Start: 2018-08-17 13:08:17 UTC Package: med-bio Source: debian-med Version: 1.13.2 Installed-Size: 101 Maintainer: Debian Med Packaging Team Architecture: all Depends: med-tasks (= 1.13.2), med-config (= 1.13.2) Recommends: abacas, acedb-other, acedb-other-belvu, acedb-other-dotter, adun.app, alien-hunter, altree, amap-align, ampliconnoise, autodock, autodock-vina, autogrid, ballview, bedtools, biomaj, blast2, bowtie, bowtie2, boxshade, bwa, cd-hit, clonalframe, clustalo, clustalw, clustalx, dialign, dialign-tx, disulfinder, dotur, dssp, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, exonerate, fastdnaml, fastlink, fasttree, fastx-toolkit, ffindex, figtree, filo, gamgi, garlic, gbrowse, gdpc, gentle, gff2aplot, gff2ps, ghemical, glam2, grinder, gromacs, hhsuite, hmmer, infernal, jalview, jellyfish, jmol, kalign, last-align, librg-utils-perl, loki, mafft, maq, maqview, massxpert, melting, mipe, mira-assembler, mlv-smile, mothur, mrbayes, mummer, muscle, mustang, ncbi-blast+, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, ncoils, neobio, njplot, perlprimer, phyml, picard-tools, plasmidomics, plink, poa, populations, primer3, probalign, probcons, proda, profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun, profphd, profphd-net, profphd-utils, proftmb, pymol, pynast, python-cogent, qiime, r-bioc-cummerbund, r-bioc-hilbertvis, r-cran-genabel, r-cran-qtl, r-other-bio3d, r-other-mott-happy, rasmol, raster3d, raxml, readseq, reprof, rnahybrid, samtools, sibsim4, sigma-align, sim4, squizz, sra-toolkit, ssake, staden-io-lib-utils, t-coffee, tabix, theseus, tigr-glimmer, tm-align, transtermhp, tree-puzzle | tree-ppuzzle, treeviewx, vcftools, velvet, wise Suggests: abyss, act, amos-assembler, amoscmp, anfo, apollo, arachne, arb, artemis, asap, augustus, autodocktools, axparafit, axpcoords, bagphenotype, bambus, bamtools, beads, beast-mcmc, big-blast, bigsdb, blimps-utils, blixem, btk-core, cactus, caftools, cain, cap3, cdbfasta, cdna-db, cinema, circos, clonalorigin, clustalw-mpi, cluster3, cmap, coalesce, codonw, compclust, concavity, conservation-code, contralign, coot, copycat, crossbow, cufflinks, cytoscape, das-proserver, dazzle, decipher, e-hive, ecell, edtsurf, eigensoft, elph, embassy-phylip, emboss-explorer, ensembl, est-db, estferret, estscan, exalt, excavator, fas, fasta, fastqc, figaro, finex, fluctuate, forester, forge, galaxy, gassst, gbioseq, gbrowse-syn, genemark, genesplicer, genetrack, genezilla, genographer, genometools, glimmerhmm, gmap, gmv, grogui, haploview, hawkeye, hexamer, hilbertvisgui, hmmer2, igv, jbrowse, jigsaw, jstreeview, kempbasu, lagan, lamarc, logol-bin, logomat-m, ltrsift, lucy, macs, mage2tab, maker2, martj, maude, mauvealigner, maxd, melting-gui, meme, mesquite, metarep, microbiomeutil, migrate, minimus, mirbase, mobyle, molekel, mosaik-aligner, mozilla-biofox, mpsqed, msatfinder, mugsy, mummergpu, murasaki, mview, ncbi-seg, ngila, norsnet, norsp, nw-align, oases, obo-edit, oligoarrayaux, omegamap, operondb, pal2nal, paml, partigene, patman, patristic, pcma, pdb2pqr, pfaat, pftools, phagefinder, phpphylotree, phy-spread, phylip, phylographer, phyloviz-core, phylowin, plato, prank, predictnls, predictprotein, proalign, profbval, profisis, profit, prot4est, pscan-tfbs, psipred, pyrophosphate-tools, python-orange, python-rdkit, python-reaper, qtlcart, r-ape, r-other-valdar-bagphenotype.library, raccoon, ray-denovoassembler, rbs-finder, rdp-classifier, recombine, repeatmasker, rmblast, roche454ace2caf, rose, rosetta, sap, seaview, seq-gen, seqan-apps, seqtk, sequenceconverter.app, sga, sift, smalt, snap, snpeff, soapdenovo, spice, splitstree, spread-phy, sra-sdk, ssaha, strap, tacg, taverna, taxinspector, tetra, tigr-assembler, tigr-glimmer-mg, tophat, trace2dbest, tracetuner, treebuilder3d, treetime, treeview, tripal, trnascan-se, twain, ugene, uniprime, vegan, vienna-rna, vmd, wgs-assembler, x-tandem-pipeline, zalign, zodiac-zeden Description: Debian Med micro-biology packages Description-md5: ed5c52e97fd9de45bfcf8410b31c75c4 Tag: field::biology, role::metapackage, suite::debian Section: misc Priority: extra Filename: pool/main/d/debian-med/med-bio_1.13.2_all.deb Size: 20540 MD5sum: e30ce877fb1a63d6565521fd054130dc SHA1: acdbc6c16f62a24af63bd9a1c126aee96198015d SHA256: 138146b21e818ebb230ab5a97d0b13dcc58fd66601e858d6231a1b88aab034fc 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-ubc.