Start: 2023-03-18 17:08:43 GMT [stretch] Package: med-bio Source: debian-med Version: 3.0.1 Installed-Size: 46 Maintainer: Debian Med Packaging Team Architecture: all Depends: med-tasks (= 3.0.1), med-config (= 3.0.1) Recommends: abacas, abyss, acedb-other, acedb-other-belvu, acedb-other-dotter, adapterremoval, adun-core, aegean, aevol, alien-hunter, alter-sequence-alignment, altree, amap-align, ampliconnoise, andi, anfo, aragorn, arden, ariba, art-nextgen-simulation-tools, artemis, artfastqgenerator, atac, augustus, autodock, autodock-vina, autogrid, axe-demultiplexer, ballview, bamtools, barrnap, bcftools, beagle, beast-mcmc, beast2-mcmc, bedtools, berkeley-express, bio-eagle, bio-rainbow, blasr, bowtie, bowtie2, boxshade, brig, bwa, cassiopee, cd-hit, cdbfasta, cgview, chimeraslayer, circlator, circos, clearcut, clonalframe, clustalo, clustalw, clustalx, codonw, concavity, conservation-code, crac, cutadapt, daligner, dascrubber, datamash, dawg, dazzdb, dialign, dialign-tx, dindel, discosnp, disulfinder, dnaclust, dssp, dwgsim, ea-utils, ecopcr, edtsurf, eigensoft, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, exonerate, falcon, fastahack, fastaq, fastdnaml, fastlink, fastml, fastqc, fastqtl, fasttree, fastx-toolkit, ffindex, figtree, filo, fitgcp, flexbar, fml-asm, freecontact, fsa, fsm-lite, gamgi, garli, garlic, gasic, gbrowse, gdpc, genometools, gentle, gff2aplot, gff2ps, ghemical, giira, glam2, graphlan, grinder, gromacs, gubbins, gwama, harvest-tools, hhsuite, hilive, hisat2, hmmer, hmmer2, hyphy-mpi | hyphy-pt, hyphygui, idba, indelible, infernal, ipig, iqtree, iva, jaligner, jellyfish, jmodeltest, jmol, kalign, khmer, kineticstools, king-probe, kissplice, kmc, kmer, kraken, lambda-align, last-align, leaff, lefse, librg-utils-perl, libvcflib-tools, logol-bin, loki, ltrsift, macs, macsyfinder, maffilter, mafft, mapdamage, mapsembler2, maq, maqview, mash, massxpert, mauve-aligner, melting, meryl, metaphlan2, metastudent, mhap, microbegps, microbiomeutil, minia, miniasm, minimap, mipe, mira-assembler, mlv-smile, mothur, mrbayes, mummer, murasaki, muscle, mustang, nanopolish, nast-ier, ncbi-blast+, ncbi-blast+-legacy, ncbi-entrez-direct, ncbi-epcr, ncbi-seg, ncbi-tools-bin, ncbi-tools-x11, ncl-tools, ncoils, neobio, njplot, norsnet, norsp, paraclu, parsinsert, parsnp, pbalign, pbbarcode, pbdagcon, pbgenomicconsensus, pbh5tools, pbhoney, pbjelly, pbsim, pbsuite, pdb2pqr, perlprimer, perm, phipack, phybin, phylip, phyml, physamp, phyutility, picard-tools, piler, pirs, placnet, plasmidomics, plast, plink, plink1.9, plip, poa, populations, poretools, prank, predictnls, predictprotein, prime-phylo, primer3, proalign, probabel, probalign, probcons, proda, prodigal, profbval, profisis, profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun, profphd, profphd-net, profphd-utils, proftmb, progressivemauve, proteinortho, prottest, pycorrfit, pymol, pynast, pyscanfcs, python-cogent, qtltools, r-bioc-annotate, r-bioc-biostrings, r-bioc-cummerbund, r-bioc-deseq2, r-bioc-dnacopy, r-bioc-ebseq, r-bioc-edger, r-bioc-genefilter, r-bioc-geneplotter, r-bioc-gviz, r-bioc-hilbertvis, r-bioc-limma, r-bioc-mergeomics, r-bioc-metagenomeseq, r-bioc-phyloseq, r-bioc-rtracklayer, r-cran-adegenet, r-cran-adephylo, r-cran-ape, r-cran-bio3d, r-cran-distory, r-cran-genabel, r-cran-phangorn, r-cran-pscbs, r-cran-qtl, r-cran-rotl, r-cran-seqinr, r-cran-treescape, r-cran-vegan, r-other-mott-happy.hbrem, rambo-k, rapmap, rasmol, raster3d, rate4site, raxml, ray, rdp-alignment, rdp-classifier, rdp-readseq, readseq, reapr, relion-bin | relion-bin+mpi, relion-bin+gui | relion-bin+mpi+gui, repeatmasker-recon, reprof, rna-star, rnahybrid, roary, rsem, rtax, saint, salmon, samtools, scrm, scythe, seaview, seer, seqan-apps, seqprep, seqtk, sga, sibsim4, sickle, sigma-align, sim4, sim4db, smalt, smithwaterman, smrtanalysis, snap, snap-aligner, sniffles, snp-sites, snpomatic, soapdenovo, soapdenovo2, sortmerna, spaced, spades, sprai, spread-phy, squizz, sra-toolkit, srst2, ssake, sspace, ssw-align, stacks, staden, staden-io-lib-utils, subread, suitename, sumaclust, sumatra, sumtrees, surankco, swarm, t-coffee, tabix, tantan, theseus, tigr-glimmer, tm-align, tophat, toppred, transdecoder, transrate-tools, transtermhp, tree-puzzle | tree-ppuzzle, treeview, treeviewx, trimmomatic, trinityrnaseq, uc-echo, varna, vcftools, velvet | velvet-long, velvetoptimiser, vsearch, wigeon, wise, zalign Suggests: acacia, adun.app, amos-assembler, amoscmp, apollo, arachne, arb, asap, autodocktools, axparafit, axpcoords, bagpipe, baitfisher, bambus, beads, bedops, biceps, big-blast, bigsdb, bio-tradis, biomaj, biomaj-watcher, bitseq, blat, blimps-utils, blixem, blobology, btk-core, cactus, caftools, cain, canu, cap3, ccs, cdna-db, cinema, clonalorigin, cluster3, cmap, cnvkit, coalesce, compclust, condetri, contrafold, contralign, coot, copycat, crossbow, crux-toolkit, cufflinks, cytoscape, das-proserver, dazzle, decipher, deepnano, diamond-aligner, e-hive, ecell, elph, embassy-phylip, emboss-explorer, emmax, emperor, ensembl, est-db, estferret, estscan, euler-sr, euler2, exabayes, exalt, examl, excavator, fasta, fasta3, ffp, figaro, finex, fluctuate, forester, forge, freebayes, galaxy, gassst, gatk, gbioseq, gbrowse-syn, genemark, genesplicer, genetrack, genezilla, genographer, getdata, glimmerhmm, gmap, gmv, grabix, grogui, haploview, hawkeye, hexamer, hilbertvisgui, htqc, igv, inspect, jalview, jbrowse, jigsaw, jstreeview, kclust, kempbasu, lagan, lamarc, lofreq, logomat-m, lucy, mach-haplotyper, mage2tab, maker2, malt, manta, martj, maude, maxd, melting-gui, meme, mesquite, metabit, metarep, metastudent-data, metastudent-data-2, metastudent-data-3, mgltools-cadd, mgltools-pmv, mgltools-vision, migrate, minimus, mirbase, mobyle, mobyle-programs, mobyle-tutorials, modeller, molekel, mosaik-aligner, mpsqed, mptp, mrs, msatfinder, mugsy, mummergpu, mview, nanocall, nextsv, ngila, ngsqctoolkit, nw-align, oases, obitools, obo-edit, oligoarrayaux, omegamap, openms, operondb, pal2nal, paleomix, paml, partigene, partitionfinder, patman, patristic, pcma, pfaat, pftools, phagefinder, phast, phpphylotree, phylographer, phylophlan, phyloviz-core, phylowin, pipasic, plato, profit, prokka, prot4est, pscan-tfbs, psipred, psortb, pssh2, pyrophosphate-tools, python-orange, python-reaper, python3-biomaj3, qcumber, qiime, qtlcart, qualimap, r-bioc-annotationhub, r-bioc-aroma.light, r-bioc-ensembldb, r-bioc-go.db, r-bioc-savr, r-cran-boolnet, r-cran-metamix, r-cran-pheatmap, r-cran-qqman, r-cran-rentrez, r-other-apmswapp, r-other-valdar-bagphenotype.library, raccoon, radiant, raxml-ng, rbs-finder, recombine, repeatmasker, rmblast, roadtrips, roche454ace2caf, roguenarok, rose, rosetta, rsat, runcircos-gui, sambamba, sap, science-workflow, segemehl, seq-gen, seqsero, sequenceconverter.app, sift, situs, snpeff, sparta, spice, splitstree, ssaha, strap, strap-base, tacg, taverna, taxinspector, tetra, tide, tigr-glimmer-mg, tnseq-transit, topp, trace2dbest, tracetuner, treebuilder3d, treetime, tripal, trnascan-se, tvc, twain, ugene, unc-fish, uniprime, varmatch, varscan, vienna-rna, vmd, x-tandem-pipeline, zodiac-zeden Description: Debian Med bioinformatics packages Description-md5: 472a50c6504872b123b928f5c13e0f5e Tag: field::biology, role::metapackage, suite::debian Section: misc Priority: extra Filename: pool/main/d/debian-med/med-bio_3.0.1_all.deb Size: 18660 MD5sum: 10b64f80ea5762265cbb0aec5a872959 SHA256: f3869d6d9e719cb9917fe4545bea317a2af385cb2c5acfe5c1c428bc664150df [stretch-lts] Package: med-bio Source: debian-med Version: 3.0.1 Installed-Size: 46 Maintainer: Debian Med Packaging Team Architecture: all Depends: med-tasks (= 3.0.1), med-config (= 3.0.1) Recommends: abacas, abyss, acedb-other, acedb-other-belvu, acedb-other-dotter, adapterremoval, adun-core, aegean, aevol, alien-hunter, alter-sequence-alignment, altree, amap-align, ampliconnoise, andi, anfo, aragorn, arden, ariba, art-nextgen-simulation-tools, artemis, artfastqgenerator, atac, augustus, autodock, autodock-vina, autogrid, axe-demultiplexer, ballview, bamtools, barrnap, bcftools, beagle, beast-mcmc, beast2-mcmc, bedtools, berkeley-express, bio-eagle, bio-rainbow, blasr, bowtie, bowtie2, boxshade, brig, bwa, cassiopee, cd-hit, cdbfasta, cgview, chimeraslayer, circlator, circos, clearcut, clonalframe, clustalo, clustalw, clustalx, codonw, concavity, conservation-code, crac, cutadapt, daligner, dascrubber, datamash, dawg, dazzdb, dialign, dialign-tx, dindel, discosnp, disulfinder, dnaclust, dssp, dwgsim, ea-utils, ecopcr, edtsurf, eigensoft, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, exonerate, falcon, fastahack, fastaq, fastdnaml, fastlink, fastml, fastqc, fastqtl, fasttree, fastx-toolkit, ffindex, figtree, filo, fitgcp, flexbar, fml-asm, freecontact, fsa, fsm-lite, gamgi, garli, garlic, gasic, gbrowse, gdpc, genometools, gentle, gff2aplot, gff2ps, ghemical, giira, glam2, graphlan, grinder, gromacs, gubbins, gwama, harvest-tools, hhsuite, hilive, hisat2, hmmer, hmmer2, hyphy-mpi | hyphy-pt, hyphygui, idba, indelible, infernal, ipig, iqtree, iva, jaligner, jellyfish, jmodeltest, jmol, kalign, khmer, kineticstools, king-probe, kissplice, kmc, kmer, kraken, lambda-align, last-align, leaff, lefse, librg-utils-perl, libvcflib-tools, logol-bin, loki, ltrsift, macs, macsyfinder, maffilter, mafft, mapdamage, mapsembler2, maq, maqview, mash, massxpert, mauve-aligner, melting, meryl, metaphlan2, metastudent, mhap, microbegps, microbiomeutil, minia, miniasm, minimap, mipe, mira-assembler, mlv-smile, mothur, mrbayes, mummer, murasaki, muscle, mustang, nanopolish, nast-ier, ncbi-blast+, ncbi-blast+-legacy, ncbi-entrez-direct, ncbi-epcr, ncbi-seg, ncbi-tools-bin, ncbi-tools-x11, ncl-tools, ncoils, neobio, njplot, norsnet, norsp, paraclu, parsinsert, parsnp, pbalign, pbbarcode, pbdagcon, pbgenomicconsensus, pbh5tools, pbhoney, pbjelly, pbsim, pbsuite, pdb2pqr, perlprimer, perm, phipack, phybin, phylip, phyml, physamp, phyutility, picard-tools, piler, pirs, placnet, plasmidomics, plast, plink, plink1.9, plip, poa, populations, poretools, prank, predictnls, predictprotein, prime-phylo, primer3, proalign, probabel, probalign, probcons, proda, prodigal, profbval, profisis, profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun, profphd, profphd-net, profphd-utils, proftmb, progressivemauve, proteinortho, prottest, pycorrfit, pymol, pynast, pyscanfcs, python-cogent, qtltools, r-bioc-annotate, r-bioc-biostrings, r-bioc-cummerbund, r-bioc-deseq2, r-bioc-dnacopy, r-bioc-ebseq, r-bioc-edger, r-bioc-genefilter, r-bioc-geneplotter, r-bioc-gviz, r-bioc-hilbertvis, r-bioc-limma, r-bioc-mergeomics, r-bioc-metagenomeseq, r-bioc-phyloseq, r-bioc-rtracklayer, r-cran-adegenet, r-cran-adephylo, r-cran-ape, r-cran-bio3d, r-cran-distory, r-cran-genabel, r-cran-phangorn, r-cran-pscbs, r-cran-qtl, r-cran-rotl, r-cran-seqinr, r-cran-treescape, r-cran-vegan, r-other-mott-happy.hbrem, rambo-k, rapmap, rasmol, raster3d, rate4site, raxml, ray, rdp-alignment, rdp-classifier, rdp-readseq, readseq, reapr, relion-bin | relion-bin+mpi, relion-bin+gui | relion-bin+mpi+gui, repeatmasker-recon, reprof, rna-star, rnahybrid, roary, rsem, rtax, saint, salmon, samtools, scrm, scythe, seaview, seer, seqan-apps, seqprep, seqtk, sga, sibsim4, sickle, sigma-align, sim4, sim4db, smalt, smithwaterman, smrtanalysis, snap, snap-aligner, sniffles, snp-sites, snpomatic, soapdenovo, soapdenovo2, sortmerna, spaced, spades, sprai, spread-phy, squizz, sra-toolkit, srst2, ssake, sspace, ssw-align, stacks, staden, staden-io-lib-utils, subread, suitename, sumaclust, sumatra, sumtrees, surankco, swarm, t-coffee, tabix, tantan, theseus, tigr-glimmer, tm-align, tophat, toppred, transdecoder, transrate-tools, transtermhp, tree-puzzle | tree-ppuzzle, treeview, treeviewx, trimmomatic, trinityrnaseq, uc-echo, varna, vcftools, velvet | velvet-long, velvetoptimiser, vsearch, wigeon, wise, zalign Suggests: acacia, adun.app, amos-assembler, amoscmp, apollo, arachne, arb, asap, autodocktools, axparafit, axpcoords, bagpipe, baitfisher, bambus, beads, bedops, biceps, big-blast, bigsdb, bio-tradis, biomaj, biomaj-watcher, bitseq, blat, blimps-utils, blixem, blobology, btk-core, cactus, caftools, cain, canu, cap3, ccs, cdna-db, cinema, clonalorigin, cluster3, cmap, cnvkit, coalesce, compclust, condetri, contrafold, contralign, coot, copycat, crossbow, crux-toolkit, cufflinks, cytoscape, das-proserver, dazzle, decipher, deepnano, diamond-aligner, e-hive, ecell, elph, embassy-phylip, emboss-explorer, emmax, emperor, ensembl, est-db, estferret, estscan, euler-sr, euler2, exabayes, exalt, examl, excavator, fasta, fasta3, ffp, figaro, finex, fluctuate, forester, forge, freebayes, galaxy, gassst, gatk, gbioseq, gbrowse-syn, genemark, genesplicer, genetrack, genezilla, genographer, getdata, glimmerhmm, gmap, gmv, grabix, grogui, haploview, hawkeye, hexamer, hilbertvisgui, htqc, igv, inspect, jalview, jbrowse, jigsaw, jstreeview, kclust, kempbasu, lagan, lamarc, lofreq, logomat-m, lucy, mach-haplotyper, mage2tab, maker2, malt, manta, martj, maude, maxd, melting-gui, meme, mesquite, metabit, metarep, metastudent-data, metastudent-data-2, metastudent-data-3, mgltools-cadd, mgltools-pmv, mgltools-vision, migrate, minimus, mirbase, mobyle, mobyle-programs, mobyle-tutorials, modeller, molekel, mosaik-aligner, mpsqed, mptp, mrs, msatfinder, mugsy, mummergpu, mview, nanocall, nextsv, ngila, ngsqctoolkit, nw-align, oases, obitools, obo-edit, oligoarrayaux, omegamap, openms, operondb, pal2nal, paleomix, paml, partigene, partitionfinder, patman, patristic, pcma, pfaat, pftools, phagefinder, phast, phpphylotree, phylographer, phylophlan, phyloviz-core, phylowin, pipasic, plato, profit, prokka, prot4est, pscan-tfbs, psipred, psortb, pssh2, pyrophosphate-tools, python-orange, python-reaper, python3-biomaj3, qcumber, qiime, qtlcart, qualimap, r-bioc-annotationhub, r-bioc-aroma.light, r-bioc-ensembldb, r-bioc-go.db, r-bioc-savr, r-cran-boolnet, r-cran-metamix, r-cran-pheatmap, r-cran-qqman, r-cran-rentrez, r-other-apmswapp, r-other-valdar-bagphenotype.library, raccoon, radiant, raxml-ng, rbs-finder, recombine, repeatmasker, rmblast, roadtrips, roche454ace2caf, roguenarok, rose, rosetta, rsat, runcircos-gui, sambamba, sap, science-workflow, segemehl, seq-gen, seqsero, sequenceconverter.app, sift, situs, snpeff, sparta, spice, splitstree, ssaha, strap, strap-base, tacg, taverna, taxinspector, tetra, tide, tigr-glimmer-mg, tnseq-transit, topp, trace2dbest, tracetuner, treebuilder3d, treetime, tripal, trnascan-se, tvc, twain, ugene, unc-fish, uniprime, varmatch, varscan, vienna-rna, vmd, x-tandem-pipeline, zodiac-zeden Description: Debian Med bioinformatics packages Description-md5: 472a50c6504872b123b928f5c13e0f5e Tag: field::biology, role::metapackage, suite::debian Section: misc Priority: extra Filename: pool/main/d/debian-med/med-bio_3.0.1_all.deb Size: 18660 MD5sum: 10b64f80ea5762265cbb0aec5a872959 SHA256: f3869d6d9e719cb9917fe4545bea317a2af385cb2c5acfe5c1c428bc664150df Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch -d stretch-lts -B /srv/piuparts.debian.org/slave/refchroot/stretch2next/reference-chroot-metadata.dat --apt med-bio=3.0.1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.1.5 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch -d stretch-lts -B /srv/piuparts.debian.org/slave/refchroot/stretch2next/reference-chroot-metadata.dat --apt med-bio=3.0.1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpfltc2e8l 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpfltc2e8l 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.9s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l/proc'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l/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/tmpfltc2e8l/dev/pts'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l/dev/pts'] 0m1.9s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l/dev/ptmx'] 0m2.0s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l/dev/ptmx'] 0m2.0s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l/dev/console'] 0m2.0s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l/dev/console'] 0m2.0s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l/dev/shm'] 0m2.0s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l/dev/shm'] 0m2.