Start: 2024-04-27 05:50:51 GMT Package: med-bio Source: debian-med Version: 3.3 Installed-Size: 48 Maintainer: Debian Med Packaging Team Architecture: all Depends: med-config (= 3.3), med-tasks (= 3.3) Recommends: abacas, abyss, acedb-other, 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, assemblytics, atac, augustus, autodock, autodock-vina, autogrid, avogadro, axe-demultiplexer, baitfisher, bali-phy, ballview, bamtools, bandage, barrnap, bcbio, bcftools, beads, beagle, beast-mcmc, beast2-mcmc, bedops, bedtools, belvu, berkeley-express, bio-eagle, bio-rainbow, bio-tradis, biosyntax, bitseq, blasr, blixem, bolt-lmm, bowtie, bowtie2, boxshade, bppphyview, bppsuite, brig, bwa, canu, cassiopee, cct, cd-hit, cdbfasta, centrifuge, cgview, changeo, chimeraslayer, chromhmm, chromimpute, circlator, circos, clearcut, clonalframe, clonalframeml, clonalorigin, clustalo, clustalw, clustalx, cnvkit, codonw, concavity, conservation-code, crac, csb, cutadapt, daligner, datamash, dawg, dazzdb, deepnano, delly, dialign, dialign-tx, diamond-aligner, dindel, discosnp, disulfinder, dnaclust, dotter, dssp, dwgsim, e-mem, ea-utils, ecopcr, edtsurf, eigensoft, elph, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, estscan, examl, exonerate, fastahack, fastaq, fastdnaml, fastlink, fastml, fastp, fastqc, fastqtl, fasttree, fastx-toolkit, ffindex, figtree, fitgcp, flexbar, fml-asm, freebayes, freecontact, fsa, fsm-lite, gamgi, garli, garlic, gasic, gatb-core, gbrowse, gdpc, gemma, genometester, genometools, gentle, gff2aplot, gff2ps, ghemical, ghmm, giira, glam2, grabix, graphlan, grinder, gromacs, gubbins, gwama, harvest-tools, hhsuite, hilive, hinge, hisat2, hmmer, hmmer2, hyphy-mpi | hyphy-pt, idba, igor, indelible, infernal, ipig, iqtree, iva, jaligner, jellyfish, jellyfish1, jmodeltest, jmol, kalign, khmer, kineticstools, king-probe, kissplice, kmc, kmer, kraken, lagan, lamarc, lambda-align, lambda-align2, last-align, leaff, lefse, librg-utils-perl, libvcflib-tools, logol, loki, ltrsift, lucy, macs, macsyfinder, maffilter, mafft, mapdamage, mapsembler2, maq, maqview, mash, mauve-aligner, melting, meryl, metaphlan2, metastudent, mhap, microbegps, microbiomeutil, minia, miniasm, minimac4, minimap, minimap2, mipe, mira-assembler, mlv-smile, mothur, mptp, mrbayes, mummer, murasaki | murasaki-mpi, muscle, mustang, nanook, 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, obitools, openms, pal2nal, paleomix, paml, paraclu, parsinsert, parsnp, patman, pbalign, pbbarcode, pbdagcon, pbgenomicconsensus, pbh5tools, pbhoney, pbjelly, pbsim, pbsuite, pdb2pqr, perlprimer, perm, pftools, phast, phipack, phybin, phylip, phyml, physamp, phyutility, phyx, picard-tools, piler, pilon, pirs, placnet, plasmidomics, plasmidseeker, plast, plink, plink1.9, plip, poa, populations, porechop, 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, pscan-chip, pscan-tfbs, psortb, pycorrfit, pymol, pynast, pyscanfcs, python-cogent, python3-biomaj3-daemon, python3-gffutils, python3-presto, python3-pybedtools, python3-pybel, python3-sqt, pyvcf, qcumber, qtltools, quorum, qutemol, r-bioc-annotate, r-bioc-biostrings, r-bioc-bitseq, r-bioc-cner, r-bioc-cummerbund, r-bioc-deseq2, r-bioc-dnacopy, r-bioc-ebseq, r-bioc-genefilter, r-bioc-geneplotter, r-bioc-gviz, r-bioc-hilbertvis, r-bioc-impute, r-bioc-limma, r-bioc-mergeomics, r-bioc-metagenomeseq, r-bioc-pcamethods, r-bioc-phyloseq, r-bioc-rtracklayer, 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-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-shazam, r-cran-tcr, r-cran-tigger, r-cran-treescape, r-cran-vegan, r-other-hms-dbmi-spp, r-other-mott-happy.hbrem, racon, radiant, rambo-k, rampler, 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, roguenarok, rsem, rtax, runcircos-gui, saint, salmon, samblaster, samtools, scoary, scrm, scythe, seaview, seer, segemehl, seqan-apps, seqmagick, seqprep, seqsero, seqtk, sga, sibsim4, sickle, sigma-align, sim4, sim4db, smalr, smalt, smithwaterman, snap, snap-aligner, sniffles, snp-sites, snpomatic, soapaligner, soapdenovo, soapdenovo2, soapsnp, sortmerna, spaced, spades, spoa, sprai, spread-phy, squizz, sra-toolkit, srst2, ssake, sspace, ssw-align, stacks, staden, staden-io-lib-utils, subread, suitename, sumaclust, sumatra, sumtrees, surankco, swarm, sweed, t-coffee, tabix, tantan, theseus, tigr-glimmer, tm-align, tnseq-transit, toil, tophat, topp, toppred, trace2dbest, tracetuner, transdecoder, transrate-tools, transtermhp, tree-puzzle | tree-ppuzzle, treeview, treeviewx, trimmomatic, trinityrnaseq, tvc, uc-echo, unanimity, unicycler, varna, vcftools, velvet | velvet-long, velvetoptimiser, viewmol, vsearch, wigeon, wise, yaha, zalign