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 med-bio=1.13.2 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-ubc.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 med-bio=1.13.2 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 4.9.0-7-amd64 #1 SMP Debian 4.9.110-3+deb9u2 (2018-08-13) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpX0oUlp 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpX0oUlp 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz'] 0m1.8s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz'] 0m1.8s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/proc'] 0m1.8s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/proc'] 0m1.8s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/dev/pts'] 0m1.8s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/dev/pts'] 0m1.8s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/dev/ptmx'] 0m1.8s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/dev/ptmx'] 0m1.8s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/dev/console'] 0m1.8s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/dev/console'] 0m1.8s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/run/shm'] 0m1.8s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/run/shm'] 0m1.8s DEBUG: sources.list: deb http://mirror-ubc.debian.org/debian/ wheezy main 0m1.8s DEBUG: Created policy-rc.d and chmodded it. 0m1.8s DEBUG: Created resolv.conf. 0m1.8s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpX0oUlp/tmp/scripts/ 0m1.8s DEBUG: Copying scriptsdir /etc/piuparts/scripts-wheezy to /srv/piuparts.debian.org/tmp/tmpX0oUlp/tmp/scripts/ 0m1.8s INFO: Running scripts post_chroot_unpack 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-get', 'update'] 0m4.0s DUMP: Hit http://mirror-ubc.debian.org wheezy Release.gpg Hit http://mirror-ubc.debian.org wheezy Release Hit http://mirror-ubc.debian.org wheezy/main amd64 Packages Hit http://mirror-ubc.debian.org wheezy/main Translation-en Reading package lists... 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-get', 'update'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-get', '-yf', 'dist-upgrade'] 0m4.2s DUMP: Reading package lists... Building dependency tree... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-get', '-yf', 'dist-upgrade'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.4s DUMP: 0c96df6df725ee7ec7aebd2b6a77fb72 - 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.4s INFO: Running scripts post_setup 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_setup_dummy_users'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_setup_dummy_users'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_setup_forbid_home'] 0m5.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_setup_forbid_home'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.3s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' `/bin/sync' -> `true' 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_setup_minimize'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_setup_minimize'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_setup_wheezy-fake-essential'] 0m6.2s 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-ubc.debian.org/debian/ wheezy/main adduser all 3.113+nmu3 [264 kB] Get:2 http://mirror-ubc.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 (22.5 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) ... 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_setup_wheezy-fake-essential'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_setup_zz_backports'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_setup_zz_backports'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-get', 'clean'] 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-get', 'clean'] 0m6.3s DEBUG: Recording chroot state 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.1s 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 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg-divert', '--list'] 0m7.1s DUMP: diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg-divert', '--list'] 0m7.1s INFO: Running scripts is_testable 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/is_testable_uninstallable'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/is_testable_uninstallable'] 0m7.2s INFO: apt-cache does not know about any of the requested packages 0m7.2s INFO: Running scripts pre_test 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_test_exceptions'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_test_exceptions'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_test_root_password'] 0m7.2s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_test_root_password'] 0m7.