Start: 2024-01-17 17:07:32 GMT Package: med-bio Source: debian-med Version: 3.8.1 Installed-Size: 44 Maintainer: Debian Med Packaging Team Architecture: all Depends: med-config (= 3.8.1), med-tasks (= 3.8.1) Recommends: abacas, abpoa, abyss, acedb-other, adapterremoval, adun-core, aegean, aevol, alien-hunter, alter-sequence-alignment, altree, amap-align, ampliconnoise, andi, any2fasta, aragorn, arden, ariba, art-nextgen-simulation-tools, artemis, artfastqgenerator, assembly-stats, assemblytics, atac, ataqv, atropos, augur, augustus, autodock, autodock-vina, autogrid, avogadro, axe-demultiplexer, baitfisher, bali-phy, ballview, bamclipper, bamkit, bamtools, bandage, barrnap, bbmap, bcalm, bcftools, beads, beagle, beast-mcmc, beast2-mcmc, bedops, bedtools, belvu, berkeley-express, bio-eagle, bio-rainbow, bio-tradis, bio-vcf, bioawk, biobambam2, biosyntax, bitseq, blasr, blixem, bolt-lmm, bowtie, bowtie2, boxshade, bppphyview, bppsuite, brig, btllib-tools, busco, bustools, bwa, canu, cassiopee, cat-bat, cct, cd-hit, cdbfasta, centrifuge, cgview, changeo, chimeraslayer, chromhmm, chromimpute, cif-tools, circlator, circos, clearcut, clonalframe, clonalframeml, clonalorigin, clustalo, clustalw, clustalx, cnvkit, codonw, comet-ms, concavity, conservation-code, covtobed, crac, csb, cutadapt, cutesv, daligner, damapper, datamash, dawg, dazzdb, delly, density-fitness, dextractor, dialign, dialign-tx, diamond-aligner, discosnp, disulfinder, dnaclust, dnarrange, dotter, drop-seq-tools, dssp, dwgsim, e-mem, ea-utils, ecopcr, edtsurf, eigensoft, elph, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, emmax, estscan, examl, exonerate, fasta3, fastahack, fastani, fastaq, fastdnaml, fastlink, fastml, fastp, fastq-pair, fastqc, fastqtl, fasttree, ffindex, figtree, filtlong, fitgcp, flash, flexbar, flye, fml-asm, freebayes, freecontact, fsa, fsm-lite, gamgi, garli, garlic, gasic, gatb-core, gbrowse, gdpc, gemma, genometester, genomethreader, genometools, genomicsdb-tools, gentle, gff2aplot, gff2ps, gffread, ggd-utils, ghemical, ghmm, glam2, gmap, grabix, graphlan, grinder, gromacs, gsort, gubbins, gwama, harvest-tools, hhsuite, hilive, hinge, hisat2, hmmer, hmmer2, hyphy-mpi | hyphy-pt, idba, igblast, igor, igv, indelible, infernal, insilicoseq, ipig, iqtree, iva, jaligner, jalview, jellyfish, jellyfish1, jmodeltest, jmol, kalign, kallisto, kaptive, khmer, kineticstools, king-probe, kissplice, kleborate, kma, kmc, kmer, kmerresistance, kraken, kraken2, lagan, lamarc, lamassemble, lambda-align, lambda-align2, last-align, lastz, leaff, lefse, libpwiz-tools, librg-utils-perl, libvcflib-tools, lighter, logol, loki, ltrsift, lucy, lumpy-sv, macs, macsyfinder, maffilter, mafft, malt, mapdamage, mapsembler2, maq, maqview, mash, massxpert, mauve-aligner, mcaller, mecat2, megadepth, megahit, megan-ce, melting, meryl, metabat, metaphlan, metastudent, mhap, microbegps, microbiomeutil, mindthegap, minexpert2, minia, miniasm, minimac4, minimap, minimap2, mipe, mira-assembler, mirtop, mlv-smile, mmb, mmseqs2, mosdepth, mothur, mptp, mrbayes, multiqc, mummer, murasaki | murasaki-mpi, muscle, muscle3, mustang, nanofilt, nanolyse, nanook, nanopolish, nanostat, nanosv, nast-ier, ncbi-acc-download, ncbi-blast+, ncbi-blast+-legacy, ncbi-entrez-direct, ncbi-epcr, ncbi-seg, ncbi-tools-bin, ncbi-tools-x11, ncl-tools, ncoils, neobio, ngmlr, njplot, norsnet, norsp, ntcard, nxtrim, obitools, openms, optimir, pal2nal, paleomix, paml, paraclu, parasail, parsinsert, parsnp, patman, pbdagcon, pbhoney, pbjelly, pbsim, pbsuite, pdb2pqr, perlprimer, perm, pftools, phast, phipack, phybin, phylip, phylonium, phyml, physamp, phyutility, phyx, picard-tools, picopore, pigx-rnaseq, piler, pilercr, pilon, pinfish, pique, pirs, pizzly, placnet, plasmidid, plasmidomics, plasmidseeker, plast, plink, plink1.9, plink2, plip, poa, populations, porechop, poretools, prank, predictnls, presto, prime-phylo, primer3, prinseq-lite, 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-net, profphd-utils, proftmb, progressivemauve, prokka, proteinortho, prottest, provean, pscan-chip, pscan-tfbs, psortb, pullseq, pycoqc, pycorrfit, pyensembl, pyfastx, pymol, pyscanfcs, python3-biomaj3-daemon, python3-cogent3, python3-emperor, python3-geneimpacts, python3-gffutils, python3-pairtools, python3-pybedtools, python3-sqt, python3-treetime, pyvcf, qcat, qcumber, qiime, qtltools, quicktree, quorum, qutemol, r-bioc-annotate, r-bioc-biostrings, r-bioc-cner, r-bioc-cummerbund, r-bioc-deseq2, r-bioc-ebseq, r-bioc-edger, r-bioc-genefilter, r-bioc-geoquery, r-bioc-hilbertvis, r-bioc-htsfilter, r-bioc-impute, r-bioc-limma, r-bioc-megadepth, r-bioc-mergeomics, r-bioc-metagenomeseq, r-bioc-mofa, r-bioc-multiassayexperiment, r-bioc-mutationalpatterns, r-bioc-pcamethods, r-bioc-phyloseq, r-bioc-rtracklayer, r-bioc-scater, r-bioc-tfbstools, r-cran-adegenet, r-cran-adephylo, r-cran-alakazam, r-cran-ape, r-cran-bio3d, r-cran-distory, r-cran-genabel, r-cran-kaos, r-cran-metamix, r-cran-phangorn, r-cran-phytools, r-cran-pscbs, r-cran-qtl, r-cran-rotl, r-cran-samr, r-cran-sdmtools, r-cran-seqinr, r-cran-seurat, r-cran-shazam, r-cran-spp, r-cran-tcr, r-cran-tigger, r-cran-treescape, r-cran-tsne, r-cran-vegan, r-cran-webgestaltr, r-cran-wgcna, r-other-ascat, r-other-mott-happy.hbrem, r-other-rajewsky-dropbead, racon, radiant, ragout, rambo-k, rampler, rapmap, rasmol, raster3d, rate4site, raxml, ray, rdp-alignment, rdp-classifier, rdp-readseq, readseq, readucks, reapr, recan, relion, relion-gui, repeatmasker-recon, reprof, resfinder, rna-star, rnahybrid, roary, rockhopper, roguenarok, rsem, rtax, runcircos-gui, saint, salmid, salmon, sambamba, samblaster, samclip, samtools, savvy-util, scoary