Suggests: acacia, adun.app, amos-assembler, amoscmp, annovar, apollo, arachne, arb, asap, atropos, autodocktools, axparafit, axpcoords, bagpipe, bambus, bax2bam, biceps, big-blast, bigsdb, biobambam2, bismark, blat, blimps-utils, blobology, braker, btk-core, cactus, caftools, cain, card-rgi, ccs, cdna-db, cellprofiler, cinema, cluster3, cmap, compclust, condetri, contrafold, contralign, coot, copycat, crossbow, crux-toolkit, cufflinks, cytoscape, dascrubber, dazzle, deepbinner, dendroscope, e-hive, ecell, embassy-phylip, emboss-explorer, emmax, emperor, ensembl, estferret, euler-sr, euler2, exabayes, exalt, excavator, falcon, fasta3, ffp, figaro, filtlong, forester, forge, galaxy, gassst, gatk, gbrowse-syn, genemark, genesplicer, genetrack, genezilla, genographer, getdata, gffread, glimmerhmm, gmap, gmv, gramalign, haploview, hawkeye, htqc, igdiscover, igv, inspect, jalview, jbrowse, jigsaw, kallisto, kempbasu, kma, kmerresistance, kraken2, lofreq, mach-haplotyper, mage2tab, maker2, malt, manta, martj, maude, maxd, meme, mesquite, metabit, metarep, metastudent-data, metastudent-data-2, metastudent-data-3, mgltools-cadd, mgltools-pmv, mgltools-vision, migrate, minimus, mirbase, mirtop, mobyle, mobyle-programs, mobyle-tutorials, modeller, molekel, mosaik-aligner, mosdepth, mpsqed, mrs, msatfinder, msxpertsuite, mugsy, multiqc, mummergpu, mview, nanocall, ncbi-igblast, nextsv, ngila, ngsqctoolkit, nw-align, oases, obo-edit, oligoarrayaux, omegamap, oncofuse, operondb, optimir, optitype, paipline, partigene, partitionfinder, patristic, pcma, pfaat, phagefinder, phpphylotree, phylographer, phylophlan, phyloviz-core, phylowin, pilercr, pipasic, plato, profit, prokka, prot4est, psipred, pssh2, pyrophosphate-tools, python-orange, python-reaper, python-treetime, python3-geneimpacts, qiime, qtlcart, qualimap, quast, r-bioc-annotationhub, r-bioc-aroma.light, r-bioc-ensembldb, r-bioc-go.db, r-bioc-savr, r-cran-boolnet, r-cran-forecast, r-cran-pheatmap, r-cran-qqman, r-cran-rentrez, r-cran-webgestaltr, r-other-apmswapp, raccoon, ragout, raxml-ng, rbs-finder, repeatmasker, rmblast, roadtrips, roche454ace2caf, rose, rsat, sailfish, sambamba, sap, science-workflow, seq-gen, seq-seq-pan, sequenceconverter.app, sibelia, sift, sina, sistr, situs, smrtanalysis, snpeff, solvate, sourmash, spaln, sparta, splitstree, ssaha, strap, strap-base, stringtie, tab2mage, tacg, taverna, taxinspector, tetra, tide, tigr-glimmer-mg, tn-seqexplorer, treebuilder3d, treetime, tripal, trnascan-se, twain, ugene, umap, umis, unc-fish, uniprime, varmatch, varscan, vcfanno, vdjtools, vienna-rna, virulencefinder, vmd, x-tandem-pipeline, zodiac-zeden Description: Debian Med bioinformatics packages Description-md5: 472a50c6504872b123b928f5c13e0f5e Tag: field::biology, role::metapackage, suite::debian Section: misc Priority: optional Filename: pool/main/d/debian-med/med-bio_3.3_all.deb Size: 20356 MD5sum: f8bcad4ac1a6292d5a36738eca629fb8 SHA256: 3100e1b95beb8e287044e2ff22e8aeae64732c7b4f60f3389f43be223e3c3da0 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-log-alternatives --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --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/buster-merged-usr_amd64.tar.gz -d buster --no-upgrade-test --apt med-bio=3.3 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.1~202403190841~1.4-4-g85045c69 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts-log-alternatives --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --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/buster-merged-usr_amd64.tar.gz -d buster --no-upgrade-test --apt med-bio=3.3 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpch7kfd_7 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/buster-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpch7kfd_7 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/buster-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/buster-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/proc'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/dev/pts'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/dev/shm'] 0m0.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main 0m0.4s DEBUG: Created policy-rc.d and chmodded it. 0m0.4s DEBUG: Created resolv.conf. 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts-log-alternatives to /srv/piuparts.debian.org/tmp/tmpch7kfd_7/tmp/scripts/ 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpch7kfd_7/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'apt-get', 'update'] 0m1.7s DUMP: Hit:1 http://deb.debian.org/debian buster InRelease Reading package lists... 