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpX0oUlp'] 0m7.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpX0oUlp'] 0m8.3s DEBUG: No broken symlinks as far as we can find. 0m8.3s INFO: Running scripts pre_install 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_install_database-server'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_install_database-server'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_install_exceptions'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_install_exceptions'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_install_extras'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_install_extras'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-cache', 'show', '--no-all-versions', 'med-bio=1.13.2'] 0m9.6s DUMP: Package: med-bio Source: debian-med Version: 1.13.2 Installed-Size: 101 Maintainer: Debian Med Packaging Team Architecture: all Depends: med-tasks (= 1.13.2), med-config (= 1.13.2) Recommends: abacas, acedb-other, acedb-other-belvu, acedb-other-dotter, adun.app, alien-hunter, altree, amap-align, ampliconnoise, autodock, autodock-vina, autogrid, ballview, bedtools, biomaj, blast2, bowtie, bowtie2, boxshade, bwa, cd-hit, clonalframe, clustalo, clustalw, clustalx, dialign, dialign-tx, disulfinder, dotur, dssp, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, exonerate, fastdnaml, fastlink, fasttree, fastx-toolkit, ffindex, figtree, filo, gamgi, garlic, gbrowse, gdpc, gentle, gff2aplot, gff2ps, ghemical, glam2, grinder, gromacs, hhsuite, hmmer, infernal, jalview, jellyfish, jmol, kalign, last-align, librg-utils-perl, loki, mafft, maq, maqview, massxpert, melting, mipe, mira-assembler, mlv-smile, mothur, mrbayes, mummer, muscle, mustang, ncbi-blast+, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, ncoils, neobio, njplot, perlprimer, phyml, picard-tools, plasmidomics, plink, poa, populations, primer3, probalign, probcons, proda, profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun, profphd, profphd-net, profphd-utils, proftmb, pymol, pynast, python-cogent, qiime, r-bioc-cummerbund, r-bioc-hilbertvis, r-cran-genabel, r-cran-qtl, r-other-bio3d, r-other-mott-happy, rasmol, raster3d, raxml, readseq, reprof, rnahybrid, samtools, sibsim4, sigma-align, sim4, squizz, sra-toolkit, ssake, staden-io-lib-utils, t-coffee, tabix, theseus, tigr-glimmer, tm-align, transtermhp, tree-puzzle | tree-ppuzzle, treeviewx, vcftools, velvet, wise Suggests: abyss, act, amos-assembler, amoscmp, anfo, apollo, arachne, arb, artemis, asap, augustus, autodocktools, axparafit, axpcoords, bagphenotype, bambus, bamtools, beads, beast-mcmc, big-blast, bigsdb, blimps-utils, blixem, btk-core, cactus, caftools, cain, cap3, cdbfasta, cdna-db, cinema, circos, clonalorigin, clustalw-mpi, cluster3, cmap, coalesce, codonw, compclust, concavity, conservation-code, contralign, coot, copycat, crossbow, cufflinks, cytoscape, das-proserver, dazzle, decipher, e-hive, ecell, edtsurf, eigensoft, elph, embassy-phylip, emboss-explorer, ensembl, est-db, estferret, estscan, exalt, excavator, fas, fasta, fastqc, figaro, finex, fluctuate, forester, forge, galaxy, gassst, gbioseq, gbrowse-syn, genemark, genesplicer, genetrack, genezilla, genographer, genometools, glimmerhmm, gmap, gmv, grogui, haploview, hawkeye, hexamer, hilbertvisgui, hmmer2, igv, jbrowse, jigsaw, jstreeview, kempbasu, lagan, lamarc, logol-bin, logomat-m, ltrsift, lucy, macs, mage2tab, maker2, martj, maude, mauvealigner, maxd, melting-gui, meme, mesquite, metarep, microbiomeutil, migrate, minimus, mirbase, mobyle, molekel, mosaik-aligner, mozilla-biofox, mpsqed, msatfinder, mugsy, mummergpu, murasaki, mview, ncbi-seg, ngila, norsnet, norsp, nw-align, oases, obo-edit, oligoarrayaux, omegamap, operondb, pal2nal, paml, partigene, patman, patristic, pcma, pdb2pqr, pfaat, pftools, phagefinder, phpphylotree, phy-spread, phylip, phylographer, phyloviz-core, phylowin, plato, prank, predictnls, predictprotein, proalign, profbval, profisis, profit, prot4est, pscan-tfbs, psipred, pyrophosphate-tools, python-orange, python-rdkit, python-reaper, qtlcart, r-ape, r-other-valdar-bagphenotype.library, raccoon, ray-denovoassembler, rbs-finder, rdp-classifier, recombine, repeatmasker, rmblast, roche454ace2caf, rose, rosetta, sap, seaview, seq-gen, seqan-apps, seqtk, sequenceconverter.app, sga, sift, smalt, snap, snpeff, soapdenovo, spice, splitstree, spread-phy, sra-sdk, ssaha, strap, tacg, taverna, taxinspector, tetra, tigr-assembler, tigr-glimmer-mg, tophat, trace2dbest, tracetuner, treebuilder3d, treetime, treeview, tripal, trnascan-se, twain, ugene, uniprime, vegan, vienna-rna, vmd, wgs-assembler, x-tandem-pipeline, zalign, zodiac-zeden