Diff of the two buildlogs: -- --- b1/build.log 2025-02-27 20:13:05.047668440 +0000 +++ b2/build.log 2025-02-27 21:11:30.124591162 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Apr 1 14:09:59 -12 2026 -I: pbuilder-time-stamp: 1775095799 +I: Current time: Fri Feb 28 10:13:16 +14 2025 +I: pbuilder-time-stamp: 1740687196 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying fix-type-cast-i386.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3075221/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3810273/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Feb 27 20:13 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3810273/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3810273/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='1cf5e35f52e04a23809d91351b66e4a6' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='3075221' - PS1='# ' - PS2='> ' + INVOCATION_ID=9ca29fa84fb84de99ed38c1b69b98a0e + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3810273 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.aqa8VV9I/pbuilderrc_G7EK --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.aqa8VV9I/b1 --logfile b1/build.log python-biopython_1.85+dfsg-2.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.aqa8VV9I/pbuilderrc_V4oO --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.aqa8VV9I/b2 --logfile b2/build.log python-biopython_1.85+dfsg-2.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3075221/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3810273/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -510,7 +542,7 @@ Get: 326 http://deb.debian.org/debian trixie/main arm64 texlive-latex-extra all 2024.20250114-1 [24.7 MB] Get: 327 http://deb.debian.org/debian trixie/main arm64 wise-data all 2.4.1-25 [76.1 kB] Get: 328 http://deb.debian.org/debian trixie/main arm64 wise arm64 2.4.1-25 [1007 kB] -Fetched 355 MB in 5s (65.3 MB/s) +Fetched 355 MB in 4s (97.3 MB/s) Preconfiguring packages ... Selecting previously unselected package m4. (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 ... 19916 files and directories currently installed.) @@ -1571,8 +1603,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Apr 2 02:12:01 UTC 2026. -Universal Time is now: Thu Apr 2 02:12:01 UTC 2026. +Local time is now: Thu Feb 27 20:16:23 UTC 2025. +Universal Time is now: Thu Feb 27 20:16:23 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... @@ -1910,7 +1942,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/python-biopython-1.85+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-biopython_1.85+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/3810273/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3810273/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/python-biopython-1.85+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../python-biopython_1.85+dfsg-2_source.changes dpkg-buildpackage: info: source package python-biopython dpkg-buildpackage: info: source version 1.85+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -2907,293 +2943,293 @@ making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. [autosummary] generating autosummary for: Tutorial/chapter_align.rst, Tutorial/chapter_appendix.rst, Tutorial/chapter_bibliography.rst, Tutorial/chapter_blast.rst, Tutorial/chapter_cluster.rst, Tutorial/chapter_contributing.rst, Tutorial/chapter_cookbook.rst, Tutorial/chapter_entrez.rst, Tutorial/chapter_graphics.rst, Tutorial/chapter_introduction.rst, ..., Tutorial/chapter_quick_start.rst, Tutorial/chapter_searchio.rst, Tutorial/chapter_seq_annot.rst, Tutorial/chapter_seq_objects.rst, Tutorial/chapter_seqio.rst, Tutorial/chapter_testing.rst, Tutorial/chapter_uniprot.rst, Tutorial/index.rst, api/index.rst, index.rst -Creating file /tmp/tmpqg6exyrl/BioSQL.rst. -Creating file /tmp/tmpqg6exyrl/BioSQL.BioSeq.rst. -Creating file /tmp/tmpqg6exyrl/BioSQL.BioSeqDatabase.rst. -Creating file /tmp/tmpqg6exyrl/BioSQL.DBUtils.rst. -Creating file /tmp/tmpqg6exyrl/BioSQL.Loader.rst. -Creating file /tmp/tmpqg6exyrl/conf.py. -Creating file /tmp/tmpqg6exyrl/index.rst. -Creating file /tmp/tmpqg6exyrl/Makefile. -Creating file /tmp/tmpqg6exyrl/make.bat. -Creating file /tmp/tmpqg6exyrl/Bio.rst. -Creating file /tmp/tmpqg6exyrl/Bio.File.rst. -Creating file /tmp/tmpqg6exyrl/Bio.LogisticRegression.rst. -Creating file /tmp/tmpqg6exyrl/Bio.MarkovModel.rst. -Creating file /tmp/tmpqg6exyrl/Bio.MaxEntropy.rst. -Creating file /tmp/tmpqg6exyrl/Bio.NaiveBayes.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Seq.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SeqFeature.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SeqRecord.rst. -Creating file /tmp/tmpqg6exyrl/Bio.bgzf.rst. -Creating file /tmp/tmpqg6exyrl/Bio.kNN.rst. -Creating file /tmp/tmpqg6exyrl/Bio.pairwise2.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Affy.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Affy.CelFile.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.AlignInfo.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.a2m.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.analysis.