, scrappie, scrm, scythe, seaview, seer, segemehl, seqan-apps, seqan-needle, seqan-raptor, seqkit, seqmagick, seqprep, seqsero, seqtk, sga, shasta, shovill, sibelia, sibsim4, sickle, sigma-align, sim4, sim4db, simka, simkamin, ska, skesa, skewer, smalt, smithwaterman, smrtanalysis, snap, snap-aligner, sniffles, snp-sites, snpeff, snpomatic, snpsift, soapaligner, soapdenovo, soapdenovo2, soapsnp, sortmerna, spaced, spades, spaln, spoa, sprai, spread-phy, squizz, sra-toolkit, srst2, ssake, sspace, ssw-align, stacks, staden, staden-io-lib-utils, stringtie, subread, suitename, sumaclust, sumatra, sumtrees, surankco, surpyvor, survivor, svim, swarm, sweed, t-coffee, tabix, tantan, terraphast, theseus, thesias, tiddit, tigr-glimmer, tm-align, tnseq-transit, toil, tombo, tophat-recondition, topp, toppred, tortoize, trace2dbest, tracetuner, transdecoder, transrate-tools, transtermhp, tree-puzzle | tree-ppuzzle, treeview, treeviewx, trf, trim-galore, trimmomatic, tvc, twopaco, uc-echo, umap-learn, umis, uncalled, unicycler, unikmer, varna, vcfanno, vcftools, velvet | velvet-long, velvetoptimiser, virulencefinder, vmatch, vsearch, vt, wham-align, wigeon, wise, xpore, yaha, yanagiba, yanosim Suggests: acacia, adun.app, agat, amos-assembler, amoscmp, anfo, annovar, apollo, arachne, arb, arvados, asap, axparafit, axpcoords, bagpipe, bambus, bax2bam, bcbio, biceps, big-blast, bigsdb, bismark, blat, blimps-utils, blobology, braker, btk-core, cactus, caftools, card-rgi, catfishq, cdna-db, cellprofiler, cinema, cluster3, cmap, conda-package-handling, condetri, contrafold, contralign, coot, copycat, covpipe, crossbow, crux-toolkit, cufflinks, cytoscape, dascrubber, dazzle, deepbinner, deepnano, dendroscope, diann, dnapi, e-hive, ecell, embassy-phylip, emboss-explorer, ensembl, ensembl-vep, epigrass, estferret, euler-sr, euler2, exabayes, exalt, excavator, ffp, fieldbioinformatics, figaro, flappie, forester, forge, galaxy, gatk, gbrowse-syn, genemark, genesplicer, genetrack, genezilla, genographer, gerp++, getdata, glimmerhmm, gmv, gramalign, graphbin, graphmap2, haploview, hawkeye, htqc, hts-nim-tools, idefix, idseq-bench, igdiscover, illustrate, inspect, jbrowse, jigsaw, kempbasu, libhdf5-dev, libhnswlib-dev, lofreq, mach-haplotyper, mage2tab, maker2, manta, marginphase, martj, maude, maxd, medaka, meme, mesquite, metabit, metaeuk, metarep, metastudent-data, metastudent-data-2, migrate, minimus, mirbase, modeller, molekel, mosaik-aligner, mpsqed, mrs, msatfinder, mugsy, mummergpu, mview, nano-snakemake, nanocall, nanocomp, nanoplot, ncbi-magicblast, nextsv, ngila, ngsqctoolkit, nw-align, oases, obo-edit, oligoarrayaux, omegamap, oncofuse, operondb, optitype, paipline, pangolin, partigene, partitionfinder, patristic, pcma, pfaat, phagefinder, phpphylotree, phylographer, phylophlan, phyloviz-core, phylowin, pigx-scrnaseq, pipasic, plato, pomoxis, pplacer, profit, profphd, prot4est, psipred, pssh2, pufferfish, purple, pyrophosphate-tools, python3-alignlib, python3-anndata, python3-cgecore, python3-cyvcf2, python3-deeptools, python3-deeptoolsintervals, python3-htseq, python3-intake, python3-loompy, python3-nanoget, python3-nanomath, python3-ncls, python3-orange, python3-py2bit, python3-pybel, python3-pychopper, python3-pyfaidx, python3-pyflow, python3-pyranges, python3-pyrle, python3-pysam, python3-tinyalign, q2-alignment, q2-composition, q2-cutadapt, q2-dada2, q2-deblur, q2-demux, q2-diversity, q2-emperor, q2-feature-classifier, q2-feature-table, q2-fragment-insertion, q2-gneiss, q2-longitudinal, q2-metadata, q2-phylogeny, q2-quality-control, q2-quality-filter, q2-sample-classifier, q2-taxa, q2-types, q2-vsearch, q2cli, q2templates, qtlcart, qtlreaper, qualimap, quast, r-bioc-annotationhub, r-bioc-aroma.light, r-bioc-beachmat, r-bioc-biocneighbors, r-bioc-biocsingular, r-bioc-bitseq, r-bioc-ctc, r-bioc-dnacopy, r-bioc-ensembldb, r-bioc-experimenthub, r-bioc-geneplotter, r-bioc-genomicalignments, r-bioc-genomicfiles, r-bioc-genomicranges, r-bioc-go.db, r-bioc-grohmm, r-bioc-gviz, r-bioc-isoformswitchanalyzer, r-bioc-mofa2, r-bioc-org.hs.eg.db, r-bioc-org.mm.eg.db, r-bioc-qusage, r-bioc-savr, r-bioc-singlecellexperiment, r-bioc-structuralvariantannotation, r-bioc-tximport, r-cran-amap, r-cran-biwt, r-cran-boolnet, r-cran-corrplot, r-cran-drinsight, r-cran-dynamictreecut, r-cran-epir, r-cran-fitdistrplus, r-cran-forecast, r-cran-gprofiler2, r-cran-minerva, r-cran-optimalcutpoints, r-cran-parmigene, r-cran-pheatmap, r-cran-qqman, r-cran-rcpphnsw, r-cran-rentrez, r-cran-sctransform, r-other-apmswapp, r-other-fastbaps, raccoon, raxml-ng, rbs-finder, relion-cuda, relion-gui-cuda, repeatmasker, resfinder-db, roadtrips, roche454ace2caf, rosa, rose, rsat, sailfish, sap, science-workflow, sepp, seq-gen, seq-seq-pan, seqcluster, seqwish, sift, signalalign, sina, sistr, situs, snippy, solvate, sourmash, sparta, splitstree, ssaha, strap, strap-base, strelka, tab2mage, tacg, tandem-genotypes, taverna, taxinspector, tetra, tide, tigr-glimmer-mg, tipp, tn-seqexplorer, tophat, treebuilder3d, trinityrnaseq, tripal, trnascan-se, twain, ufasta, ugene, umap, unc-fish, uniprime, varmatch, varscan, vdjtools, vg, vienna-rna, viewmol, vmd, x-tandem-pipeline, zodiac-zeden Description: Debian Med bioinformatics packages Description-md5: 472a50c6504872b123b928f5c13e0f5e Tag: field::biology, role::metapackage, suite::debian Section: metapackages Priority: optional Filename: pool/main/d/debian-med/med-bio_3.8.1_all.deb Size: 14364 MD5sum: b9b30bb9abd8d2214aaa49b59e4773a4 SHA256: 72c61ba134a3bcc5694390cc130c8d2a8259cad5daa15bf4cd2fb6650bfb155f 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 --scriptsdir /etc/piuparts/scripts-no-usr-share-doc --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt med-bio=3.8.1 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 1.2 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 --scriptsdir /etc/piuparts/scripts-no-usr-share-doc --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt med-bio=3.8.1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-27-amd64 #1 SMP Debian 5.10.205-2 (2023-12-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpedsqhkew 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpedsqhkew 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m1.7s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/proc'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/proc'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/dev/pts'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/dev/pts'] 0m1.7s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/dev/ptmx'] 0m1.7s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/dev/ptmx'] 0m1.7s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/dev/console'] 0m1.7s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/dev/console'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/dev/shm'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/dev/shm'] 0m1.7s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m1.7s DEBUG: Created policy-rc.d and chmodded it. 0m1.7s DEBUG: Created resolv.conf. 0m1.7s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpedsqhkew/tmp/scripts/ 0m1.7s DEBUG: Copying scriptsdir /etc/piuparts/scripts-no-usr-share-doc to /srv/piuparts.debian.org/tmp/tmpedsqhkew/tmp/scripts/ 0m1.7s INFO: Running scripts post_chroot_unpack 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'apt-get', 'update'] 0m5.6s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9659 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7107 kB] Fetched 17.0 MB in 3s (6185 kB/s) Reading package lists... 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'apt-get', 'update'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'apt-get', '-yf', 'dist-upgrade'] 0m6.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: libacl1 libtinfo6 ncurses-base ncurses-bin 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1073 kB of archives. After this operation, 1024 B of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20240113-1 [431 kB] Get:2 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.4+20240113-1 [268 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libacl1 amd64 2.3.1-6 [31.9 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20240113-1 [342 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1073 kB in 0s (9809 kB/s) (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 ... 5230 files and directories currently installed.) Preparing to unpack .../libacl1_2.3.1-6_amd64.deb ... Unpacking libacl1:amd64 (2.3.1-6) over (2.3.1-4) ... Setting up libacl1:amd64 (2.3.1-6) ... (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 ... 5230 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.4+20240113-1_amd64.deb ... Unpacking libtinfo6:amd64 (6.4+20240113-1) over (6.4+20231209-1) ... Setting up libtinfo6:amd64 (6.4+20240113-1) ... Processing triggers for libc-bin (2.37-13) ... 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'apt-get', '-yf', 'dist-upgrade'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.2s DUMP: f36d9fa4be47cfb64e2b14613ba3a8c6 - 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.2s INFO: Running scripts post_setup 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_setup_disable_usr_share_doc'] 0m7.2s DUMP: dpkg-query: no packages found matching systemd dpkg-query: no packages found matching systemd-sysv dpkg-query: no packages found matching sysv-rc 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_setup_disable_usr_share_doc'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_setup_dummy_users'] 0m7.9s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_setup_dummy_users'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_setup_forbid_home'] 0m7.9s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_setup_forbid_home'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.0s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_setup_minimize'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_setup_minimize'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_setup_zz_backports'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_setup_zz_backports'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'apt-get', 'clean'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'apt-get', 'clean'] 0m8.0s DEBUG: Recording chroot state 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.4s DUMP: install ok installed apt apt 2.7.9 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bsdutils bsdutils 1:2.39.3-6 install ok installed coreutils coreutils 9.4-3+b1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.83 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.16 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.2 install ok installed e2fsprogs e2fsprogs 1.47.0-2+b1 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-13-base:amd64 gcc-13-base 13.2.0-9 install ok installed gpgv gpgv 2.2.40-1.1+b1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.1-6 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.7.9 install ok installed libattr1:amd64 libattr1 1:2.5.1-5 install ok installed libaudit-common libaudit-common 1:3.1.2-1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-1 install ok installed libblkid1:amd64 libblkid1 2.39.3-6 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b2 install ok installed libc-bin libc-bin 2.37-13 install ok installed libc6:amd64 libc6 2.37-13 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-1 install ok installed libcap2:amd64 libcap2 1:2.66-4+b2 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-4+b1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2+b1 install ok installed libffi8:amd64 libffi8 3.4.4-2 install ok installed libgcc-s1:amd64 libgcc-s1 13.2.0-9 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2 install ok installed libgnutls30:amd64 libgnutls30 3.8.2-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.4-1+b2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1+b2 install ok installed liblzma5:amd64 liblzma5 5.4.5-0.3 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.39.3-6 install ok installed libnettle8:amd64 libnettle8 3.9.