Description-en: Debian Med micro-biology packages This metapackage will install Debian packages related to molecular biology, structural biology and bioinformatics for use in life sciences. Description-md5: ed5c52e97fd9de45bfcf8410b31c75c4 Tag: field::biology, role::metapackage, suite::debian Section: misc Priority: extra Filename: pool/main/d/debian-med/med-bio_1.13.2_all.deb Size: 20540 MD5sum: e30ce877fb1a63d6565521fd054130dc SHA1: acdbc6c16f62a24af63bd9a1c126aee96198015d SHA256: 138146b21e818ebb230ab5a97d0b13dcc58fd66601e858d6231a1b88aab034fc 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-cache', 'show', '--no-all-versions', 'med-bio=1.13.2'] 0m9.6s DEBUG: metapackage: Package: piuparts-depends-dummy Version: 0.invalid.0 Architecture: all Maintainer: piuparts developers team Description: Dummy package to satisfy dependencies - created by piuparts This package was created automatically by piuparts and can safely be removed Depends: med-tasks (= 1.13.2), med-config (= 1.13.2) 0m9.6s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmphmiL72/piuparts-depends-dummy'] 0m9.6s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmphmiL72/piuparts-depends-dummy.deb'. 0m9.6s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmphmiL72/piuparts-depends-dummy'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m9.6s DUMP: 0.9.7.9+deb7u7 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m9.6s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmphmiL72/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmpX0oUlp/tmp 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg', '-i', './tmp/piuparts-depends-dummy.deb'] 0m9.7s 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 med-tasks (= 1.13.2); however: Package med-tasks is not installed. piuparts-depends-dummy depends on med-config (= 1.13.2); however: Package med-config is not installed. dpkg: error processing piuparts-depends-dummy (--install): dependency problems - leaving unconfigured Errors were encountered while processing: piuparts-depends-dummy 0m9.7s DEBUG: Command failed (status=1), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg', '-i', './tmp/piuparts-depends-dummy.deb'] 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-get', '-yf', 'install'] 0m10.8s DUMP: Reading package lists... Building dependency tree... Reading state information... Correcting dependencies... Done The following extra packages will be installed: blends-common med-config med-tasks menu tasksel tasksel-data Suggested packages: blends-doc menu-l10n gksu kdebase-bin kdebase-runtime ktsuss sux Recommended packages: laptop-detect The following NEW packages will be installed: blends-common med-config med-tasks menu tasksel tasksel-data 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 1 not fully installed or removed. Need to get 642 kB of archives. After this operation, 3339 kB of additional disk space will be used. Get:1 http://mirror-ubc.debian.org/debian/ wheezy/main tasksel-data all 3.14.1 [20.6 kB] Get:2 http://mirror-ubc.debian.org/debian/ wheezy/main tasksel all 3.14.1 [94.8 kB] Get:3 http://mirror-ubc.debian.org/debian/ wheezy/main med-tasks all 1.13.2 [12.0 kB] Get:4 http://mirror-ubc.debian.org/debian/ wheezy/main menu amd64 2.1.46 [480 kB] Get:5 http://mirror-ubc.debian.org/debian/ wheezy/main blends-common all 0.6.16.2 [23.4 kB] Get:6 http://mirror-ubc.debian.org/debian/ wheezy/main med-config all 1.13.2 [11.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 642 kB in 0s (13.5 MB/s) Selecting previously unselected package tasksel-data. (Reading database ... 