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch 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/tmpfltc2e8l/tmp/scripts/ 0m2.0s INFO: Running scripts post_chroot_unpack 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-get', 'update'] 0m3.1s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-get', 'update'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-get', '-yf', 'dist-upgrade'] 0m3.4s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-get', '-yf', 'dist-upgrade'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.7s DUMP: 660e5103244a20b75ca08c3f8741e16e - 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.7s INFO: Running scripts post_setup 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_setup_dummy_users'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_setup_dummy_users'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_setup_forbid_home'] 0m4.8s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_setup_forbid_home'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.8s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_setup_minimize'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_setup_minimize'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_setup_zz_backports'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_setup_zz_backports'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.8s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.10 install ok installed base-files base-files 9.9+deb9u13 install ok installed base-passwd base-passwd 3.5.43 install ok installed bash bash 4.4-5 install ok installed bsdutils bsdutils 1:2.29.2-1+deb9u1 install ok installed coreutils coreutils 8.26-3 install ok installed dash dash 0.5.8-2.4 install ok installed debconf debconf 1.5.61 install ok installed debian-archive-keyring debian-archive-keyring 2017.5+deb9u1 install ok installed debianutils debianutils 4.8.1.1 install ok installed diffutils diffutils 1:3.5-3 install ok installed dpkg dpkg 1.18.25 install ok installed e2fslibs:amd64 e2fslibs 1.43.4-2+deb9u1 install ok installed e2fsprogs e2fsprogs 1.43.4-2+deb9u1 install ok installed findutils findutils 4.6.0+git+20161106-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gpgv gpgv 2.1.18-8~deb9u4 install ok installed grep grep 2.27-2 install ok installed gzip gzip 1.6-5+b1 install ok installed hostname hostname 3.18+b1 install ok installed init-system-helpers init-system-helpers 1.48 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.4.10 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.6.7-2 install ok installed libaudit1:amd64 libaudit1 1:2.6.7-2 install ok installed libblkid1:amd64 libblkid1 2.29.2-1+deb9u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-8.1 install ok installed libc-bin libc-bin 2.24-11+deb9u4 install ok installed libc6:amd64 libc6 2.24-11+deb9u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2+deb9u1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-12+deb9u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.227 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libgcc1:amd64 libgcc1 1:6.3.0-18+deb9u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.7.6-2+deb9u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed liblz4-1:amd64 liblz4-1 0.0~r131-2+b1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.2+b1 install ok installed libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libncursesw5:amd64 libncursesw5 6.0+20161126-1+deb9u2 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.6 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.6 install ok installed libpam-runtime libpam-runtime 1.1.8-3.6 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.6 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libselinux1:amd64 libselinux1 2.6-3+b3 install ok installed libsemanage-common libsemanage-common 2.6-2 install ok installed libsemanage1:amd64 libsemanage1 2.6-2 install ok installed libsepol1:amd64 libsepol1 2.6-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u1 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u12 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u12 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.29.2-1+deb9u1 install ok installed login login 1:4.4-4.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed ncurses-base ncurses-base 6.0+20161126-1+deb9u2 install ok installed ncurses-bin ncurses-bin 6.0+20161126-1+deb9u2 install ok installed passwd passwd 1:4.4-4.1 install ok installed perl-base perl-base 5.24.1-3+deb9u7 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59.9 install ok installed tar tar 1.29b-1.1 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.8s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stretch2next/reference-chroot-metadata.dat 0m4.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l'] 0m5.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l'] 0m5.1s INFO: Running scripts is_testable 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/is_testable_uninstallable'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/is_testable_uninstallable'] 0m5.1s INFO: Running scripts pre_test 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_test_exceptions'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_test_exceptions'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_test_root_password'] 0m5.1s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_test_root_password'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-cache', 'show', '--no-all-versions', 'med-bio'] 0m5.4s DUMP: Package: med-bio Source: debian-med Version: 3.0.1 Installed-Size: 46 Maintainer: Debian Med Packaging Team Architecture: all Depends: med-tasks (= 3.0.1), med-config (= 3.0.1) Recommends: abacas, abyss, acedb-other, acedb-other-belvu, acedb-other-dotter, adapterremoval, adun-core, aegean, aevol, alien-hunter, alter-sequence-alignment, altree, amap-align, ampliconnoise, andi, anfo, aragorn, arden, ariba, art-nextgen-simulation-tools, artemis, artfastqgenerator, atac, augustus, autodock, autodock-vina, autogrid, axe-demultiplexer, ballview, bamtools, barrnap, bcftools, beagle, beast-mcmc, beast2-mcmc, bedtools, berkeley-express, bio-eagle, bio-rainbow, blasr, bowtie, bowtie2, boxshade, brig, bwa, cassiopee, cd-hit, cdbfasta, cgview, chimeraslayer, circlator, circos, clearcut, clonalframe, clustalo, clustalw, clustalx, codonw, concavity, conservation-code, crac, cutadapt, daligner, dascrubber, datamash, dawg, dazzdb, dialign, dialign-tx, dindel, discosnp, disulfinder, dnaclust, dssp, dwgsim, ea-utils, ecopcr, edtsurf, eigensoft, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, exonerate, falcon, fastahack, fastaq, fastdnaml, fastlink, fastml, fastqc, fastqtl, fasttree, fastx-toolkit, ffindex, figtree, filo, fitgcp, flexbar, fml-asm, freecontact, fsa, fsm-lite, gamgi, garli, garlic, gasic, gbrowse, gdpc, genometools, gentle, gff2aplot, gff2ps, ghemical, giira, glam2, graphlan, grinder, gromacs, gubbins, gwama, harvest-tools, hhsuite, hilive, hisat2, hmmer, hmmer2, hyphy-mpi | hyphy-pt, hyphygui, idba, indelible, infernal, ipig, iqtree, iva, jaligner, jellyfish, jmodeltest, jmol, kalign, khmer, kineticstools, king-probe, kissplice, kmc, kmer, kraken, lambda-align, last-align, leaff, lefse, librg-utils-perl, libvcflib-tools, logol-bin, loki, ltrsift, macs, macsyfinder, maffilter, mafft, mapdamage, mapsembler2, maq, maqview, mash, massxpert, mauve-aligner, melting, meryl, metaphlan2, metastudent, mhap, microbegps, microbiomeutil, minia, miniasm, minimap, mipe, mira-assembler, mlv-smile, mothur, mrbayes, mummer, murasaki, muscle, mustang, nanopolish, nast-ier, ncbi-blast+, ncbi-blast+-legacy, ncbi-entrez-direct, ncbi-epcr, ncbi-seg, ncbi-tools-bin, ncbi-tools-x11, ncl-tools, ncoils, neobio, njplot, norsnet, norsp, paraclu, parsinsert, parsnp, pbalign, pbbarcode, pbdagcon, pbgenomicconsensus, pbh5tools, pbhoney, pbjelly, pbsim, pbsuite, pdb2pqr, perlprimer, perm, phipack, phybin, phylip, phyml, physamp, phyutility, picard-tools, piler, pirs, placnet, plasmidomics, plast, plink, plink1.9, plip, poa, populations, poretools, prank, predictnls, predictprotein, prime-phylo, primer3, proalign, probabel, probalign, probcons, proda, prodigal, profbval, profisis, profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun, profphd, profphd-net, profphd-utils, proftmb, progressivemauve, proteinortho, prottest, pycorrfit, pymol, pynast, pyscanfcs, python-cogent, qtltools, r-bioc-annotate, r-bioc-biostrings, r-bioc-cummerbund, r-bioc-deseq2, r-bioc-dnacopy, r-bioc-ebseq, r-bioc-edger, r-bioc-genefilter, r-bioc-geneplotter, r-bioc-gviz, r-bioc-hilbertvis, r-bioc-limma, r-bioc-mergeomics, r-bioc-metagenomeseq, r-bioc-phyloseq, r-bioc-rtracklayer, r-cran-adegenet, r-cran-adephylo, r-cran-ape, r-cran-bio3d, r-cran-distory, r-cran-genabel, r-cran-phangorn, r-cran-pscbs, r-cran-qtl, r-cran-rotl, r-cran-seqinr, r-cran-treescape, r-cran-vegan, r-other-mott-happy.hbrem, rambo-k, rapmap, rasmol, raster3d, rate4site, raxml, ray, rdp-alignment, rdp-classifier, rdp-readseq, readseq, reapr, relion-bin | relion-bin+mpi, relion-bin+gui | relion-bin+mpi+gui, repeatmasker-recon, reprof, rna-star, rnahybrid, roary, rsem, rtax, saint, salmon, samtools, scrm, scythe, seaview, seer, seqan-apps, seqprep, seqtk, sga, sibsim4, sickle, sigma-align, sim4, sim4db, smalt, smithwaterman, smrtanalysis, snap, snap-aligner, sniffles, snp-sites, snpomatic, soapdenovo, soapdenovo2, sortmerna, spaced, spades, sprai, spread-phy, squizz, sra-toolkit, srst2, ssake, sspace, ssw-align, stacks, staden, staden-io-lib-utils, subread, suitename, sumaclust, sumatra, sumtrees, surankco, swarm, t-coffee, tabix, tantan, theseus, tigr-glimmer, tm-align, tophat, toppred, transdecoder, transrate-tools, transtermhp, tree-puzzle | tree-ppuzzle, treeview, treeviewx, trimmomatic, trinityrnaseq, uc-echo, varna, vcftools, velvet | velvet-long, velvetoptimiser, vsearch, wigeon, wise, zalign Suggests: acacia, adun.app, amos-assembler, amoscmp, apollo, arachne, arb, asap, autodocktools, axparafit, axpcoords, bagpipe, baitfisher, bambus, beads, bedops, biceps, big-blast, bigsdb, bio-tradis, biomaj, biomaj-watcher, bitseq, blat, blimps-utils, blixem, blobology, btk-core, cactus, caftools, cain, canu, cap3, ccs, cdna-db, cinema, clonalorigin, cluster3, cmap, cnvkit, coalesce, compclust, condetri, contrafold, contralign, coot, copycat, crossbow, crux-toolkit, cufflinks, cytoscape, das-proserver, dazzle, decipher, deepnano, diamond-aligner, e-hive, ecell, elph, embassy-phylip, emboss-explorer, emmax, emperor, ensembl, est-db, estferret, estscan, euler-sr, euler2, exabayes, exalt, examl, excavator, fasta, fasta3, ffp, figaro, finex, fluctuate, forester, forge, freebayes, galaxy, gassst, gatk, gbioseq, gbrowse-syn, genemark, genesplicer, genetrack, genezilla, genographer, getdata, glimmerhmm, gmap, gmv, grabix, grogui, haploview, hawkeye, hexamer, hilbertvisgui, htqc, igv, inspect, jalview, jbrowse, jigsaw, jstreeview, kclust, kempbasu, lagan, lamarc, lofreq, logomat-m, lucy, mach-haplotyper, mage2tab, maker2, malt, manta, martj, maude, maxd, melting-gui, meme, mesquite, metabit, metarep, metastudent-data, metastudent-data-2, metastudent-data-3, mgltools-cadd, mgltools-pmv, mgltools-vision, migrate, minimus, mirbase, mobyle, mobyle-programs, mobyle-tutorials, modeller, molekel, mosaik-aligner, mpsqed, mptp, mrs, msatfinder, mugsy, mummergpu, mview, nanocall, nextsv, ngila, ngsqctoolkit, nw-align, oases, obitools, obo-edit, oligoarrayaux, omegamap, openms, operondb, pal2nal, paleomix, paml, partigene, partitionfinder, patman, patristic, pcma, pfaat, pftools, phagefinder, phast, phpphylotree, phylographer, phylophlan, phyloviz-core, phylowin, pipasic, plato, profit, prokka, prot4est, pscan-tfbs, psipred, psortb, pssh2, pyrophosphate-tools, python-orange, python-reaper, python3-biomaj3, qcumber, qiime, qtlcart, qualimap, r-bioc-annotationhub, r-bioc-aroma.light, r-bioc-ensembldb, r-bioc-go.db, r-bioc-savr, r-cran-boolnet, r-cran-metamix, r-cran-pheatmap, r-cran-qqman, r-cran-rentrez, r-other-apmswapp, r-other-valdar-bagphenotype.library, raccoon, radiant, raxml-ng, rbs-finder, recombine, repeatmasker, rmblast, roadtrips, roche454ace2caf, roguenarok, rose, rosetta, rsat, runcircos-gui, sambamba, sap, science-workflow, segemehl, seq-gen, seqsero, sequenceconverter.app, sift, situs, snpeff, sparta, spice, splitstree, ssaha, strap, strap-base, tacg, taverna, taxinspector, tetra, tide, tigr-glimmer-mg, tnseq-transit, topp, trace2dbest, tracetuner, treebuilder3d, treetime, tripal, trnascan-se, tvc, twain, ugene, unc-fish, uniprime, varmatch, varscan, vienna-rna, vmd, x-tandem-pipeline, zodiac-zeden Description-en: Debian Med bioinformatics packages This metapackage will install Debian packages for use in molecular biology, structural biology and other biological sciences. Description-md5: 472a50c6504872b123b928f5c13e0f5e Tag: field::biology, role::metapackage, suite::debian Section: misc Priority: extra Filename: pool/main/d/debian-med/med-bio_3.0.1_all.deb Size: 18660 MD5sum: 10b64f80ea5762265cbb0aec5a872959 SHA256: f3869d6d9e719cb9917fe4545bea317a2af385cb2c5acfe5c1c428bc664150df 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-cache', 'show', '--no-all-versions', 'med-bio'] 0m5.4s INFO: apt-cache knows about the following packages: med-bio 0m5.4s INFO: Running scripts pre_install 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_database-server'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_database-server'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_exceptions'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_exceptions'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_extras'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_extras'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-cache', 'policy'] 0m5.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian stretch/main amd64 Packages release v=9.13,o=Debian,a=oldoldstable,n=stretch,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-cache', 'policy'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-cache', 'policy', 'med-bio'] 0m5.6s DUMP: med-bio: Installed: (none) Candidate: 3.0.1 Version table: 3.0.1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-cache', 'policy', 'med-bio'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-get', '-y', 'install', 'med-bio'] 0m7.7s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: blends-common liblocale-gettext-perl med-config med-tasks menu tasksel tasksel-data Suggested packages: blends-doc acacia adun.app amos-assembler amoscmp apollo arachne arb asap autodocktools axparafit axpcoords bagpipe baitfisher bambus beads bedops biceps big-blast bigsdb bio-tradis biomaj biomaj-watcher bitseq blat blimps-utils blixem blobology btk-core cactus caftools cain canu cap3 ccs cdna-db cinema clonalorigin cluster3 cmap cnvkit coalesce compclust condetri contrafold contralign coot copycat crossbow crux-toolkit cufflinks cytoscape das-proserver dazzle decipher deepnano diamond-aligner e-hive ecell elph embassy-phylip emboss-explorer emmax emperor ensembl est-db estferret estscan euler-sr euler2 exabayes exalt examl excavator fasta fasta3 ffp figaro finex fluctuate forester forge freebayes galaxy gassst gatk gbioseq gbrowse-syn genemark genesplicer genetrack genezilla genographer getdata glimmerhmm gmap gmv grabix grogui haploview hawkeye hexamer hilbertvisgui htqc igv inspect jalview jbrowse jigsaw jstreeview kclust kempbasu lagan lamarc lofreq logomat-m lucy mach-haplotyper mage2tab maker2 malt manta martj maude maxd melting-gui meme mesquite metabit metarep metastudent-data metastudent-data-2 metastudent-data-3 mgltools-cadd mgltools-pmv mgltools-vision migrate minimus mirbase mobyle mobyle-programs mobyle-tutorials modeller molekel mosaik-aligner mpsqed mptp mrs msatfinder mugsy mummergpu mview nanocall nextsv ngila ngsqctoolkit nw-align oases obitools obo-edit oligoarrayaux omegamap openms operondb pal2nal paleomix paml partigene partitionfinder patman patristic pcma pfaat pftools phagefinder phast phpphylotree phylographer phylophlan phyloviz-core phylowin pipasic plato profit prokka prot4est pscan-tfbs psipred psortb pssh2 pyrophosphate-tools python-orange python-reaper python3-biomaj3 qcumber qiime qtlcart qualimap r-bioc-annotationhub r-bioc-aroma.light r-bioc-ensembldb r-bioc-go.db r-bioc-savr r-cran-boolnet r-cran-metamix r-cran-pheatmap r-cran-qqman r-cran-rentrez r-other-apmswapp r-other-valdar-bagphenotype.library raccoon radiant raxml-ng rbs-finder recombine repeatmasker rmblast roadtrips roche454ace2caf roguenarok rose rosetta rsat runcircos-gui sambamba sap science-workflow segemehl seq-gen seqsero sequenceconverter.app sift situs snpeff sparta spice splitstree ssaha strap strap-base tacg taverna taxinspector tetra tide tigr-glimmer-mg tnseq-transit topp trace2dbest tracetuner treebuilder3d treetime tripal trnascan-se tvc twain ugene unc-fish uniprime varmatch varscan vienna-rna vmd x-tandem-pipeline zodiac-zeden menu-l10n gksu | kde-runtime | ktsuss Recommended packages: abacas abyss acedb-other acedb-other-belvu acedb-other-dotter adapterremoval adun-core aegean aevol alien-hunter alter-sequence-alignment altree amap-align ampliconnoise andi anfo aragorn arden ariba art-nextgen-simulation-tools artemis artfastqgenerator atac augustus autodock autodock-vina autogrid axe-demultiplexer ballview bamtools barrnap bcftools beagle beast-mcmc beast2-mcmc bedtools berkeley-express bio-eagle bio-rainbow blasr bowtie bowtie2 boxshade brig bwa cassiopee cd-hit cdbfasta cgview chimeraslayer circlator circos clearcut clonalframe clustalo clustalw clustalx codonw concavity conservation-code crac cutadapt daligner dascrubber datamash dawg dazzdb dialign dialign-tx dindel discosnp disulfinder dnaclust dssp dwgsim ea-utils