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.bed.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.bigbed.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.bigmaf.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.bigpsl.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.chain.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.clustal.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.emboss.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.exonerate.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.fasta.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.hhr.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.interfaces.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.maf.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.mauve.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.msf.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.nexus.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.phylip.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.psl.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.sam.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.stockholm.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.tabular.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.Applications.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Align.substitution_matrices.rst. -Creating file /tmp/tmpqg6exyrl/Bio.AlignIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.AlignIO.ClustalIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.AlignIO.EmbossIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.AlignIO.FastaIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.AlignIO.Interfaces.rst. -Creating file /tmp/tmpqg6exyrl/Bio.AlignIO.MafIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.AlignIO.MauveIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.AlignIO.MsfIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.AlignIO.NexusIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.AlignIO.PhylipIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.AlignIO.StockholmIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Application.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Blast.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Blast.Applications.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Blast.NCBIWWW.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Blast.NCBIXML.rst. -Creating file /tmp/tmpqg6exyrl/Bio.CAPS.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Cluster.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Compass.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Data.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Data.CodonTable.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Data.IUPACData.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Data.PDBData.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Emboss.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Emboss.Applications.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Emboss.Primer3.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Emboss.PrimerSearch.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Entrez.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Entrez.Parser.rst. -Creating file /tmp/tmpqg6exyrl/Bio.ExPASy.rst. -Creating file /tmp/tmpqg6exyrl/Bio.ExPASy.Enzyme.rst. -Creating file /tmp/tmpqg6exyrl/Bio.ExPASy.Prodoc.rst. -Creating file /tmp/tmpqg6exyrl/Bio.ExPASy.Prosite.rst. -Creating file /tmp/tmpqg6exyrl/Bio.ExPASy.ScanProsite.rst. -Creating file /tmp/tmpqg6exyrl/Bio.ExPASy.cellosaurus.rst. -Creating file /tmp/tmpqg6exyrl/Bio.GenBank.rst. -Creating file /tmp/tmpqg6exyrl/Bio.GenBank.Record.rst. -Creating file /tmp/tmpqg6exyrl/Bio.GenBank.Scanner.rst. -Creating file /tmp/tmpqg6exyrl/Bio.GenBank.utils.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Geo.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Geo.Record.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Graphics.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Graphics.BasicChromosome.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Graphics.ColorSpiral.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Graphics.Comparative.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Graphics.DisplayRepresentation.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Graphics.Distribution.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Graphics.KGML_vis.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Graphics.GenomeDiagram.rst. -Creating file /tmp/tmpqg6exyrl/Bio.HMM.rst. -Creating file /tmp/tmpqg6exyrl/Bio.HMM.DynamicProgramming.rst. -Creating file /tmp/tmpqg6exyrl/Bio.HMM.MarkovModel.rst. -Creating file /tmp/tmpqg6exyrl/Bio.HMM.Trainer.rst. -Creating file /tmp/tmpqg6exyrl/Bio.HMM.Utilities.rst. -Creating file /tmp/tmpqg6exyrl/Bio.KEGG.rst. -Creating file /tmp/tmpqg6exyrl/Bio.KEGG.REST.rst. -Creating file /tmp/tmpqg6exyrl/Bio.KEGG.Compound.rst. -Creating file /tmp/tmpqg6exyrl/Bio.KEGG.Enzyme.rst. -Creating file /tmp/tmpqg6exyrl/Bio.KEGG.Gene.rst. -Creating file /tmp/tmpqg6exyrl/Bio.KEGG.KGML.rst. -Creating file /tmp/tmpqg6exyrl/Bio.KEGG.KGML.KGML_parser.rst. -Creating file /tmp/tmpqg6exyrl/Bio.KEGG.KGML.KGML_pathway.rst. -Creating file /tmp/tmpqg6exyrl/Bio.KEGG.Map.