6768 files and directories currently installed.) Unpacking tasksel-data (from .../tasksel-data_3.14.1_all.deb) ... Selecting previously unselected package tasksel. Unpacking tasksel (from .../tasksel_3.14.1_all.deb) ... Selecting previously unselected package med-tasks. Unpacking med-tasks (from .../med-tasks_1.13.2_all.deb) ... Selecting previously unselected package menu. Unpacking menu (from .../archives/menu_2.1.46_amd64.deb) ... Selecting previously unselected package blends-common. Unpacking blends-common (from .../blends-common_0.6.16.2_all.deb) ... Selecting previously unselected package med-config. Unpacking med-config (from .../med-config_1.13.2_all.deb) ... Setting up menu (2.1.46) ... Processing triggers for menu ... Setting up blends-common (0.6.16.2) ... Setting up med-config (1.13.2) ... Adding group `med' (GID 150) ... Done. Setting up tasksel (3.14.1) ... Setting up med-tasks (1.13.2) ... Setting up piuparts-depends-dummy (0.invalid.0) ... Setting up tasksel-data (3.14.1) ... Processing triggers for menu ... 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-get', '-yf', 'install'] 0m10.8s INFO: Installation of ['./tmp/piuparts-depends-dummy.deb'] ok 0m10.8s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmpX0oUlp/./tmp/piuparts-depends-dummy.deb 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m10.8s DUMP: piuparts-depends-dummy install ok installed 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m10.9s DUMP: (Reading database ... 7143 files and directories currently installed.) Removing piuparts-depends-dummy ... 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-get', 'clean'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-get', 'clean'] 0m10.9s DEBUG: Recording chroot state 0m11.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpX0oUlp'] 0m12.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpX0oUlp'] 0m12.8s DEBUG: No broken symlinks as far as we can find. 0m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-cache', 'policy'] 0m13.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror-ubc.debian.org/debian/ wheezy/main Translation-en 500 http://mirror-ubc.debian.org/debian/ wheezy/main amd64 Packages release v=7.11,o=Debian,a=oldoldstable,n=wheezy,l=Debian,c=main origin mirror-ubc.debian.org Pinned packages: 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-cache', 'policy'] 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-cache', 'policy', 'med-bio'] 0m13.7s DUMP: med-bio: Installed: (none) Candidate: 1.13.2 Version table: 1.13.2 0 500 http://mirror-ubc.debian.org/debian/ wheezy/main amd64 Packages 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-cache', 'policy', 'med-bio'] 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-get', '-y', 'install', 'med-bio=1.13.2'] 0m14.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Suggested packages: abyss act amos-assembler amoscmp anfo apollo arachne arb artemis asap augustus autodocktools axparafit axpcoords bagphenotype bambus bamtools beads beast-mcmc big-blast bigsdb blimps-utils blixem btk-core cactus caftools cain cap3 cdbfasta cdna-db cinema circos clonalorigin clustalw-mpi cluster3 cmap coalesce codonw compclust concavity conservation-code contralign coot copycat crossbow cufflinks cytoscape das-proserver dazzle decipher e-hive ecell edtsurf eigensoft elph embassy-phylip emboss-explorer ensembl est-db estferret estscan exalt excavator fas fastqc figaro finex fluctuate forester forge galaxy gassst gbioseq gbrowse-syn genemark genesplicer genetrack genezilla genographer genometools glimmerhmm gmap gmv grogui haploview hawkeye hexamer hilbertvisgui hmmer2 igv jbrowse jigsaw jstreeview kempbasu lagan lamarc logol-bin logomat-m ltrsift lucy macs mage2tab maker2 martj maude mauvealigner maxd melting-gui meme mesquite metarep microbiomeutil migrate minimus mirbase mobyle molekel mosaik-aligner mozilla-biofox mpsqed msatfinder mugsy mummergpu murasaki mview ncbi-seg ngila norsnet norsp nw-align oases obo-edit oligoarrayaux omegamap operondb pal2nal paml partigene patman patristic pcma pdb2pqr pfaat pftools phagefinder phpphylotree phy-spread phylographer phyloviz-core phylowin plato prank predictnls predictprotein proalign profbval profisis profit prot4est pscan-tfbs psipred pyrophosphate-tools python-orange python-rdkit python-reaper qtlcart r-ape r-other-valdar-bagphenotype.library raccoon ray-denovoassembler rbs-finder rdp-classifier recombine repeatmasker rmblast roche454ace2caf rose rosetta seaview seq-gen seqan-apps seqtk sequenceconverter.app sga smalt snap snpeff soapdenovo spice splitstree spread-phy sra-sdk ssaha strap tacg taverna taxinspector tetra tigr-assembler