0m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'apt-get', 'update'] 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s DUMP: f6fc0f2636004ef589309651dfd778f4 - 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s INFO: Running scripts post_setup 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_setup_dummy_users'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_setup_dummy_users'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_setup_forbid_home'] 0m3.7s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_setup_forbid_home'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.8s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_setup_minimize'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_setup_minimize'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_setup_zz_backports'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_setup_zz_backports'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'apt-get', 'clean'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'apt-get', 'clean'] 0m3.8s DEBUG: Recording chroot state 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.3s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.2.3 install ok installed base-files base-files 10.3+deb10u13 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-4 install ok installed bsdutils bsdutils 1:2.33.1-0.1 install ok installed coreutils coreutils 8.30-3 install ok installed dash dash 0.5.10.2-5 install ok installed debconf debconf 1.5.71+deb10u1 install ok installed debian-archive-keyring debian-archive-keyring 2019.1+deb10u1 install ok installed debianutils debianutils 4.8.6.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.8 install ok installed e2fsprogs e2fsprogs 1.44.5-1+deb10u3 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed findutils findutils 4.6.0+git+20190209-2 install ok installed gcc-8-base:amd64 gcc-8-base 8.3.0-6 install ok installed gpgv gpgv 2.2.12-1+deb10u2 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3+deb10u1 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56+nmu1 install ok installed libacl1:amd64 libacl1 2.2.53-4 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.2.3 install ok installed libattr1:amd64 libattr1 1:2.4.48-4 install ok installed libaudit-common libaudit-common 1:2.8.4-3 install ok installed libaudit1:amd64 libaudit1 1:2.8.4-3 install ok installed libblkid1:amd64 libblkid1 2.33.1-0.1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-9.2~deb10u1 install ok installed libc-bin libc-bin 2.28-10+deb10u1 install ok installed libc6:amd64 libc6 2.28-10+deb10u1 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2 install ok installed libcom-err2:amd64 libcom-err2 1.44.5-1+deb10u3 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.249 install ok installed libext2fs2:amd64 libext2fs2 1.44.5-1+deb10u3 install ok installed libfdisk1:amd64 libfdisk1 2.33.1-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libgcc1:amd64 libgcc1 1:8.3.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.4-5+deb10u1 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4+deb10u1 install ok installed libgnutls30:amd64 libgnutls30 3.6.7-4+deb10u8 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1+deb10u1 install ok installed liblz4-1:amd64 liblz4-1 1.8.3-1+deb10u1 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+deb10u1 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-2+deb10u2 install ok installed libnettle6:amd64 libnettle6 3.4.1-1+deb10u1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.15-2+deb10u1 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre3:amd64 libpcre3 2:8.39-12 install ok installed libseccomp2:amd64 libseccomp2 2.3.3-4 install ok installed libselinux1:amd64 libselinux1 2.8-1+b1 install ok installed libsemanage-common libsemanage-common 2.8-2 install ok installed libsemanage1:amd64 libsemanage1 2.8-2 install ok installed libsepol1:amd64 libsepol1 2.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.33.1-0.1 install ok installed libss2:amd64 libss2 1.44.5-1+deb10u3 install ok installed libstdc++6:amd64 libstdc++6 8.3.0-6 install ok installed libsystemd0:amd64 libsystemd0 241-7~deb10u8 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-2+deb10u2 install ok installed libudev1:amd64 libudev1 241-7~deb10u8 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libzstd1:amd64 libzstd1 1.3.8+dfsg-3+deb10u2 install ok installed login login 1:4.5-1.