ecopcr edtsurf eigensoft embassy-domainatrix embassy-domalign embassy-domsearch emboss exonerate falcon fastahack fastaq fastdnaml fastlink fastml fastqc fastqtl fasttree fastx-toolkit ffindex figtree filo fitgcp flexbar fml-asm freecontact fsa fsm-lite gamgi garli garlic gasic gbrowse gdpc genometools gentle gff2aplot gff2ps ghemical giira glam2 graphlan grinder gromacs gubbins gwama harvest-tools hhsuite hilive hisat2 hmmer hmmer2 hyphy-mpi | hyphy-pt hyphygui idba indelible infernal ipig iqtree iva jaligner jellyfish jmodeltest jmol kalign khmer kineticstools king-probe kissplice kmc kmer kraken lambda-align last-align leaff lefse librg-utils-perl libvcflib-tools logol-bin loki ltrsift macs macsyfinder maffilter mafft mapdamage mapsembler2 maq maqview mash massxpert mauve-aligner melting meryl metaphlan2 metastudent mhap microbegps microbiomeutil minia miniasm minimap mipe mira-assembler mlv-smile mothur mrbayes mummer murasaki muscle mustang nanopolish nast-ier ncbi-blast+ ncbi-blast+-legacy ncbi-entrez-direct ncbi-epcr ncbi-seg ncbi-tools-bin ncbi-tools-x11 ncl-tools ncoils neobio njplot norsnet norsp paraclu parsinsert parsnp pbalign pbbarcode pbdagcon pbgenomicconsensus pbh5tools pbhoney pbjelly pbsim pbsuite pdb2pqr perlprimer perm phipack phybin phylip phyml physamp phyutility picard-tools piler pirs placnet plasmidomics plast plink plink1.9 plip poa populations poretools prank predictnls predictprotein prime-phylo primer3 proalign probabel probalign probcons proda prodigal profbval profisis profnet-bval profnet-chop profnet-con profnet-isis profnet-md profnet-norsnet profnet-prof profnet-snapfun profphd profphd-net profphd-utils proftmb progressivemauve proteinortho prottest pycorrfit pymol pynast pyscanfcs python-cogent qtltools r-bioc-annotate r-bioc-biostrings r-bioc-cummerbund r-bioc-deseq2 r-bioc-dnacopy r-bioc-ebseq r-bioc-edger r-bioc-genefilter r-bioc-geneplotter r-bioc-gviz r-bioc-hilbertvis r-bioc-limma r-bioc-mergeomics r-bioc-metagenomeseq r-bioc-phyloseq r-bioc-rtracklayer r-cran-adegenet r-cran-adephylo r-cran-ape r-cran-bio3d r-cran-distory r-cran-genabel r-cran-phangorn r-cran-pscbs r-cran-qtl r-cran-rotl r-cran-seqinr r-cran-treescape r-cran-vegan r-other-mott-happy.hbrem rambo-k rapmap rasmol raster3d rate4site raxml ray rdp-alignment rdp-classifier rdp-readseq readseq reapr relion-bin | relion-bin+mpi relion-bin+gui | relion-bin+mpi+gui repeatmasker-recon reprof rna-star rnahybrid roary rsem rtax saint salmon samtools scrm scythe seaview seer seqan-apps seqprep seqtk sga sibsim4 sickle sigma-align sim4 sim4db smalt smithwaterman smrtanalysis snap snap-aligner sniffles snp-sites snpomatic soapdenovo soapdenovo2 sortmerna spaced spades sprai spread-phy squizz sra-toolkit srst2 ssake sspace ssw-align stacks staden staden-io-lib-utils subread suitename sumaclust sumatra sumtrees surankco swarm t-coffee tabix tantan theseus tigr-glimmer tm-align tophat toppred transdecoder transrate-tools transtermhp tree-puzzle | tree-ppuzzle treeview treeviewx trimmomatic trinityrnaseq uc-echo varna vcftools velvet | velvet-long velvetoptimiser vsearch wigeon wise zalign laptop-detect The following NEW packages will be installed: blends-common liblocale-gettext-perl med-bio med-config med-tasks menu tasksel tasksel-data 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. Need to get 584 kB of archives. After this operation, 2321 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian stretch/main amd64 liblocale-gettext-perl amd64 1.07-3+b1 [18.7 kB] Get:2 http://deb.debian.org/debian stretch/main amd64 tasksel-data all 3.39 [18.1 kB] Get:3 http://deb.debian.org/debian stretch/main amd64 tasksel all 3.39 [94.6 kB] Get:4 http://deb.debian.org/debian stretch/main amd64 menu amd64 2.1.47+b1 [380 kB] Get:5 http://deb.debian.org/debian stretch/main amd64 blends-common all 0.6.96 [23.3 kB] Get:6 http://deb.debian.org/debian stretch/main amd64 med-tasks all 3.0.1 [14.3 kB] Get:7 http://deb.debian.org/debian stretch/main amd64 med-config all 3.0.1 [17.1 kB] Get:8 http://deb.debian.org/debian stretch/main amd64 med-bio all 3.0.1 [18.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 584 kB in 0s (1478 kB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4411 files and directories currently installed.) Preparing to unpack .../0-liblocale-gettext-perl_1.07-3+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b1) ... Selecting previously unselected package tasksel-data. Preparing to unpack .../1-tasksel-data_3.39_all.deb ... Unpacking tasksel-data (3.39) ... Selecting previously unselected package tasksel. Preparing to unpack .../2-tasksel_3.39_all.deb ... Unpacking tasksel (3.39) ... Selecting previously unselected package menu. Preparing to unpack .../3-menu_2.1.47+b1_amd64.deb ... Unpacking menu (2.1.47+b1) ... Selecting previously unselected package blends-common. Preparing to unpack .../4-blends-common_0.6.96_all.deb ... Unpacking blends-common (0.6.96) ... Selecting previously unselected package med-tasks. Preparing to unpack .../5-med-tasks_3.0.1_all.deb ... Unpacking med-tasks (3.0.1) ... Selecting previously unselected package med-config. Preparing to unpack .../6-med-config_3.0.1_all.deb ... Unpacking med-config (3.0.1) ... Selecting previously unselected package med-bio. Preparing to unpack .../7-med-bio_3.0.1_all.deb ... Unpacking med-bio (3.0.1) ... Setting up menu (2.1.47+b1) ... Setting up liblocale-gettext-perl (1.07-3+b1) ... Processing triggers for menu (2.1.47+b1) ... Setting up blends-common (0.6.96) ... Setting up med-config (3.0.1) ... Adding group `med' (GID 150) ... Done. Setting up tasksel-data (3.39) ... Setting up tasksel (3.39) ... Setting up med-tasks (3.0.1) ... Setting up med-bio (3.0.1) ... Processing triggers for menu (2.1.47+b1) ... 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-get', '-y', 'install', 'med-bio'] 0m7.7s INFO: Running scripts post_install 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_install_exceptions'] 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_install_exceptions'] 0m7.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l'] 0m8.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l'] 0m8.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpfltc2e8l to stretch-lts 0m8.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main deb http://security.debian.org stretch/updates main 0m8.0s INFO: Running scripts pre_distupgrade 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_distupgrade_exceptions'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_distupgrade_exceptions'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-get', 'update'] 0m9.5s DUMP: Get:1 http://security.debian.org stretch/updates InRelease [59.1 kB] Ign:2 http://deb.debian.org/debian stretch InRelease Hit:3 http://deb.debian.org/debian stretch Release Get:4 http://security.debian.org stretch/updates/main amd64 Packages [782 kB] Get:5 http://security.debian.org stretch/updates/main Translation-en [368 kB] Fetched 1209 kB in 0s (2112 kB/s) Reading package lists... 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-get', 'update'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-get', '-yf', 'dist-upgrade'] 0m13.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt debian-archive-keyring dpkg e2fslibs e2fsprogs gzip libapt-pkg5.0 libcomerr2 libgcrypt20 liblz4-1 liblzma5 libss2 libsystemd0 libudev1 login passwd tar zlib1g 18 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 9594 kB of archives. After this operation, 50.2 kB of additional disk space will be used. Get:1 http://security.debian.org stretch/updates/main amd64 tar amd64 1.29b-1.1+deb9u1 [760 kB] Get:2 http://security.debian.org stretch/updates/main amd64 dpkg amd64 1.18.26 [2117 kB] Get:3 http://security.debian.org stretch/updates/main amd64 e2fslibs amd64 1.43.4-2+deb9u2 [208 kB] Get:4 http://security.debian.org stretch/updates/main amd64 e2fsprogs amd64 1.43.4-2+deb9u2 [948 kB] Get:5 http://security.debian.org stretch/updates/main amd64 gzip amd64 1.6-5+deb9u1 [114 kB] Get:6 http://security.debian.org stretch/updates/main amd64 login amd64 1:4.4-4.1+deb9u1 [790 kB] Get:7 http://security.debian.org stretch/updates/main amd64 debian-archive-keyring all 2017.5+deb9u2 [92.4 kB] Get:8 http://security.debian.org stretch/updates/main amd64 liblz4-1 amd64 0.0~r131-2+deb9u1 [33.2 kB] Get:9 http://security.debian.org stretch/updates/main amd64 liblzma5 amd64 5.2.2-1.2+deb9u1 [234 kB] Get:10 http://security.debian.org stretch/updates/main amd64 zlib1g amd64 