tigr-glimmer-mg tophat trace2dbest tracetuner treebuilder3d treetime tripal trnascan-se twain ugene uniprime vegan vienna-rna vmd wgs-assembler x-tandem-pipeline zalign zodiac-zeden Recommended packages: abacas acedb-other acedb-other-belvu acedb-other-dotter adun.app alien-hunter altree amap-align ampliconnoise autodock autodock-vina autogrid ballview bedtools biomaj blast2 bowtie bowtie2 boxshade bwa cd-hit clonalframe clustalo clustalw clustalx dialign dialign-tx disulfinder dotur dssp embassy-domainatrix embassy-domalign embassy-domsearch emboss exonerate fastdnaml fastlink fasttree fastx-toolkit ffindex figtree filo gamgi garlic gbrowse gdpc gentle gff2aplot gff2ps ghemical glam2 grinder gromacs hhsuite hmmer infernal jalview jellyfish jmol kalign last-align librg-utils-perl loki mafft maq maqview massxpert melting mipe mira-assembler mlv-smile mothur mrbayes mummer muscle mustang ncbi-blast+ ncbi-epcr ncbi-tools-bin ncbi-tools-x11 ncoils neobio njplot perlprimer phyml picard-tools plasmidomics plink poa populations primer3 probalign probcons proda profnet-bval profnet-chop profnet-con profnet-isis profnet-md profnet-norsnet profnet-prof profnet-snapfun profphd profphd-net profphd-utils proftmb pymol pynast python-cogent qiime r-bioc-cummerbund r-bioc-hilbertvis r-cran-genabel r-cran-qtl r-other-bio3d r-other-mott-happy rasmol raster3d raxml readseq reprof rnahybrid samtools sibsim4 sigma-align squizz sra-toolkit ssake staden-io-lib-utils t-coffee tabix theseus tigr-glimmer tm-align transtermhp tree-puzzle tree-ppuzzle treeviewx vcftools velvet wise The following NEW packages will be installed: med-bio 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 20.5 kB of archives. After this operation, 103 kB of additional disk space will be used. Get:1 http://mirror-ubc.debian.org/debian/ wheezy/main med-bio all 1.13.2 [20.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 20.5 kB in 0s (1254 kB/s) Selecting previously unselected package med-bio. (Reading database ... 7143 files and directories currently installed.) Unpacking med-bio (from .../med-bio_1.13.2_all.deb) ... Setting up med-bio (1.13.2) ... 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-get', '-y', 'install', 'med-bio=1.13.2'] 0m14.5s INFO: Running scripts post_install 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_install_exceptions'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_install_exceptions'] 0m14.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpX0oUlp'] 0m15.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpX0oUlp'] 0m15.6s DEBUG: No broken symlinks as far as we can find. 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m15.6s 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 blends-common blends-common 0.6.16.2 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 med-bio med-bio 1.13.2 install ok installed med-config med-config 1.13.2 install ok installed med-tasks med-tasks 1.13.2 install ok installed menu menu 2.1.46 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 tasksel tasksel 3.14.1 install ok installed tasksel-data tasksel-data 3.14.1 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 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m16.1s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', '-ac', '--ignore-obsolete'] 0m16.6s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', '-ac', '--ignore-obsolete'] 0m16.6s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m16.7s DUMP: 0.15.1 0m16.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m16.7s INFO: Running adequate version 0.15.1 now. 0m16.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'med-bio'] 0m16.7s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'med-bio'] 0m16.7s INFO: Running scripts pre_remove 0m16.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m16.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m16.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m16.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m16.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m17.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m17.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m17.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_remove_exceptions'] 0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/pre_remove_exceptions'] 0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-get', 'remove', 'menu', 'med-tasks', 'med-config', 'tasksel', 'tasksel-data', 'blends-common', 'med-bio'] 0m17.