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.33.1-0.1 install ok installed ncurses-base ncurses-base 6.1+20181013-2+deb10u2 install ok installed ncurses-bin ncurses-bin 6.1+20181013-2+deb10u2 install ok installed passwd passwd 1:4.5-1.1 install ok installed perl-base perl-base 5.28.1-6+deb10u1 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.93-8 install ok installed tar tar 1.30+dfsg-6 install ok installed tzdata tzdata 2021a-0+deb10u6 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+deb10u1 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'dpkg-divert', '--list'] 0m4.3s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged 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 local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'dpkg-divert', '--list'] 0m4.3s INFO: Running scripts is_testable 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/is_testable_uninstallable'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/is_testable_uninstallable'] 0m4.3s INFO: apt-cache does not know about any of the requested packages 0m4.3s INFO: Running scripts pre_test 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_test_exceptions'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_test_exceptions'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_test_root_password'] 0m4.3s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_test_root_password'] 0m4.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7'] 0m4.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7'] 0m5.2s DEBUG: No broken symlinks as far as we can find. 0m5.2s INFO: Running scripts pre_install 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_install_database-server'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_install_database-server'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_install_exceptions'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_install_exceptions'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_install_extras'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_install_extras'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_install_log_alternatives'] 0m5.3s DUMP: Adding 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' dpkg-divert: warning: diverting file '/usr/bin/update-alternatives' from an Essential package with rename is dangerous, use --no-rename 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_install_log_alternatives'] 0m5.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7'] 0m5.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7'] 0m6.3s DEBUG: No broken symlinks as far as we can find. 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'apt-cache', 'policy'] 0m7.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldoldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'apt-cache', 'policy'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'apt-cache', 'policy', 'med-bio'] 0m7.3s DUMP: med-bio: Installed: (none) Candidate: 3.3 Version table: 3.3 500 500 http://deb.debian.org/debian buster/main amd64 Packages 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'apt-cache', 'policy', 'med-bio'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'apt-get', '-y', 'install', 'med-bio=3.3'] 0m9.3s 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 annovar apollo arachne arb asap atropos autodocktools axparafit axpcoords bagpipe bambus bax2bam biceps big-blast bigsdb biobambam2 bismark blat blimps-utils blobology braker btk-core cactus caftools cain card-rgi ccs cdna-db cellprofiler cinema cluster3 cmap compclust condetri contrafold contralign coot copycat crossbow crux-toolkit cufflinks cytoscape dascrubber dazzle deepbinner dendroscope e-hive ecell embassy-phylip emboss-explorer emmax emperor ensembl estferret euler-sr euler2 exabayes exalt excavator falcon fasta3 ffp figaro filtlong forester forge galaxy gassst gatk gbrowse-syn genemark genesplicer genetrack genezilla genographer getdata gffread glimmerhmm gmap gmv gramalign haploview hawkeye htqc igdiscover igv inspect jalview jbrowse jigsaw kallisto kempbasu kma kmerresistance kraken2 lofreq mach-haplotyper mage2tab maker2 malt manta martj maude maxd meme mesquite metabit metarep metastudent-data metastudent-data-2 metastudent-data-3 mgltools-cadd mgltools-pmv mgltools-vision migrate minimus mirbase mirtop mobyle mobyle-programs mobyle-tutorials modeller molekel mosaik-aligner mosdepth mpsqed mrs msatfinder msxpertsuite mugsy multiqc mummergpu mview nanocall ncbi-igblast nextsv ngila ngsqctoolkit nw-align oases obo-edit oligoarrayaux omegamap oncofuse operondb optimir optitype paipline partigene partitionfinder patristic pcma pfaat phagefinder phpphylotree phylographer phylophlan phyloviz-core phylowin pilercr pipasic plato profit prokka prot4est psipred pssh2 pyrophosphate-tools python-orange python-reaper python-treetime python3-geneimpacts qiime qtlcart qualimap quast r-bioc-annotationhub