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-9.1+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-9.1+b1 install ok installed libpam-runtime libpam-runtime 1.5.2-9.1 install ok installed libpam0g:amd64 libpam0g 1.5.2-9.1+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-1+b2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b2 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-6 install ok installed libss2:amd64 libss2 1.47.0-2+b1 install ok installed libssl3:amd64 libssl3 3.1.4-2 install ok installed libstdc++6:amd64 libstdc++6 13.2.0-9 install ok installed libsystemd0:amd64 libsystemd0 255.2-4 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libudev1:amd64 libudev1 255.2-4 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed libuuid1:amd64 libuuid1 2.39.3-6 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-3+b1 install ok installed logsave logsave 1.47.0-2+b1 install ok installed mawk mawk 1.3.4.20231126-1 install ok installed mount mount 2.39.3-6 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed passwd passwd 1:4.13+dfsg1-3+b1 install ok installed perl-base perl-base 5.38.2-3 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.08-5 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2023d-1 install ok installed usr-is-merged usr-is-merged 38 install ok installed util-linux util-linux 2.39.3-6 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3+b1 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'dpkg-divert', '--list'] 0m8.4s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'dpkg-divert', '--list'] 0m8.4s INFO: Running scripts is_testable 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/is_testable_uninstallable'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/is_testable_uninstallable'] 0m8.4s INFO: apt-cache does not know about any of the requested packages 0m8.4s INFO: Running scripts pre_test 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_test_exceptions'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_test_exceptions'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_test_root_password'] 0m8.5s DUMP: New password: Retype new password: passwd: password updated successfully 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_test_root_password'] 0m8.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpedsqhkew'] 0m8.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpedsqhkew'] 0m9.4s DEBUG: No broken symlinks as far as we can find. 0m9.4s INFO: Running scripts pre_install 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_install_database-server'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_install_database-server'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_install_exceptions'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_install_exceptions'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_install_extras'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_install_extras'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpedsqhkew'] 0m9.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpedsqhkew'] 0m10.5s DEBUG: No broken symlinks as far as we can find. 0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'apt-cache', 'policy'] 0m12.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'apt-cache', 'policy'] 0m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'apt-cache', 'policy', 'med-bio'] 0m12.3s DUMP: med-bio: Installed: (none) Candidate: 3.8.1 Version table: 3.8.1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'apt-cache', 'policy', 'med-bio'] 0m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'apt-get', '-y', 'install', 'med-bio=3.8.1'] 0m14.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: adduser blends-common liblocale-gettext-perl med-config med-tasks menu sensible-utils tasksel tasksel-data Suggested packages: perl cron quota blends-doc acacia adun.app agat amos-assembler amoscmp anfo annovar apollo arachne arb arvados asap axparafit axpcoords bagpipe bambus bax2bam bcbio biceps big-blast bigsdb bismark blat blimps-utils blobology braker btk-core cactus caftools card-rgi catfishq cdna-db cellprofiler cinema cluster3 cmap conda-package-handling condetri contrafold contralign coot copycat covpipe crossbow crux-toolkit cufflinks cytoscape dascrubber dazzle deepbinner deepnano dendroscope diann dnapi e-hive ecell embassy-phylip emboss-explorer ensembl ensembl-vep epigrass estferret euler-sr euler2 exabayes exalt excavator ffp fieldbioinformatics figaro flappie forester forge galaxy gatk gbrowse-syn genemark genesplicer genetrack genezilla genographer gerp++ getdata glimmerhmm gmv gramalign graphbin graphmap2 haploview hawkeye htqc hts-nim-tools idefix idseq-bench igdiscover illustrate inspect jbrowse jigsaw kempbasu libhdf5-dev libhnswlib-dev lofreq mach-haplotyper mage2tab maker2 manta marginphase martj maude maxd medaka meme mesquite metabit metaeuk metarep metastudent-data metastudent-data-2 migrate