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Medline.rst. -Creating file /tmp/tmpqg6exyrl/Bio.NMR.rst. -Creating file /tmp/tmpqg6exyrl/Bio.NMR.NOEtools.rst. -Creating file /tmp/tmpqg6exyrl/Bio.NMR.xpktools.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Nexus.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Nexus.Nexus.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Nexus.Nodes.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Nexus.StandardData.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Nexus.Trees.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.AbstractPropertyMap.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.Atom.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.Chain.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.DSSP.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.Dice.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.Entity.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.FragmentMapper.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.HSExposure.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.MMCIF2Dict.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.MMCIFParser.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.Model.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.NACCESS.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.NeighborSearch.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.PDBExceptions.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.PDBIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.PDBList.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.PDBMLParser.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.PDBParser.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.PICIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.PSEA.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.Polypeptide.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.Residue.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.ResidueDepth.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.SASA.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.SCADIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.Selection.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.Structure.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.StructureAlignment.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.StructureBuilder.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.Superimposer.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.alphafold_db.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.binary_cif.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.cealign.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.ic_data.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.ic_rebuild.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.internal_coords.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.mmcifio.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.parse_pdb_header.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.qcprot.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.vectors.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.mmtf.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.mmtf.DefaultParser.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PDB.mmtf.mmtfio.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Pathway.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Pathway.Rep.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Pathway.Rep.Graph.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Pathway.Rep.MultiGraph.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Phylo.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Phylo.BaseTree.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Phylo.CDAO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Phylo.CDAOIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Phylo.Consensus.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Phylo.NeXML.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Phylo.NeXMLIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Phylo.Newick.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Phylo.NewickIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Phylo.NexusIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Phylo.PhyloXML.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Phylo.PhyloXMLIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Phylo.TreeConstruction.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Phylo.Applications.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Phylo.PAML.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Phylo.PAML.baseml.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Phylo.PAML.chi2.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Phylo.PAML.codeml.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Phylo.PAML.yn00.