r-bioc-aroma.light r-bioc-ensembldb r-bioc-go.db r-bioc-savr r-cran-boolnet r-cran-forecast r-cran-pheatmap r-cran-qqman r-cran-rentrez r-cran-webgestaltr r-other-apmswapp raccoon ragout raxml-ng rbs-finder repeatmasker rmblast roadtrips roche454ace2caf rose rsat sailfish sambamba sap science-workflow seq-gen seq-seq-pan sequenceconverter.app sibelia sift sina sistr situs smrtanalysis snpeff solvate sourmash spaln sparta splitstree ssaha strap strap-base stringtie tab2mage tacg taverna taxinspector tetra tide tigr-glimmer-mg tn-seqexplorer treebuilder3d treetime tripal trnascan-se twain ugene umap umis unc-fish uniprime varmatch varscan vcfanno vdjtools vienna-rna virulencefinder vmd x-tandem-pipeline zodiac-zeden menu-l10n gksu | kde-runtime | ktsuss Recommended packages: abacas abyss acedb-other 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 assemblytics atac augustus autodock autodock-vina autogrid avogadro axe-demultiplexer baitfisher bali-phy ballview bamtools bandage barrnap bcbio bcftools beads beagle beast-mcmc beast2-mcmc bedops bedtools belvu berkeley-express bio-eagle bio-rainbow bio-tradis biosyntax bitseq blasr blixem bolt-lmm bowtie bowtie2 boxshade bppphyview bppsuite brig bwa canu cassiopee cct cd-hit cdbfasta centrifuge cgview changeo chimeraslayer chromhmm chromimpute circlator circos clearcut clonalframe clonalframeml clonalorigin clustalo clustalw clustalx cnvkit codonw concavity conservation-code crac csb cutadapt daligner datamash dawg dazzdb deepnano delly dialign dialign-tx diamond-aligner dindel discosnp disulfinder dnaclust dotter dssp dwgsim e-mem ea-utils ecopcr edtsurf eigensoft elph embassy-domainatrix embassy-domalign embassy-domsearch emboss estscan examl exonerate fastahack fastaq fastdnaml fastlink fastml fastp fastqc fastqtl fasttree fastx-toolkit ffindex figtree fitgcp flexbar fml-asm freebayes freecontact fsa fsm-lite gamgi garli garlic gasic gatb-core gbrowse gdpc gemma genometester genometools gentle gff2aplot gff2ps ghemical ghmm giira glam2 grabix graphlan grinder gromacs gubbins gwama harvest-tools hhsuite hilive hinge hisat2 hmmer hmmer2 hyphy-mpi | hyphy-pt idba igor indelible infernal ipig iqtree iva jaligner jellyfish jellyfish1 jmodeltest jmol kalign khmer kineticstools king-probe kissplice kmc kmer kraken lagan lamarc lambda-align lambda-align2 last-align leaff lefse librg-utils-perl libvcflib-tools logol loki ltrsift lucy macs macsyfinder maffilter mafft mapdamage mapsembler2 maq maqview mash mauve-aligner melting meryl metaphlan2 metastudent mhap microbegps microbiomeutil minia miniasm minimac4 minimap minimap2 mipe mira-assembler mlv-smile mothur mptp mrbayes mummer murasaki | murasaki-mpi muscle mustang nanook 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 obitools openms pal2nal paleomix paml paraclu parsinsert parsnp patman pbalign pbbarcode pbdagcon pbgenomicconsensus pbh5tools pbhoney pbjelly pbsim pbsuite pdb2pqr perlprimer perm pftools phast phipack phybin phylip phyml physamp phyutility phyx picard-tools piler pilon pirs placnet plasmidomics plasmidseeker plast plink plink1.9 plip poa populations porechop 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 pscan-chip pscan-tfbs psortb pycorrfit pymol pynast pyscanfcs python-cogent python3-biomaj3-daemon python3-gffutils python3-presto python3-pybedtools python3-pybel python3-sqt pyvcf qcumber qtltools quorum qutemol r-bioc-annotate r-bioc-biostrings r-bioc-bitseq r-bioc-cner r-bioc-cummerbund r-bioc-deseq2 r-bioc-dnacopy r-bioc-ebseq r-bioc-genefilter r-bioc-geneplotter r-bioc-gviz r-bioc-hilbertvis r-bioc-impute r-bioc-limma r-bioc-mergeomics r-bioc-metagenomeseq r-bioc-pcamethods r-bioc-phyloseq r-bioc-rtracklayer 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-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-shazam r-cran-tcr r-cran-tigger r-cran-treescape r-cran-vegan r-other-hms-dbmi-spp r-other-mott-happy.hbrem racon radiant rambo-k rampler 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 roguenarok rsem rtax runcircos-gui saint salmon samblaster samtools scoary scrm scythe seaview seer segemehl seqan-apps seqmagick seqprep seqsero seqtk sga sibsim4 sickle sigma-align sim4 sim4db smalr smalt smithwaterman snap snap-aligner sniffles snp-sites snpomatic soapaligner soapdenovo soapdenovo2 soapsnp sortmerna spaced spades spoa sprai spread-phy squizz sra-toolkit srst2 ssake sspace ssw-align stacks staden staden-io-lib-utils subread suitename sumaclust sumatra sumtrees surankco swarm sweed t-coffee tabix tantan theseus tigr-glimmer tm-align tnseq-transit toil tophat topp toppred trace2dbest tracetuner transdecoder transrate-tools