minimus mirbase modeller molekel mosaik-aligner mpsqed mrs msatfinder mugsy mummergpu mview nano-snakemake nanocall nanocomp nanoplot ncbi-magicblast nextsv ngila ngsqctoolkit nw-align oases obo-edit oligoarrayaux omegamap oncofuse operondb optitype paipline pangolin partigene partitionfinder patristic pcma pfaat phagefinder phpphylotree phylographer phylophlan phyloviz-core phylowin pigx-scrnaseq pipasic plato pomoxis pplacer profit profphd prot4est psipred pssh2 pufferfish purple pyrophosphate-tools python3-alignlib python3-anndata python3-cgecore python3-cyvcf2 python3-deeptools python3-deeptoolsintervals python3-htseq python3-intake python3-loompy python3-nanoget python3-nanomath python3-ncls python3-orange python3-py2bit python3-pybel python3-pychopper python3-pyfaidx python3-pyflow python3-pyranges python3-pyrle python3-pysam python3-tinyalign q2-alignment q2-composition q2-cutadapt q2-dada2 q2-deblur q2-demux q2-diversity q2-emperor q2-feature-classifier q2-feature-table q2-fragment-insertion q2-gneiss q2-longitudinal q2-metadata q2-phylogeny q2-quality-control q2-quality-filter q2-sample-classifier q2-taxa q2-types q2-vsearch q2cli q2templates qtlcart qtlreaper qualimap quast r-bioc-annotationhub r-bioc-aroma.light r-bioc-beachmat r-bioc-biocneighbors r-bioc-biocsingular r-bioc-bitseq r-bioc-ctc r-bioc-dnacopy r-bioc-ensembldb r-bioc-experimenthub r-bioc-geneplotter r-bioc-genomicalignments r-bioc-genomicfiles r-bioc-genomicranges r-bioc-go.db r-bioc-grohmm r-bioc-gviz r-bioc-isoformswitchanalyzer r-bioc-mofa2 r-bioc-org.hs.eg.db r-bioc-org.mm.eg.db r-bioc-qusage r-bioc-savr r-bioc-singlecellexperiment r-bioc-structuralvariantannotation r-bioc-tximport r-cran-amap r-cran-biwt r-cran-boolnet r-cran-corrplot r-cran-drinsight r-cran-dynamictreecut r-cran-epir r-cran-fitdistrplus r-cran-forecast r-cran-gprofiler2 r-cran-minerva r-cran-optimalcutpoints r-cran-parmigene r-cran-pheatmap r-cran-qqman r-cran-rcpphnsw r-cran-rentrez r-cran-sctransform r-other-apmswapp r-other-fastbaps raccoon raxml-ng rbs-finder relion-cuda relion-gui-cuda repeatmasker resfinder-db roadtrips roche454ace2caf rosa rose rsat sailfish sap science-workflow sepp seq-gen seq-seq-pan seqcluster seqwish sift signalalign sina sistr situs snippy solvate sourmash sparta splitstree ssaha strap strap-base strelka tab2mage tacg tandem-genotypes taverna taxinspector tetra tide tigr-glimmer-mg tipp tn-seqexplorer tophat treebuilder3d trinityrnaseq tripal trnascan-se twain ufasta ugene umap unc-fish uniprime varmatch varscan vdjtools vg vienna-rna viewmol vmd x-tandem-pipeline zodiac-zeden menu-l10n gksu | kde-cli-tools | ktsuss Recommended packages: abacas abpoa abyss acedb-other adapterremoval adun-core aegean aevol alien-hunter alter-sequence-alignment altree amap-align ampliconnoise andi any2fasta aragorn arden ariba art-nextgen-simulation-tools artemis artfastqgenerator assembly-stats assemblytics atac ataqv atropos augur augustus autodock autodock-vina autogrid avogadro axe-demultiplexer baitfisher bali-phy ballview bamclipper bamkit bamtools bandage barrnap bbmap bcalm bcftools beads beagle beast-mcmc beast2-mcmc bedops bedtools belvu berkeley-express bio-eagle bio-rainbow bio-tradis bio-vcf bioawk biobambam2 biosyntax bitseq blasr blixem bolt-lmm bowtie bowtie2 boxshade bppphyview bppsuite brig btllib-tools busco bustools bwa canu cassiopee cat-bat cct cd-hit cdbfasta centrifuge cgview changeo chimeraslayer chromhmm chromimpute cif-tools circlator circos clearcut clonalframe clonalframeml clonalorigin clustalo clustalw clustalx cnvkit codonw comet-ms concavity conservation-code covtobed crac csb cutadapt cutesv daligner damapper datamash dawg dazzdb delly density-fitness dextractor dialign dialign-tx diamond-aligner discosnp disulfinder dnaclust dnarrange dotter drop-seq-tools dssp dwgsim e-mem ea-utils ecopcr edtsurf eigensoft elph embassy-domainatrix embassy-domalign embassy-domsearch emboss emmax estscan examl exonerate fasta3 fastahack fastani fastaq fastdnaml fastlink fastml fastp fastq-pair fastqc fastqtl fasttree ffindex figtree filtlong fitgcp flash flexbar flye fml-asm freebayes freecontact fsa fsm-lite gamgi garli garlic gasic gatb-core gbrowse gdpc gemma genometester genomethreader genometools genomicsdb-tools gentle gff2aplot gff2ps gffread ggd-utils ghemical ghmm glam2 gmap grabix graphlan grinder gromacs gsort gubbins gwama harvest-tools hhsuite hilive hinge hisat2 hmmer hmmer2 hyphy-mpi | hyphy-pt idba igblast igor igv indelible infernal insilicoseq ipig iqtree iva jaligner jalview jellyfish jellyfish1 jmodeltest jmol kalign kallisto kaptive khmer kineticstools king-probe kissplice kleborate kma kmc kmer kmerresistance kraken kraken2 lagan lamarc lamassemble lambda-align lambda-align2 last-align lastz leaff lefse libpwiz-tools librg-utils-perl libvcflib-tools lighter logol loki ltrsift lucy lumpy-sv macs macsyfinder maffilter mafft malt mapdamage mapsembler2 maq maqview mash massxpert mauve-aligner mcaller mecat2 megadepth megahit megan-ce melting meryl metabat metaphlan metastudent mhap microbegps microbiomeutil mindthegap minexpert2 minia miniasm minimac4 minimap minimap2 mipe mira-assembler mirtop mlv-smile mmb mmseqs2 mosdepth mothur mptp mrbayes multiqc mummer murasaki | murasaki-mpi muscle muscle3 mustang nanofilt nanolyse nanook nanopolish nanostat nanosv nast-ier ncbi-acc-download ncbi-blast+ ncbi-blast+-legacy ncbi-entrez-direct ncbi-epcr ncbi-seg ncbi-tools-bin ncbi-tools-x11 ncl-tools ncoils neobio ngmlr njplot norsnet norsp ntcard nxtrim obitools openms optimir pal2nal paleomix paml paraclu parasail parsinsert parsnp patman pbdagcon pbhoney pbjelly pbsim pbsuite pdb2pqr perlprimer perm pftools