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: blends-common med-bio med-config med-tasks menu tasksel tasksel-data 0 upgraded, 0 newly installed, 7 to remove and 0 not upgraded. After this operation, 3443 kB disk space will be freed. (Reading database ... 7176 files and directories currently installed.) Removing med-bio ... Removing med-config ... Removing blends-common ... Removing med-tasks ... Removing menu ... Removing tasksel-data ... Removing tasksel ... 0m17.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-get', 'remove', 'menu', 'med-tasks', 'med-config', 'tasksel', 'tasksel-data', 'blends-common', 'med-bio'] 0m17.7s INFO: Running scripts post_remove 0m17.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_remove_exceptions'] 0m17.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_remove_exceptions'] 0m17.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg', '--purge', 'menu', 'med-tasks', 'med-config', 'tasksel', 'tasksel-data', 'blends-common'] 0m18.0s DUMP: (Reading database ... 6778 files and directories currently installed.) Removing menu ... Purging configuration files for menu ... dpkg: warning: ignoring request to remove med-tasks which isn't installed Removing med-config ... Purging configuration files for med-config ... Removing tasksel ... Purging configuration files for tasksel ... dpkg: warning: ignoring request to remove tasksel-data which isn't installed Removing blends-common ... Purging configuration files for blends-common ... 0m18.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg', '--purge', 'menu', 'med-tasks', 'med-config', 'tasksel', 'tasksel-data', 'blends-common'] 0m18.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg', '--purge', 'med-bio'] 0m18.0s DUMP: (Reading database ... 6768 files and directories currently installed.) Removing med-bio ... Purging configuration files for med-bio ... 0m18.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg', '--purge', 'med-bio'] 0m18.0s INFO: Running scripts post_purge 0m18.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_purge_exceptions'] 0m18.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_purge_exceptions'] 0m18.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg', '--purge', '--pending'] 0m18.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg', '--purge', '--pending'] 0m18.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg', '--remove', '--pending'] 0m18.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg', '--remove', '--pending'] 0m18.0s INFO: Running scripts post_test 0m18.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_test_exceptions'] 0m18.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'tmp/scripts/post_test_exceptions'] 0m18.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpX0oUlp'] 0m18.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpX0oUlp'] 0m19.2s DEBUG: No broken symlinks as far as we can find. 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg-divert', '--list'] 0m19.2s DUMP: diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'dpkg-divert', '--list'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-get', 'clean'] 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpX0oUlp', 'apt-get', 'clean'] 0m19.3s DEBUG: Recording chroot state 0m20.3s INFO: PASS: Installation and purging test. 0m20.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/run/shm'] 0m20.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/run/shm'] 0m20.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/dev/console'] 0m20.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/dev/console'] 0m20.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/dev/ptmx'] 0m20.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/dev/ptmx'] 0m20.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/dev/pts'] 0m20.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/dev/pts'] 0m20.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/proc'] 0m20.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpX0oUlp/proc'] 0m20.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpX0oUlp'] 0m20.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpX0oUlp'] 0m20.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpX0oUlp 0m20.9s INFO: PASS: All tests. 0m20.9s INFO: piuparts run ends. ret=0 End: 2018-08-17 13:08:38 UTC