transtermhp tree-puzzle | tree-ppuzzle treeview treeviewx trimmomatic trinityrnaseq tvc uc-echo unanimity unicycler varna vcftools velvet | velvet-long velvetoptimiser viewmol vsearch wigeon wise yaha 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 591 kB of archives. After this operation, 2334 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian buster/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get:2 http://deb.debian.org/debian buster/main amd64 tasksel-data all 3.53 [17.9 kB] Get:3 http://deb.debian.org/debian buster/main amd64 tasksel all 3.53 [95.0 kB] Get:4 http://deb.debian.org/debian buster/main amd64 menu amd64 2.1.47+b1 [380 kB] Get:5 http://deb.debian.org/debian buster/main amd64 blends-common all 0.7.2 [24.7 kB] Get:6 http://deb.debian.org/debian buster/main amd64 med-config all 3.3 [18.7 kB] Get:7 http://deb.debian.org/debian buster/main amd64 med-tasks all 3.3 [15.9 kB] Get:8 http://deb.debian.org/debian buster/main amd64 med-bio all 3.3 [20.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 591 kB in 0s (1526 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 ... 6465 files and directories currently installed.) Preparing to unpack .../0-liblocale-gettext-perl_1.07-3+b4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package tasksel-data. Preparing to unpack .../1-tasksel-data_3.53_all.deb ... Unpacking tasksel-data (3.53) ... Selecting previously unselected package tasksel. Preparing to unpack .../2-tasksel_3.53_all.deb ... Unpacking tasksel (3.53) ... 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_0.7.2_all.deb ... Unpacking blends-common (0.7.2) ... Selecting previously unselected package med-config. Preparing to unpack .../5-med-config_3.3_all.deb ... Unpacking med-config (3.3) ... Selecting previously unselected package med-tasks. Preparing to unpack .../6-med-tasks_3.3_all.deb ... Unpacking med-tasks (3.3) ... Selecting previously unselected package med-bio. Preparing to unpack .../7-med-bio_3.3_all.deb ... Unpacking med-bio (3.3) ... Setting up menu (2.1.47+b1) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up tasksel (3.53) ... Setting up tasksel-data (3.53) ... Setting up med-tasks (3.3) ... Processing triggers for menu (2.1.47+b1) ... Setting up blends-common (0.7.2) ... Setting up med-config (3.3) ... Adding group `med' (GID 150) ... Done. Setting up med-bio (3.3) ... 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'apt-get', '-y', 'install', 'med-bio=3.3'] 0m9.3s INFO: Running scripts post_install 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_install_exceptions'] 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_install_exceptions'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_install_log_alternatives'] 0m9.4s DUMP: Removing 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_install_log_alternatives'] 0m9.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7'] 0m9.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7'] 0m10.3s DEBUG: No broken symlinks as far as we can find. 0m10.4s INFO: /bin converted to /usr/bin by /usr merge 0m10.4s INFO: /lib converted to /usr/lib by /usr merge 0m10.4s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m10.4s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m10.4s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m10.4s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m10.4s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m10.4s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m10.4s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m10.4s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m10.4s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m10.4s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m10.4s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m10.4s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m10.4s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m10.4s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m10.4s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m10.4s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m10.4s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m10.4s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m10.4s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m10.4s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m10.4s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m10.4s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m10.4s INFO: /sbin converted to /usr/sbin by /usr merge 0m10.