phast phipack phybin phylip phylonium phyml physamp phyutility phyx picard-tools picopore pigx-rnaseq piler pilercr pilon pinfish pique pirs pizzly placnet plasmidid plasmidomics plasmidseeker plast plink plink1.9 plink2 plip poa populations porechop poretools prank predictnls presto prime-phylo primer3 prinseq-lite 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-net profphd-utils proftmb progressivemauve prokka proteinortho prottest provean pscan-chip pscan-tfbs psortb pullseq pycoqc pycorrfit pyensembl pyfastx pymol pyscanfcs python3-biomaj3-daemon python3-cogent3 python3-emperor python3-geneimpacts python3-gffutils python3-pairtools python3-pybedtools python3-sqt python3-treetime pyvcf qcat qcumber qiime qtltools quicktree quorum qutemol r-bioc-annotate r-bioc-biostrings r-bioc-cner r-bioc-cummerbund r-bioc-deseq2 r-bioc-ebseq r-bioc-edger r-bioc-genefilter r-bioc-geoquery r-bioc-hilbertvis r-bioc-htsfilter r-bioc-impute r-bioc-limma r-bioc-megadepth r-bioc-mergeomics r-bioc-metagenomeseq r-bioc-mofa r-bioc-multiassayexperiment r-bioc-mutationalpatterns r-bioc-pcamethods r-bioc-phyloseq r-bioc-rtracklayer r-bioc-scater r-bioc-tfbstools r-cran-adegenet r-cran-adephylo r-cran-alakazam r-cran-ape r-cran-bio3d r-cran-distory r-cran-genabel r-cran-kaos r-cran-metamix r-cran-phangorn r-cran-phytools r-cran-pscbs r-cran-qtl r-cran-rotl r-cran-samr r-cran-sdmtools r-cran-seqinr r-cran-seurat r-cran-shazam r-cran-spp r-cran-tcr r-cran-tigger r-cran-treescape r-cran-tsne r-cran-vegan r-cran-webgestaltr r-cran-wgcna r-other-ascat r-other-mott-happy.hbrem r-other-rajewsky-dropbead racon radiant ragout rambo-k rampler rapmap rasmol raster3d rate4site raxml ray rdp-alignment rdp-classifier rdp-readseq readseq readucks reapr recan relion relion-gui repeatmasker-recon reprof resfinder rna-star rnahybrid roary rockhopper roguenarok rsem rtax runcircos-gui saint salmid salmon sambamba samblaster samclip samtools savvy-util scoary scrappie scrm scythe seaview seer segemehl seqan-apps seqan-needle seqan-raptor seqkit seqmagick seqprep seqsero seqtk sga shasta shovill sibelia sibsim4 sickle sigma-align sim4 sim4db simka simkamin ska skesa skewer smalt smithwaterman smrtanalysis snap snap-aligner sniffles snp-sites snpeff snpomatic snpsift soapaligner soapdenovo soapdenovo2 soapsnp sortmerna spaced spades spaln spoa sprai spread-phy squizz sra-toolkit srst2 ssake sspace ssw-align stacks staden staden-io-lib-utils stringtie subread suitename sumaclust sumatra sumtrees surankco surpyvor survivor svim swarm sweed t-coffee tabix tantan terraphast theseus thesias tiddit tigr-glimmer tm-align tnseq-transit toil tombo tophat-recondition topp toppred tortoize trace2dbest tracetuner transdecoder transrate-tools transtermhp tree-puzzle | tree-ppuzzle treeview treeviewx trf trim-galore trimmomatic tvc twopaco uc-echo umap-learn umis uncalled unicycler unikmer varna vcfanno vcftools velvet | velvet-long velvetoptimiser virulencefinder vmatch vsearch vt wham-align wigeon wise xpore yaha yanagiba yanosim laptop-detect The following NEW packages will be installed: adduser blends-common liblocale-gettext-perl med-bio med-config med-tasks menu sensible-utils tasksel tasksel-data 0 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. Need to get 639 kB of archives. After this operation, 2975 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-6+b1 [15.2 kB] Get:2 http://deb.debian.org/debian sid/main amd64 tasksel-data all 3.73 [18.0 kB] Get:3 http://deb.debian.org/debian sid/main amd64 tasksel all 3.73 [51.2 kB] Get:4 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:5 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.20 [19.3 kB] Get:6 http://deb.debian.org/debian sid/main amd64 menu amd64 2.1.50 [346 kB] Get:7 http://deb.debian.org/debian sid/main amd64 blends-common all 0.7.6 [14.9 kB] Get:8 http://deb.debian.org/debian sid/main amd64 med-config all 3.8.1 [11.1 kB] Get:9 http://deb.debian.org/debian sid/main amd64 med-tasks all 3.8.1 [8704 B] Get:10 http://deb.debian.org/debian sid/main amd64 med-bio all 3.8.1 [14.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 639 kB in 0s (4640 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 ... 5232 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-6+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-6+b1) ... Selecting previously unselected package tasksel-data. Preparing to unpack .../tasksel-data_3.73_all.deb ... Unpacking tasksel-data (3.73) ... Selecting previously unselected package tasksel. Preparing to unpack .../archives/tasksel_3.73_all.deb ... Unpacking tasksel (3.73) ... Selecting previously unselected package adduser. Preparing to unpack .../archives/adduser_3.137_all.deb ... Unpacking adduser (3.137) ... Setting up adduser (3.137) ... Selecting previously unselected package sensible-utils. (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 ... 5464 files and directories currently installed.) Preparing to unpack .../0-sensible-utils_0.0.20_all.deb ... Unpacking sensible-utils (0.0.20) ... Selecting previously unselected package menu. Preparing to unpack .../1-menu_2.1.50_amd64.deb ... Unpacking menu (2.1.50) ... Selecting previously unselected package blends-common. Preparing to unpack .../2-blends-common_0.7.6_all.deb ... Unpacking blends-common (0.7.6) ... Selecting previously unselected package med-config. Preparing to unpack .../3-med-config_3.8.1_all.deb ... Unpacking med-config (3.8.1) ... Selecting previously unselected package med-tasks. Preparing to unpack .../4-med-tasks_3.8.1_all.deb ... Unpacking med-tasks (3.8.1) ... Selecting previously unselected package med-bio. Preparing to unpack .../5-med-bio_3.8.1_all.deb ... Unpacking med-bio (3.8.1) ... Setting up sensible-utils (0.0.20) ... Setting up menu (2.1.50) ... Setting up liblocale-gettext-perl (1.07-6+b1) ... Setting up tasksel (3.73) ... Setting up tasksel-data (3.73) ... Setting up med-tasks (3.8.1) ... Processing triggers for menu (2.1.50) ... Setting up blends-common (0.7.6) ... Setting up med-config (3.8.1) ... info: Selecting GID from range 100 to 999 ... info: Adding group `med' (GID 150) ... Setting up med-bio (3.8.1) ... 