1.49.0', 'mira-assembler'] 0m32.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libboost-regex1.49.0 libboost-thread1.49.0 libexpat1 libicu48 libtcmalloc-minimal4 mira-assembler 0 upgraded, 0 newly installed, 6 to remove and 0 not upgraded. After this operation, 32.8 MB disk space will be freed. (Reading database ... 6849 files and directories currently installed.) Removing mira-assembler ... Removing libboost-regex1.49.0 ... Removing libboost-thread1.49.0 ... Removing libexpat1:amd64 ... Removing libicu48:amd64 ... Removing libtcmalloc-minimal4 ... 0m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-get', 'remove', 'libboost-thread1.49.0', 'libtcmalloc-minimal4', 'libicu48:amd64', 'libexpat1:amd64', 'libboost-regex1.49.0', 'mira-assembler'] 0m32.9s INFO: Running scripts post_remove 0m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_remove_exceptions'] 0m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_remove_exceptions'] 0m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_remove_extras'] 0m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_remove_extras'] 0m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg', '--purge', 'libboost-thread1.49.0', 'libtcmalloc-minimal4', 'libicu48:amd64', 'libexpat1:amd64', 'libboost-regex1.49.0'] 0m33.0s DUMP: (Reading database ... 6768 files and directories currently installed.) Removing libboost-thread1.49.0 ... Purging configuration files for libboost-thread1.49.0 ... Removing libtcmalloc-minimal4 ... Purging configuration files for libtcmalloc-minimal4 ... Removing libicu48:amd64 ... Purging configuration files for libicu48:amd64 ... Removing libexpat1:amd64 ... Purging configuration files for libexpat1:amd64 ... Removing libboost-regex1.49.0 ... Purging configuration files for libboost-regex1.49.0 ... 0m33.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg', '--purge', 'libboost-thread1.49.0', 'libtcmalloc-minimal4', 'libicu48:amd64', 'libexpat1:amd64', 'libboost-regex1.49.0'] 0m33.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg', '--purge', 'mira-assembler'] 0m33.0s DUMP: dpkg: warning: ignoring request to remove mira-assembler which isn't installed 0m33.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg', '--purge', 'mira-assembler'] 0m33.0s INFO: Running scripts post_purge 0m33.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_purge_exceptions'] 0m33.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_purge_exceptions'] 0m33.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg', '--purge', '--pending'] 0m33.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg', '--purge', '--pending'] 0m33.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg', '--remove', '--pending'] 0m33.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg', '--remove', '--pending'] 0m33.1s INFO: Running scripts post_test 0m33.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_test_exceptions'] 0m33.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'tmp/scripts/post_test_exceptions'] 0m33.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfRUL4E'] 0m34.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfRUL4E'] 0m35.7s DEBUG: No broken symlinks as far as we can find. 0m35.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg-divert', '--list'] 0m35.7s 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 0m35.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'dpkg-divert', '--list'] 0m35.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-get', 'clean'] 0m35.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfRUL4E', 'apt-get', 'clean'] 0m35.8s DEBUG: Recording chroot state 0m38.2s INFO: PASS: Installation and purging test. 0m39.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/run/shm'] 0m39.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/run/shm'] 0m39.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/dev/console'] 0m39.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/dev/console'] 0m39.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/dev/ptmx'] 0m39.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/dev/ptmx'] 0m39.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/dev/pts'] 0m39.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/dev/pts'] 0m39.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/proc'] 0m39.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfRUL4E/proc'] 0m39.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpfRUL4E'] 0m39.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpfRUL4E'] 0m39.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpfRUL4E 0m39.6s INFO: PASS: All tests. 0m39.6s INFO: piuparts run ends. ret=0 End: 2018-02-12 20:45:33 UTC