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PopGen.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PopGen.GenePop.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PopGen.GenePop.Controller.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PopGen.GenePop.EasyController.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PopGen.GenePop.FileParser.rst. -Creating file /tmp/tmpqg6exyrl/Bio.PopGen.GenePop.LargeFileParser.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Restriction.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Restriction.PrintFormat.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Restriction.Restriction_Dictionary.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SCOP.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SCOP.Cla.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SCOP.Des.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SCOP.Dom.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SCOP.Hie.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SCOP.Raf.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SCOP.Residues.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SVDSuperimposer.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SearchIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SearchIO.BlatIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SearchIO.FastaIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SearchIO.BlastIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SearchIO.BlastIO.blast_tab.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SearchIO.BlastIO.blast_xml.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SearchIO.ExonerateIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SearchIO.ExonerateIO.exonerate_cigar.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SearchIO.ExonerateIO.exonerate_text.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SearchIO.ExonerateIO.exonerate_vulgar.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SearchIO.HHsuiteIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SearchIO.HHsuiteIO.hhsuite2_text.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SearchIO.HmmerIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SearchIO.HmmerIO.hmmer2_text.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SearchIO.HmmerIO.hmmer3_domtab.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SearchIO.HmmerIO.hmmer3_tab.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SearchIO.HmmerIO.hmmer3_text.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SearchIO.InterproscanIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SearchIO.InterproscanIO.interproscan_xml.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SeqIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SeqIO.AbiIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SeqIO.AceIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SeqIO.FastaIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SeqIO.GckIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SeqIO.GfaIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SeqIO.IgIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SeqIO.InsdcIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SeqIO.Interfaces.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SeqIO.NibIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SeqIO.PdbIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SeqIO.PhdIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SeqIO.PirIO.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SeqIO.QualityIO.rst. -Creating file 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/tmp/tmpqg6exyrl/Bio.Sequencing.Phd.rst. -Creating file /tmp/tmpqg6exyrl/Bio.Sequencing.Applications.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SwissProt.rst. -Creating file /tmp/tmpqg6exyrl/Bio.SwissProt.KeyWList.rst. -Creating file /tmp/tmpqg6exyrl/Bio.TogoWS.rst. -Creating file /tmp/tmpqg6exyrl/Bio.UniGene.rst. -Creating file /tmp/tmpqg6exyrl/Bio.UniProt.rst. -Creating file /tmp/tmpqg6exyrl/Bio.UniProt.GOA.rst. -Creating file /tmp/tmpqg6exyrl/Bio.codonalign.rst. -Creating file /tmp/tmpqg6exyrl/Bio.codonalign.codonalignment.rst. -Creating file /tmp/tmpqg6exyrl/Bio.codonalign.codonseq.rst. -Creating file /tmp/tmpqg6exyrl/Bio.motifs.rst. -Creating file /tmp/tmpqg6exyrl/Bio.motifs.alignace.rst. -Creating file /tmp/tmpqg6exyrl/Bio.motifs.clusterbuster.rst. -Creating file /tmp/tmpqg6exyrl/Bio.motifs.mast.rst. -Creating file /tmp/tmpqg6exyrl/Bio.motifs.matrix.rst. -Creating file /tmp/tmpqg6exyrl/Bio.motifs.meme.rst. -Creating file /tmp/tmpqg6exyrl/Bio.motifs.minimal.rst. -Creating file /tmp/tmpqg6exyrl/Bio.motifs.pfm.rst. -Creating file /tmp/tmpqg6exyrl/Bio.motifs.thresholds.rst. -Creating file /tmp/tmpqg6exyrl/Bio.motifs.transfac.rst. -Creating file /tmp/tmpqg6exyrl/Bio.motifs.xms.rst. -Creating file /tmp/tmpqg6exyrl/Bio.motifs.applications.rst. -Creating file /tmp/tmpqg6exyrl/Bio.motifs.jaspar.rst. -Creating file /tmp/tmpqg6exyrl/Bio.motifs.jaspar.db.rst. -Creating file /tmp/tmpqg6exyrl/Bio.phenotype.rst. -Creating file /tmp/tmpqg6exyrl/Bio.phenotype.phen_micro.rst. -Creating file /tmp/tmpqg6exyrl/Bio.phenotype.pm_fitting.rst. -File /tmp/tmpqg6exyrl/conf.py already exists, skipping. -File /tmp/tmpqg6exyrl/index.rst already exists, skipping. -File /tmp/tmpqg6exyrl/Makefile already exists, skipping. -File /tmp/tmpqg6exyrl/make.bat already exists, skipping. +Creating file /tmp/tmpxou5smmy/BioSQL.rst. +Creating file /tmp/tmpxou5smmy/BioSQL.BioSeq.rst. +Creating file /tmp/tmpxou5smmy/BioSQL.BioSeqDatabase.rst. +Creating file /tmp/tmpxou5smmy/BioSQL.DBUtils.rst. +Creating file /tmp/tmpxou5smmy/BioSQL.Loader.rst. +Creating file /tmp/tmpxou5smmy/conf.py. +Creating file /tmp/tmpxou5smmy/index.rst. +Creating file /tmp/tmpxou5smmy/Makefile. +Creating file /tmp/tmpxou5smmy/make.bat. +Creating file /tmp/tmpxou5smmy/Bio.rst. +Creating file /tmp/tmpxou5smmy/Bio.File.rst. +Creating file /tmp/tmpxou5smmy/Bio.LogisticRegression.rst. +Creating file /tmp/tmpxou5smmy/Bio.MarkovModel.rst. +Creating file /tmp/tmpxou5smmy/Bio.MaxEntropy.rst. +Creating file /tmp/tmpxou5smmy/Bio.NaiveBayes.rst. +Creating file /tmp/tmpxou5smmy/Bio.Seq.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqFeature.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqRecord.rst. +Creating file /tmp/tmpxou5smmy/Bio.bgzf.rst. +Creating file /tmp/tmpxou5smmy/Bio.kNN.rst. +Creating file /tmp/tmpxou5smmy/Bio.pairwise2.rst. +Creating file /tmp/tmpxou5smmy/Bio.Affy.rst. +Creating file /tmp/tmpxou5smmy/Bio.Affy.CelFile.rst. +Creating file /tmp/tmpxou5smmy/Bio.Align.rst. +Creating file 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/tmp/tmpxou5smmy/Bio.Entrez.Parser.rst. +Creating file /tmp/tmpxou5smmy/Bio.ExPASy.rst. +Creating file /tmp/tmpxou5smmy/Bio.ExPASy.Enzyme.rst. +Creating file /tmp/tmpxou5smmy/Bio.ExPASy.Prodoc.rst. +Creating file /tmp/tmpxou5smmy/Bio.ExPASy.Prosite.rst. +Creating file /tmp/tmpxou5smmy/Bio.ExPASy.ScanProsite.rst. +Creating file /tmp/tmpxou5smmy/Bio.ExPASy.cellosaurus.rst. +Creating file /tmp/tmpxou5smmy/Bio.GenBank.rst. +Creating file /tmp/tmpxou5smmy/Bio.GenBank.Record.rst. +Creating file /tmp/tmpxou5smmy/Bio.GenBank.Scanner.rst. +Creating file /tmp/tmpxou5smmy/Bio.GenBank.utils.rst. +Creating file /tmp/tmpxou5smmy/Bio.Geo.rst. +Creating file /tmp/tmpxou5smmy/Bio.Geo.Record.rst. +Creating file /tmp/tmpxou5smmy/Bio.Graphics.rst. +Creating file /tmp/tmpxou5smmy/Bio.Graphics.BasicChromosome.rst. +Creating file /tmp/tmpxou5smmy/Bio.Graphics.ColorSpiral.rst. +Creating file /tmp/tmpxou5smmy/Bio.Graphics.Comparative.rst. +Creating file /tmp/tmpxou5smmy/Bio.Graphics.DisplayRepresentation.rst. +Creating file /tmp/tmpxou5smmy/Bio.Graphics.Distribution.rst. +Creating file /tmp/tmpxou5smmy/Bio.Graphics.KGML_vis.rst. +Creating file /tmp/tmpxou5smmy/Bio.Graphics.GenomeDiagram.rst. +Creating file /tmp/tmpxou5smmy/Bio.HMM.rst. +Creating file /tmp/tmpxou5smmy/Bio.HMM.DynamicProgramming.rst. +Creating file /tmp/tmpxou5smmy/Bio.HMM.MarkovModel.rst. +Creating file /tmp/tmpxou5smmy/Bio.HMM.Trainer.rst. +Creating file /tmp/tmpxou5smmy/Bio.HMM.Utilities.rst. +Creating file /tmp/tmpxou5smmy/Bio.KEGG.rst. +Creating file /tmp/tmpxou5smmy/Bio.KEGG.REST.rst. +Creating file /tmp/tmpxou5smmy/Bio.KEGG.Compound.rst. +Creating file /tmp/tmpxou5smmy/Bio.KEGG.Enzyme.rst. +Creating file /tmp/tmpxou5smmy/Bio.KEGG.Gene.rst. +Creating file /tmp/tmpxou5smmy/Bio.KEGG.KGML.rst. +Creating file /tmp/tmpxou5smmy/Bio.KEGG.KGML.KGML_parser.rst. +Creating file /tmp/tmpxou5smmy/Bio.KEGG.KGML.KGML_pathway.rst. +Creating file /tmp/tmpxou5smmy/Bio.KEGG.Map.rst. +Creating file /tmp/tmpxou5smmy/Bio.Medline.rst. +Creating file /tmp/tmpxou5smmy/Bio.NMR.rst. +Creating file /tmp/tmpxou5smmy/Bio.NMR.NOEtools.rst. +Creating file /tmp/tmpxou5smmy/Bio.NMR.xpktools.rst. +Creating file /tmp/tmpxou5smmy/Bio.Nexus.rst. +Creating file /tmp/tmpxou5smmy/Bio.Nexus.Nexus.rst. +Creating file /tmp/tmpxou5smmy/Bio.Nexus.Nodes.rst. +Creating file /tmp/tmpxou5smmy/Bio.Nexus.StandardData.rst. +Creating file /tmp/tmpxou5smmy/Bio.Nexus.Trees.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.AbstractPropertyMap.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.Atom.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.Chain.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.DSSP.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.Dice.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.Entity.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.FragmentMapper.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.HSExposure.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.MMCIF2Dict.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.MMCIFParser.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.Model.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.NACCESS.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.NeighborSearch.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.PDBExceptions.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.PDBIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.PDBList.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.PDBMLParser.