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'apt-get', '-y', 'install', 'med-bio=3.8.1'] 0m14.0s INFO: Running scripts post_install 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_install_exceptions'] 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_install_exceptions'] 0m14.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpedsqhkew'] 0m14.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpedsqhkew'] 0m14.6s DEBUG: No broken symlinks as far as we can find. 0m14.6s INFO: /bin converted to /usr/bin by /usr merge 0m14.6s INFO: /lib converted to /usr/lib by /usr merge 0m14.6s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m14.6s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m14.6s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m14.6s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m14.6s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m14.6s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m14.6s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m14.6s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m14.6s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m14.6s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m14.6s INFO: /sbin converted to /usr/sbin by /usr merge 0m14.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', '-ac', '--ignore-obsolete'] 0m15.4s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', '-ac', '--ignore-obsolete'] 0m15.4s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m15.4s DUMP: 0.15.6 0m15.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m15.4s INFO: Running adequate version 0.15.6 now. 0m15.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'med-bio'] 0m15.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'med-bio'] 0m15.5s INFO: Running scripts pre_remove 0m15.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m15.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m15.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_remove_exceptions'] 0m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/pre_remove_exceptions'] 0m16.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m16.4s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.7.9 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed blends-common blends-common 0.7.6 install ok installed bsdutils bsdutils 1:2.39.3-6 install ok installed coreutils coreutils 9.4-3+b1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.83 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.16 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.2 install ok installed e2fsprogs e2fsprogs 1.47.0-2+b1 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-13-base:amd64 gcc-13-base 13.2.0-9 install ok installed gpgv gpgv 2.2.40-1.1+b1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.1-6 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.7.9 install ok installed libattr1:amd64 libattr1 1:2.5.1-5 install ok installed libaudit-common libaudit-common 1:3.1.2-1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-1 install ok installed libblkid1:amd64 libblkid1 2.39.3-6 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b2 install ok installed libc-bin libc-bin 2.37-13 install ok installed libc6:amd64 libc6 2.37-13 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-1 install ok installed libcap2:amd64 libcap2 1:2.66-4+b2 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-4+b1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2+b1 install ok installed libffi8:amd64 libffi8 3.4.4-2 install ok installed libgcc-s1:amd64 libgcc-s1 13.2.0-9 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2 install ok installed libgnutls30:amd64 libgnutls30 3.8.2-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.4-1+b2 install ok installed liblocale-gettext-perl liblocale-gettext-perl 1.07-6+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1+b2 install ok installed liblzma5:amd64 liblzma5 5.4.5-0.3 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.39.3-6 install ok installed libnettle8:amd64 libnettle8 3.9.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-9.1+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-9.1+b1 install ok installed libpam-runtime libpam-runtime 1.5.2-9.1 install ok installed libpam0g:amd64 libpam0g 1.5.2-9.1+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-1+b2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b2 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-6 install ok installed libss2:amd64 libss2 1.47.0-2+b1 install ok installed libssl3:amd64 libssl3 3.1.4-2 install ok installed libstdc++6:amd64 libstdc++6 13.2.0-9 install ok installed libsystemd0:amd64 libsystemd0 255.2-4 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libudev1:amd64 libudev1 255.2-4 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed libuuid1:amd64 libuuid1 2.39.3-6 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-3+b1 install ok installed logsave logsave 1.47.0-2+b1 install ok installed mawk mawk 1.3.4.20231126-1 install ok installed med-bio med-bio 3.8.1 install ok installed med-config med-config 3.8.1 install ok installed med-tasks med-tasks 3.8.1 install ok installed menu menu 2.1.50 install ok installed mount mount 2.39.3-6 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed passwd passwd 1:4.13+dfsg1-3+b1 install ok installed perl-base perl-base 5.38.2-3 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.20 install ok installed sysvinit-utils sysvinit-utils 3.08-5 install ok installed tar tar 1.35+dfsg-3 install ok installed tasksel tasksel 3.73 install ok installed tasksel-data tasksel-data 3.73 install ok installed tzdata tzdata 2023d-1 install ok installed usr-is-merged usr-is-merged 38 install ok installed util-linux util-linux 2.39.3-6 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3+b1 0m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m16.