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', '-ac', '--ignore-obsolete'] 0m11.5s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', '-ac', '--ignore-obsolete'] 0m11.5s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m11.5s DUMP: 0.15.6 0m11.5s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m11.5s INFO: Running adequate version 0.15.6 now. 0m11.5s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'med-bio'] 0m11.6s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'med-bio'] 0m11.6s INFO: Running scripts pre_remove 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_remove_exceptions'] 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/pre_remove_exceptions'] 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m13.7s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.2.3 install ok installed base-files base-files 10.3+deb10u13 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-4 install ok installed blends-common blends-common 0.7.2 install ok installed bsdutils bsdutils 1:2.33.1-0.1 install ok installed coreutils coreutils 8.30-3 install ok installed dash dash 0.5.10.2-5 install ok installed debconf debconf 1.5.71+deb10u1 install ok installed debian-archive-keyring debian-archive-keyring 2019.1+deb10u1 install ok installed debianutils debianutils 4.8.6.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.8 install ok installed e2fsprogs e2fsprogs 1.44.5-1+deb10u3 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed findutils findutils 4.6.0+git+20190209-2 install ok installed gcc-8-base:amd64 gcc-8-base 8.3.0-6 install ok installed gpgv gpgv 2.2.12-1+deb10u2 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3+deb10u1 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56+nmu1 install ok installed libacl1:amd64 libacl1 2.2.53-4 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.2.3 install ok installed libattr1:amd64 libattr1 1:2.4.48-4 install ok installed libaudit-common libaudit-common 1:2.8.4-3 install ok installed libaudit1:amd64 libaudit1 1:2.8.4-3 install ok installed libblkid1:amd64 libblkid1 2.33.1-0.1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-9.2~deb10u1 install ok installed libc-bin libc-bin 2.28-10+deb10u1 install ok installed libc6:amd64 libc6 2.28-10+deb10u1 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2 install ok installed libcom-err2:amd64 libcom-err2 1.44.5-1+deb10u3 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.249 install ok installed libext2fs2:amd64 libext2fs2 1.44.5-1+deb10u3 install ok installed libfdisk1:amd64 libfdisk1 2.33.1-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libgcc1:amd64 libgcc1 1:8.3.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.4-5+deb10u1 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4+deb10u1 install ok installed libgnutls30:amd64 libgnutls30 3.6.7-4+deb10u8 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1+deb10u1 install ok installed liblocale-gettext-perl liblocale-gettext-perl 1.07-3+b4 install ok installed liblz4-1:amd64 liblz4-1 1.8.3-1+deb10u1 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+deb10u1 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-2+deb10u2 install ok installed libnettle6:amd64 libnettle6 3.4.1-1+deb10u1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.15-2+deb10u1 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre3:amd64 libpcre3 2:8.39-12 install ok installed libseccomp2:amd64 libseccomp2 2.3.3-4 install ok installed libselinux1:amd64 libselinux1 2.8-1+b1 install ok installed libsemanage-common libsemanage-common 2.8-2 install ok installed libsemanage1:amd64 libsemanage1 2.8-2 install ok installed libsepol1:amd64 libsepol1 2.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.33.1-0.1 install ok installed libss2:amd64 libss2 1.44.5-1+deb10u3 install ok installed libstdc++6:amd64 libstdc++6 8.3.0-6 install ok installed libsystemd0:amd64 libsystemd0 241-7~deb10u8 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-2+deb10u2 install ok installed libudev1:amd64 libudev1 241-7~deb10u8 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libzstd1:amd64 libzstd1 1.3.8+dfsg-3+deb10u2 install ok installed login login 1:4.5-1.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed med-bio med-bio 3.3 install ok installed med-config med-config 3.3 install ok installed med-tasks med-tasks 3.3 install ok installed menu menu 2.1.47+b1 install ok installed mount mount 2.33.1-0.1 install ok installed ncurses-base ncurses-base 6.1+20181013-2+deb10u2 install ok installed ncurses-bin ncurses-bin 6.1+20181013-2+deb10u2 install ok installed passwd passwd 1:4.5-1.1 install ok installed perl-base perl-base 5.28.1-6+deb10u1 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.93-8 install ok installed tar tar 1.30+dfsg-6 install ok installed tasksel tasksel 3.53 install ok installed tasksel-data tasksel-data 3.53 install ok installed tzdata tzdata 2021a-0+deb10u6 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+deb10u1 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'apt-get', 'remove', 'blends-common', 'liblocale-gettext-perl', 'med-config', 'med-tasks', 'menu', 'tasksel', 'tasksel-data', 'med-bio'] 0m14.8s 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, 2334 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 ... 