1:1.2.8.dfsg-5+deb9u1 [87.8 kB] Get:11 http://security.debian.org stretch/updates/main amd64 libapt-pkg5.0 amd64 1.4.11 [917 kB] Get:12 http://security.debian.org stretch/updates/main amd64 apt amd64 1.4.11 [1232 kB] Get:13 http://security.debian.org stretch/updates/main amd64 libsystemd0 amd64 232-25+deb9u14 [282 kB] Get:14 http://security.debian.org stretch/updates/main amd64 libcomerr2 amd64 1.43.4-2+deb9u2 [63.8 kB] Get:15 http://security.debian.org stretch/updates/main amd64 libss2 amd64 1.43.4-2+deb9u2 [68.0 kB] Get:16 http://security.debian.org stretch/updates/main amd64 passwd amd64 1:4.4-4.1+deb9u1 [997 kB] Get:17 http://security.debian.org stretch/updates/main amd64 libudev1 amd64 232-25+deb9u14 [126 kB] Get:18 http://security.debian.org stretch/updates/main amd64 libgcrypt20 amd64 1.7.6-2+deb9u4 [523 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 9594 kB in 0s (48.8 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4815 files and directories currently installed.) Preparing to unpack .../tar_1.29b-1.1+deb9u1_amd64.deb ... Unpacking tar (1.29b-1.1+deb9u1) over (1.29b-1.1) ... Setting up tar (1.29b-1.1+deb9u1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4815 files and directories currently installed.) Preparing to unpack .../gzip_1.6-5+deb9u1_amd64.deb ... Unpacking gzip (1.6-5+deb9u1) over (1.6-5+b1) ... Setting up gzip (1.6-5+deb9u1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4815 files and directories currently installed.) Preparing to unpack .../libapt-pkg5.0_1.4.11_amd64.deb ... Unpacking libapt-pkg5.0:amd64 (1.4.11) over (1.4.10) ... Setting up libapt-pkg5.0:amd64 (1.4.11) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4815 files and directories currently installed.) Preparing to unpack .../archives/apt_1.4.11_amd64.deb ... Unpacking apt (1.4.11) over (1.4.10) ... Setting up apt (1.4.11) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4815 files and directories currently installed.) Preparing to unpack .../libsystemd0_232-25+deb9u14_amd64.deb ... Unpacking libsystemd0:amd64 (232-25+deb9u14) over (232-25+deb9u12) ... Setting up libsystemd0:amd64 (232-25+deb9u14) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4815 files and directories currently installed.) Preparing to unpack .../libcomerr2_1.43.4-2+deb9u2_amd64.deb ... Unpacking libcomerr2:amd64 (1.43.4-2+deb9u2) over (1.43.4-2+deb9u1) ... Setting up libcomerr2:amd64 (1.43.4-2+deb9u2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4815 files and directories currently installed.) Preparing to unpack .../libss2_1.43.4-2+deb9u2_amd64.deb ... Unpacking libss2:amd64 (1.43.4-2+deb9u2) over (1.43.4-2+deb9u1) ... Setting up libss2:amd64 (1.43.4-2+deb9u2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4815 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.4-4.1+deb9u1_amd64.deb ... Unpacking passwd (1:4.4-4.1+deb9u1) over (1:4.4-4.1) ... Setting up passwd (1:4.4-4.1+deb9u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4815 files and directories currently installed.) Preparing to unpack .../libudev1_232-25+deb9u14_amd64.deb ... Unpacking libudev1:amd64 (232-25+deb9u14) over (232-25+deb9u12) ... Setting up libudev1:amd64 (232-25+deb9u14) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4815 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.7.6-2+deb9u4_amd64.deb ... Unpacking libgcrypt20:amd64 (1.7.6-2+deb9u4) over (1.7.6-2+deb9u3) ... Setting up libgcrypt20:amd64 (1.7.6-2+deb9u4) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-get', '-yf', 'dist-upgrade'] 0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m13.6s DUMP: f0660a0a38f941b755664f52e8306b99 - 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-cache', 'show', '--no-all-versions', 'med-bio'] 0m13.8s DUMP: Package: med-bio Source: debian-med Version: 3.0.1 Installed-Size: 46 Maintainer: Debian Med Packaging Team Architecture: all Depends: med-tasks (= 3.0.1), med-config (= 3.0.1) Recommends: abacas, abyss, acedb-other, acedb-other-belvu, acedb-other-dotter, adapterremoval, adun-core, aegean, aevol, alien-hunter, alter-sequence-alignment, altree, amap-align, ampliconnoise, andi, anfo, aragorn, arden, ariba, art-nextgen-simulation-tools, artemis, artfastqgenerator, atac, augustus, autodock, autodock-vina, autogrid, axe-demultiplexer, ballview, bamtools, barrnap, bcftools, beagle, beast-mcmc, beast2-mcmc, bedtools, berkeley-express, bio-eagle, bio-rainbow, blasr, bowtie, bowtie2, boxshade, brig, bwa, cassiopee, cd-hit, cdbfasta, cgview, chimeraslayer, circlator, circos, clearcut, clonalframe, clustalo, clustalw, clustalx, codonw, concavity, conservation-code, crac, cutadapt, daligner, dascrubber, datamash, dawg, dazzdb, dialign, dialign-tx, dindel, discosnp, disulfinder, dnaclust, dssp, dwgsim, ea-utils, ecopcr, edtsurf, eigensoft, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, exonerate, falcon, fastahack, fastaq, fastdnaml, fastlink, fastml, fastqc, fastqtl, fasttree, fastx-toolkit, ffindex, figtree, filo, fitgcp, flexbar, fml-asm, freecontact, fsa, fsm-lite, gamgi, garli, garlic, gasic, gbrowse, gdpc, genometools, gentle, gff2aplot, gff2ps, ghemical, giira, glam2, graphlan, grinder, gromacs, gubbins, gwama, harvest-tools, hhsuite, hilive, hisat2, hmmer, hmmer2, hyphy-mpi | hyphy-pt, hyphygui, idba, indelible, infernal, ipig, iqtree, iva, jaligner, jellyfish, jmodeltest, jmol, kalign, khmer, kineticstools, king-probe, kissplice, kmc, kmer, kraken, lambda-align, last-align, leaff, lefse, librg-utils-perl, libvcflib-tools, logol-bin, loki, ltrsift, macs, macsyfinder, maffilter, mafft, mapdamage, mapsembler2, maq, maqview, mash, massxpert, mauve-aligner, melting, meryl, metaphlan2, metastudent, mhap, microbegps, microbiomeutil, minia, miniasm, minimap, mipe, mira-assembler, mlv-smile, mothur, mrbayes, mummer, murasaki, muscle, mustang, nanopolish, nast-ier, ncbi-blast+, ncbi-blast+-legacy, ncbi-entrez-direct, ncbi-epcr, ncbi-seg, ncbi-tools-bin, ncbi-tools-x11, ncl-tools, ncoils, neobio, njplot, norsnet, norsp, paraclu, parsinsert, parsnp, pbalign, pbbarcode, pbdagcon, pbgenomicconsensus, pbh5tools, pbhoney, pbjelly, pbsim, pbsuite, pdb2pqr, perlprimer, perm, phipack, phybin, phylip, phyml, physamp, phyutility, picard-tools, piler, pirs, placnet, plasmidomics, plast, plink, plink1.9, plip, poa, populations, poretools, prank, predictnls, predictprotein, prime-phylo, primer3, proalign, probabel, probalign, probcons, proda, prodigal, profbval, profisis, profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun, profphd, profphd-net, profphd-utils, proftmb, progressivemauve, proteinortho, prottest, pycorrfit, pymol, pynast, pyscanfcs, python-cogent, qtltools, r-bioc-annotate, r-bioc-biostrings, r-bioc-cummerbund, r-bioc-deseq2, r-bioc-dnacopy, r-bioc-ebseq, r-bioc-edger, r-bioc-genefilter, r-bioc-geneplotter, r-bioc-gviz, r-bioc-hilbertvis, r-bioc-limma, r-bioc-mergeomics, r-bioc-metagenomeseq, r-bioc-phyloseq, r-bioc-rtracklayer, r-cran-adegenet, r-cran-adephylo, r-cran-ape, r-cran-bio3d, r-cran-distory, r-cran-genabel, r-cran-phangorn, r-cran-pscbs, r-cran-qtl, r-cran-rotl, r-cran-seqinr, r-cran-treescape, r-cran-vegan, r-other-mott-happy.hbrem, rambo-k, rapmap, rasmol, raster3d, rate4site, raxml, ray, rdp-alignment, rdp-classifier, rdp-readseq, readseq, reapr, relion-bin | relion-bin+mpi, relion-bin+gui | relion-bin+mpi+gui, repeatmasker-recon, reprof, rna-star, rnahybrid, roary, rsem, rtax, saint, salmon, samtools, scrm, scythe, seaview, seer, seqan-apps, seqprep, seqtk, sga, sibsim4, sickle, sigma-align, sim4, sim4db, smalt, smithwaterman, smrtanalysis, snap, snap-aligner, sniffles, snp-sites, snpomatic, soapdenovo, soapdenovo2, sortmerna, spaced, spades, sprai, spread-phy, squizz, sra-toolkit, srst2, ssake, sspace, ssw-align, stacks, staden, staden-io-lib-utils, subread, suitename, sumaclust, sumatra, sumtrees, surankco, swarm, t-coffee, tabix, tantan, theseus, tigr-glimmer, tm-align, tophat, toppred, transdecoder, transrate-tools, transtermhp, tree-puzzle | tree-ppuzzle, treeview, treeviewx, trimmomatic, trinityrnaseq, uc-echo, varna, vcftools, velvet | velvet-long, velvetoptimiser, vsearch, wigeon, wise, zalign Suggests: acacia, adun.app, amos-assembler, amoscmp, apollo, arachne, arb, asap, autodocktools, axparafit, axpcoords, bagpipe, baitfisher, bambus, beads, bedops, biceps, big-blast, bigsdb, bio-tradis, biomaj, biomaj-watcher, bitseq, blat, blimps-utils, blixem, blobology, btk-core, cactus, caftools, cain, canu, cap3, ccs, cdna-db, cinema, clonalorigin, cluster3, cmap, cnvkit, coalesce, compclust, condetri, contrafold, contralign, coot, copycat, crossbow, crux-toolkit, cufflinks, cytoscape, das-proserver, dazzle, decipher, deepnano, diamond-aligner, e-hive, ecell, elph, embassy-phylip, emboss-explorer, emmax, emperor, ensembl, est-db, estferret, estscan, euler-sr, euler2, exabayes, exalt, examl, excavator, fasta, fasta3, ffp, figaro, finex, fluctuate, forester, forge, freebayes, galaxy, gassst, gatk, gbioseq, gbrowse-syn, genemark, genesplicer, genetrack, genezilla, genographer, getdata, glimmerhmm, gmap, gmv, grabix, grogui, haploview, hawkeye, hexamer, hilbertvisgui, htqc, igv, inspect, jalview, jbrowse, jigsaw, jstreeview, kclust, kempbasu, lagan, lamarc, lofreq, logomat-m, lucy, mach-haplotyper, mage2tab, maker2, malt, manta, martj, maude, maxd, melting-gui, meme, mesquite, metabit, metarep, metastudent-data, metastudent-data-2, metastudent-data-3, mgltools-cadd, mgltools-pmv, mgltools-vision, migrate, minimus, mirbase, mobyle, mobyle-programs, mobyle-tutorials, modeller, molekel, mosaik-aligner, mpsqed, mptp, mrs, msatfinder, mugsy, mummergpu, mview, nanocall, nextsv, ngila, ngsqctoolkit, nw-align, oases, obitools, obo-edit, oligoarrayaux, omegamap, openms, operondb, pal2nal, paleomix, paml, partigene, partitionfinder, patman, patristic, pcma, pfaat, pftools, phagefinder, phast, phpphylotree, phylographer, phylophlan, phyloviz-core, phylowin, pipasic, plato, profit, prokka, prot4est, pscan-tfbs, psipred, psortb, pssh2, pyrophosphate-tools, python-orange, python-reaper, python3-biomaj3, qcumber, qiime, qtlcart, qualimap, r-bioc-annotationhub, r-bioc-aroma.light, r-bioc-ensembldb, r-bioc-go.db, r-bioc-savr, r-cran-boolnet, r-cran-metamix, r-cran-pheatmap, r-cran-qqman, r-cran-rentrez, r-other-apmswapp, r-other-valdar-bagphenotype.library, raccoon, radiant, raxml-ng, rbs-finder, recombine, repeatmasker, rmblast, roadtrips, roche454ace2caf, roguenarok, rose, rosetta, rsat, runcircos-gui, sambamba, sap, science-workflow, segemehl, seq-gen, seqsero, sequenceconverter.app, sift, situs, snpeff, sparta, spice, splitstree, ssaha, strap, strap-base, tacg, taverna, taxinspector, tetra, tide, tigr-glimmer-mg, tnseq-transit, topp, trace2dbest, tracetuner, treebuilder3d, treetime, tripal, trnascan-se, tvc, twain, ugene, unc-fish, uniprime, varmatch, varscan, vienna-rna, vmd, x-tandem-pipeline, zodiac-zeden Description-en: Debian Med bioinformatics packages This metapackage will install Debian packages for use in molecular biology, structural biology and other biological sciences. Description-md5: 472a50c6504872b123b928f5c13e0f5e Tag: field::biology, role::metapackage, suite::debian Section: misc Priority: extra Filename: pool/main/d/debian-med/med-bio_3.0.1_all.deb Size: 18660 MD5sum: 10b64f80ea5762265cbb0aec5a872959 SHA256: f3869d6d9e719cb9917fe4545bea317a2af385cb2c5acfe5c1c428bc664150df 0m13.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-cache', 'show', '--no-all-versions', 'med-bio'] 0m13.8s INFO: apt-cache knows about the following packages: med-bio 0m13.8s INFO: Running scripts pre_install 0m13.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_database-server'] 0m13.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_database-server'] 0m13.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_exceptions'] 0m13.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_exceptions'] 0m13.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_extras'] 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_extras'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_foreign_architecture'] 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_foreign_architecture'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-cache', 'policy'] 0m14.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://security.debian.org stretch/updates/main amd64 Packages release v=9,o=Debian,a=oldoldstable,n=stretch,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian stretch/main amd64 Packages release v=9.13,o=Debian,a=oldoldstable,n=stretch,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-cache', 'policy'] 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-cache', 'policy', 'med-bio'] 0m14.0s DUMP: med-bio: Installed: 3.0.1 Candidate: 3.0.1 Version table: *** 3.0.1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 100 /var/lib/dpkg/status 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-cache', 'policy', 'med-bio'] 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-get', '-y', 'install', 'med-bio'] 0m14.3s DUMP: Reading package lists... Building dependency tree... Reading state information... med-bio is already the newest version (3.0.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-get', '-y', 'install', 'med-bio'] 0m14.3s INFO: Running scripts post_install 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_install_exceptions'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_install_exceptions'] 0m14.3s INFO: Running scripts post_distupgrade 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_distupgrade_exceptions'] 0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_distupgrade_exceptions'] 0m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_distupgrade_zz_backports'] 0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_distupgrade_zz_backports'] 0m14.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l'] 0m14.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l'] 0m14.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l'] 0m14.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l'] 0m14.9s INFO: Running scripts pre_install 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_database-server'] 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_database-server'] 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_exceptions'] 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_exceptions'] 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_extras'] 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_extras'] 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_foreign_architecture'] 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_foreign_architecture'] 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-cache', 'policy'] 0m15.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://security.debian.org stretch/updates/main amd64 Packages release v=9,o=Debian,a=oldoldstable,n=stretch,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian stretch/main amd64 Packages release v=9.13,o=Debian,a=oldoldstable,n=stretch,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m15.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-cache', 'policy'] 0m15.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-cache', 'policy', 'med-bio'] 0m15.0s DUMP: med-bio: Installed: 3.0.1 Candidate: 3.0.1 Version table: *** 3.0.1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 100 /var/lib/dpkg/status 0m15.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-cache', 'policy', 'med-bio'] 0m15.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-get', '-y', 'install', 'med-bio=3.0.1'] 0m15.3s DUMP: Reading package lists... Building dependency tree... Reading state information... med-bio is already the newest version (3.0.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m15.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-get', '-y', 'install', 'med-bio=3.0.1'] 0m15.3s INFO: Running scripts post_install 0m15.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_install_exceptions'] 0m15.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_install_exceptions'] 0m15.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l'] 0m15.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l'] 0m15.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', '-ac', '--ignore-obsolete'] 0m16.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', '-ac', '--ignore-obsolete'] 0m16.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m16.3s DUMP: 0.15.6 0m16.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m16.3s INFO: Running adequate version 0.15.6 now. 0m16.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'med-bio'] 0m16.4s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'med-bio'] 0m16.4s INFO: Running scripts pre_remove 0m16.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m16.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m16.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m17.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m17.