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'apt-get', 'remove', 'adduser', 'blends-common', 'liblocale-gettext-perl', 'med-config', 'med-tasks', 'menu', 'sensible-utils', 'tasksel', 'tasksel-data', 'med-bio'] 0m17.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: adduser blends-common liblocale-gettext-perl med-bio med-config med-tasks menu sensible-utils tasksel tasksel-data 0 upgraded, 0 newly installed, 10 to remove and 0 not upgraded. After this operation, 2975 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 ... 5739 files and directories currently installed.) Removing med-bio (3.8.1) ... Removing med-config (3.8.1) ... Removing blends-common (0.7.6) ... Removing adduser (3.137) ... Removing med-tasks (3.8.1) ... Removing menu (2.1.50) ... Removing sensible-utils (0.0.20) ... Removing tasksel (3.73) ... Removing tasksel-data (3.73) ... Removing liblocale-gettext-perl (1.07-6+b1) ... 0m17.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'apt-get', 'remove', 'adduser', 'blends-common', 'liblocale-gettext-perl', 'med-config', 'med-tasks', 'menu', 'sensible-utils', 'tasksel', 'tasksel-data', 'med-bio'] 0m17.6s INFO: Running scripts post_remove 0m17.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_remove_exceptions'] 0m17.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_remove_exceptions'] 0m17.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'dpkg', '--purge', 'adduser', 'blends-common', 'liblocale-gettext-perl', 'med-config', 'med-tasks', 'menu', 'sensible-utils', 'tasksel', 'tasksel-data'] 0m17.8s DUMP: (Reading database ... 5245 files and directories currently installed.) Purging configuration files for adduser (3.137) ... Purging configuration files for blends-common (0.7.6) ... dpkg: warning: ignoring request to remove liblocale-gettext-perl which isn't installed Purging configuration files for med-config (3.8.1) ... dpkg: warning: ignoring request to remove med-tasks which isn't installed Purging configuration files for menu (2.1.50) ... dpkg: warning: ignoring request to remove sensible-utils which isn't installed Purging configuration files for tasksel (3.73) ... dpkg: warning: ignoring request to remove tasksel-data which isn't installed 0m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'dpkg', '--purge', 'adduser', 'blends-common', 'liblocale-gettext-perl', 'med-config', 'med-tasks', 'menu', 'sensible-utils', 'tasksel', 'tasksel-data'] 0m17.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'dpkg', '--purge', 'med-bio'] 0m17.8s DUMP: dpkg: warning: ignoring request to remove med-bio which isn't installed 0m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'dpkg', '--purge', 'med-bio'] 0m17.8s INFO: Running scripts post_purge 0m17.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_purge_exceptions'] 0m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_purge_exceptions'] 0m17.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'dpkg', '--purge', '--pending'] 0m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'dpkg', '--purge', '--pending'] 0m17.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'dpkg', '--remove', '--pending'] 0m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'dpkg', '--remove', '--pending'] 0m17.8s INFO: Running scripts post_test 0m17.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_test_exceptions'] 0m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'tmp/scripts/post_test_exceptions'] 0m17.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpedsqhkew'] 0m18.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpedsqhkew'] 0m18.8s DEBUG: No broken symlinks as far as we can find. 0m18.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'dpkg-divert', '--list'] 0m18.9s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'dpkg-divert', '--list'] 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'apt-get', 'clean'] 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpedsqhkew', 'apt-get', 'clean'] 0m18.9s DEBUG: Recording chroot state 0m19.5s INFO: PASS: Installation and purging test. 0m19.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/dev/shm'] 0m19.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/dev/shm'] 0m19.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/dev/console'] 0m19.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/dev/console'] 0m19.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/dev/ptmx'] 0m19.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/dev/ptmx'] 0m19.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/dev/pts'] 0m19.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/dev/pts'] 0m19.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/proc'] 0m20.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpedsqhkew/proc'] 0m20.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpedsqhkew'] 0m20.1s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpedsqhkew'] 0m20.1s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpedsqhkew 0m20.1s INFO: PASS: All tests. 0m20.1s INFO: piuparts run ends. ret=0 End: 2024-01-17 17:07:52 GMT