6866 files and directories currently installed.) Removing med-bio (3.3) ... Removing med-config (3.3) ... Removing blends-common (0.7.2) ... Removing med-tasks (3.3) ... Removing menu (2.1.47+b1) ... Removing tasksel (3.53) ... Removing tasksel-data (3.53) ... Removing liblocale-gettext-perl (1.07-3+b4) ... 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'apt-get', 'remove', 'blends-common', 'liblocale-gettext-perl', 'med-config', 'med-tasks', 'menu', 'tasksel', 'tasksel-data', 'med-bio'] 0m14.8s INFO: Running scripts post_remove 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_remove_exceptions'] 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_remove_exceptions'] 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'dpkg', '--purge', 'blends-common', 'liblocale-gettext-perl', 'med-config', 'med-tasks', 'menu', 'tasksel', 'tasksel-data'] 0m15.0s DUMP: (Reading database ... 6475 files and directories currently installed.) Purging configuration files for blends-common (0.7.2) ... dpkg: warning: ignoring request to remove liblocale-gettext-perl which isn't installed Purging configuration files for med-config (3.3) ... 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 (3.53) ... dpkg: warning: ignoring request to remove tasksel-data which isn't installed 0m15.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'dpkg', '--purge', 'blends-common', 'liblocale-gettext-perl', 'med-config', 'med-tasks', 'menu', 'tasksel', 'tasksel-data'] 0m15.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'dpkg', '--purge', 'med-bio'] 0m15.0s DUMP: dpkg: warning: ignoring request to remove med-bio which isn't installed 0m15.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'dpkg', '--purge', 'med-bio'] 0m15.0s INFO: Running scripts post_purge 0m15.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_purge_exceptions'] 0m15.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_purge_exceptions'] 0m15.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'dpkg', '--purge', '--pending'] 0m15.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'dpkg', '--purge', '--pending'] 0m15.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'dpkg', '--remove', '--pending'] 0m15.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'dpkg', '--remove', '--pending'] 0m15.1s INFO: Running scripts post_test 0m15.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_test_exceptions'] 0m15.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'tmp/scripts/post_test_exceptions'] 0m15.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7'] 0m15.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7'] 0m16.1s DEBUG: No broken symlinks as far as we can find. 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'dpkg-divert', '--list'] 0m16.1s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged 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 local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'dpkg-divert', '--list'] 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'apt-get', 'clean'] 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7', 'apt-get', 'clean'] 0m16.1s DEBUG: Recording chroot state 0m16.7s INFO: PASS: Installation and purging test. 0m17.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/dev/shm'] 0m17.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/dev/shm'] 0m17.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/dev/console'] 0m17.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/dev/console'] 0m17.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/dev/ptmx'] 0m17.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/dev/ptmx'] 0m17.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/dev/pts'] 0m17.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/dev/pts'] 0m17.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/proc'] 0m17.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7/proc'] 0m17.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7'] 0m17.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpch7kfd_7'] 0m17.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpch7kfd_7 0m17.5s INFO: PASS: All tests. 0m17.5s INFO: piuparts run ends. ret=0 End: 2024-04-27 05:51:09 GMT