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_remove_exceptions'] 0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/pre_remove_exceptions'] 0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m17.2s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.11 install ok installed base-files base-files 9.9+deb9u13 install ok installed base-passwd base-passwd 3.5.43 install ok installed bash bash 4.4-5 install ok installed blends-common blends-common 0.6.96 install ok installed bsdutils bsdutils 1:2.29.2-1+deb9u1 install ok installed coreutils coreutils 8.26-3 install ok installed dash dash 0.5.8-2.4 install ok installed debconf debconf 1.5.61 install ok installed debian-archive-keyring debian-archive-keyring 2017.5+deb9u2 install ok installed debianutils debianutils 4.8.1.1 install ok installed diffutils diffutils 1:3.5-3 install ok installed dpkg dpkg 1.18.26 install ok installed e2fslibs:amd64 e2fslibs 1.43.4-2+deb9u2 install ok installed e2fsprogs e2fsprogs 1.43.4-2+deb9u2 install ok installed findutils findutils 4.6.0+git+20161106-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gpgv gpgv 2.1.18-8~deb9u4 install ok installed grep grep 2.27-2 install ok installed gzip gzip 1.6-5+deb9u1 install ok installed hostname hostname 3.18+b1 install ok installed init-system-helpers init-system-helpers 1.48 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.4.11 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.6.7-2 install ok installed libaudit1:amd64 libaudit1 1:2.6.7-2 install ok installed libblkid1:amd64 libblkid1 2.29.2-1+deb9u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-8.1 install ok installed libc-bin libc-bin 2.24-11+deb9u4 install ok installed libc6:amd64 libc6 2.24-11+deb9u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2+deb9u2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-12+deb9u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.227 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libgcc1:amd64 libgcc1 1:6.3.0-18+deb9u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.7.6-2+deb9u4 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed liblocale-gettext-perl liblocale-gettext-perl 1.07-3+b1 install ok installed liblz4-1:amd64 liblz4-1 0.0~r131-2+deb9u1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.2+deb9u1 install ok installed libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libncursesw5:amd64 libncursesw5 6.0+20161126-1+deb9u2 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.6 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.6 install ok installed libpam-runtime libpam-runtime 1.1.8-3.6 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.6 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libselinux1:amd64 libselinux1 2.6-3+b3 install ok installed libsemanage-common libsemanage-common 2.6-2 install ok installed libsemanage1:amd64 libsemanage1 2.6-2 install ok installed libsepol1:amd64 libsepol1 2.6-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u2 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u14 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u14 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.29.2-1+deb9u1 install ok installed login login 1:4.4-4.1+deb9u1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed med-bio med-bio 3.0.1 install ok installed med-config med-config 3.0.1 install ok installed med-tasks med-tasks 3.0.1 install ok installed menu menu 2.1.47+b1 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed ncurses-base ncurses-base 6.0+20161126-1+deb9u2 install ok installed ncurses-bin ncurses-bin 6.0+20161126-1+deb9u2 install ok installed passwd passwd 1:4.4-4.1+deb9u1 install ok installed perl-base perl-base 5.24.1-3+deb9u7 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59.9 install ok installed tar tar 1.29b-1.1+deb9u1 install ok installed tasksel tasksel 3.39 install ok installed tasksel-data tasksel-data 3.39 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5+deb9u1 0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-get', 'remove', 'blends-common', 'liblocale-gettext-perl', 'med-config', 'med-tasks', 'menu', 'tasksel', 'tasksel-data', 'med-bio'] 0m18.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: blends-common liblocale-gettext-perl med-bio med-config med-tasks menu tasksel tasksel-data 0 upgraded, 0 newly installed, 8 to remove and 0 not upgraded. After this operation, 2321 kB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4815 files and directories currently installed.) Removing med-bio (3.0.1) ... Removing med-config (3.0.1) ... Removing blends-common (0.6.96) ... Removing med-tasks (3.0.1) ... Removing menu (2.1.47+b1) ... Removing tasksel (3.39) ... Removing tasksel-data (3.39) ... Removing liblocale-gettext-perl (1.07-3+b1) ... 0m18.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-get', 'remove', 'blends-common', 'liblocale-gettext-perl', 'med-config', 'med-tasks', 'menu', 'tasksel', 'tasksel-data', 'med-bio'] 0m18.2s INFO: Running scripts post_remove 0m18.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_remove_exceptions'] 0m18.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_remove_exceptions'] 0m18.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'dpkg', '--purge', 'blends-common', 'liblocale-gettext-perl', 'med-config', 'med-tasks', 'menu', 'tasksel', 'tasksel-data'] 0m18.4s DUMP: (Reading database ... 4422 files and directories currently installed.) Purging configuration files for blends-common (0.6.96) ... dpkg: warning: ignoring request to remove liblocale-gettext-perl which isn't installed Purging configuration files for med-config (3.0.1) ... dpkg: warning: ignoring request to remove med-tasks which isn't installed Purging configuration files for menu (2.1.47+b1) ... Purging configuration files for tasksel (3.39) ... dpkg: warning: ignoring request to remove tasksel-data which isn't installed 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'dpkg', '--purge', 'blends-common', 'liblocale-gettext-perl', 'med-config', 'med-tasks', 'menu', 'tasksel', 'tasksel-data'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'dpkg', '--purge', 'med-bio'] 0m18.4s DUMP: dpkg: warning: ignoring request to remove med-bio which isn't installed 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'dpkg', '--purge', 'med-bio'] 0m18.4s INFO: Running scripts post_purge 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_purge_exceptions'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_purge_exceptions'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'dpkg', '--purge', '--pending'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'dpkg', '--purge', '--pending'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'dpkg', '--remove', '--pending'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'dpkg', '--remove', '--pending'] 0m18.5s INFO: Running scripts post_test 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_test_exceptions'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'tmp/scripts/post_test_exceptions'] 0m18.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l'] 0m18.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l'] 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'dpkg-divert', '--list'] 0m18.8s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m18.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'dpkg-divert', '--list'] 0m18.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-get', 'clean'] 0m18.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l', 'apt-get', 'clean'] 0m18.8s DEBUG: Recording chroot state 0m19.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l/dev/shm'] 0m19.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l/dev/shm'] 0m19.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l/dev/console'] 0m19.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l/dev/console'] 0m19.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l/dev/ptmx'] 0m19.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l/dev/ptmx'] 0m19.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l/dev/pts'] 0m19.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l/dev/pts'] 0m19.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l/proc'] 0m19.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l/proc'] 0m19.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l'] 0m19.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpfltc2e8l'] 0m19.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpfltc2e8l 0m19.6s INFO: PASS: Upgrading between Debian distributions. 0m19.6s INFO: PASS: All tests. 0m19.6s INFO: piuparts run ends. ret=0 End: 2023-03-18 17:09:03 GMT