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.PDBParser.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.PICIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.PSEA.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.Polypeptide.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.Residue.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.ResidueDepth.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.SASA.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.SCADIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.Selection.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.Structure.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.StructureAlignment.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.StructureBuilder.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.Superimposer.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.alphafold_db.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.binary_cif.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.cealign.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.ic_data.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.ic_rebuild.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.internal_coords.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.mmcifio.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.parse_pdb_header.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.qcprot.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.vectors.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.mmtf.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.mmtf.DefaultParser.rst. +Creating file /tmp/tmpxou5smmy/Bio.PDB.mmtf.mmtfio.rst. +Creating file /tmp/tmpxou5smmy/Bio.Pathway.rst. +Creating file /tmp/tmpxou5smmy/Bio.Pathway.Rep.rst. +Creating file /tmp/tmpxou5smmy/Bio.Pathway.Rep.Graph.rst. +Creating file /tmp/tmpxou5smmy/Bio.Pathway.Rep.MultiGraph.rst. +Creating file /tmp/tmpxou5smmy/Bio.Phylo.rst. +Creating file /tmp/tmpxou5smmy/Bio.Phylo.BaseTree.rst. +Creating file /tmp/tmpxou5smmy/Bio.Phylo.CDAO.rst. +Creating file /tmp/tmpxou5smmy/Bio.Phylo.CDAOIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.Phylo.Consensus.rst. +Creating file /tmp/tmpxou5smmy/Bio.Phylo.NeXML.rst. +Creating file /tmp/tmpxou5smmy/Bio.Phylo.NeXMLIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.Phylo.Newick.rst. +Creating file /tmp/tmpxou5smmy/Bio.Phylo.NewickIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.Phylo.NexusIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.Phylo.PhyloXML.rst. +Creating file /tmp/tmpxou5smmy/Bio.Phylo.PhyloXMLIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.Phylo.TreeConstruction.rst. +Creating file /tmp/tmpxou5smmy/Bio.Phylo.Applications.rst. +Creating file /tmp/tmpxou5smmy/Bio.Phylo.PAML.rst. +Creating file /tmp/tmpxou5smmy/Bio.Phylo.PAML.baseml.rst. +Creating file /tmp/tmpxou5smmy/Bio.Phylo.PAML.chi2.rst. +Creating file /tmp/tmpxou5smmy/Bio.Phylo.PAML.codeml.rst. +Creating file /tmp/tmpxou5smmy/Bio.Phylo.PAML.yn00.rst. +Creating file /tmp/tmpxou5smmy/Bio.PopGen.rst. +Creating file /tmp/tmpxou5smmy/Bio.PopGen.GenePop.rst. +Creating file /tmp/tmpxou5smmy/Bio.PopGen.GenePop.Controller.rst. +Creating file /tmp/tmpxou5smmy/Bio.PopGen.GenePop.EasyController.rst. +Creating file /tmp/tmpxou5smmy/Bio.PopGen.GenePop.FileParser.rst. +Creating file /tmp/tmpxou5smmy/Bio.PopGen.GenePop.LargeFileParser.rst. +Creating file /tmp/tmpxou5smmy/Bio.Restriction.rst. +Creating file /tmp/tmpxou5smmy/Bio.Restriction.PrintFormat.rst. +Creating file /tmp/tmpxou5smmy/Bio.Restriction.Restriction_Dictionary.rst. +Creating file /tmp/tmpxou5smmy/Bio.SCOP.rst. +Creating file /tmp/tmpxou5smmy/Bio.SCOP.Cla.rst. +Creating file /tmp/tmpxou5smmy/Bio.SCOP.Des.rst. +Creating file /tmp/tmpxou5smmy/Bio.SCOP.Dom.rst. +Creating file /tmp/tmpxou5smmy/Bio.SCOP.Hie.rst. +Creating file /tmp/tmpxou5smmy/Bio.SCOP.Raf.rst. +Creating file /tmp/tmpxou5smmy/Bio.SCOP.Residues.rst. +Creating file /tmp/tmpxou5smmy/Bio.SVDSuperimposer.rst. +Creating file /tmp/tmpxou5smmy/Bio.SearchIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SearchIO.BlatIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SearchIO.FastaIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SearchIO.BlastIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SearchIO.BlastIO.blast_tab.rst. +Creating file /tmp/tmpxou5smmy/Bio.SearchIO.BlastIO.blast_xml.rst. +Creating file /tmp/tmpxou5smmy/Bio.SearchIO.ExonerateIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SearchIO.ExonerateIO.exonerate_cigar.rst. +Creating file /tmp/tmpxou5smmy/Bio.SearchIO.ExonerateIO.exonerate_text.rst. +Creating file /tmp/tmpxou5smmy/Bio.SearchIO.ExonerateIO.exonerate_vulgar.rst. +Creating file /tmp/tmpxou5smmy/Bio.SearchIO.HHsuiteIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SearchIO.HHsuiteIO.hhsuite2_text.rst. +Creating file /tmp/tmpxou5smmy/Bio.SearchIO.HmmerIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SearchIO.HmmerIO.hmmer2_text.rst. +Creating file /tmp/tmpxou5smmy/Bio.SearchIO.HmmerIO.hmmer3_domtab.rst. +Creating file /tmp/tmpxou5smmy/Bio.SearchIO.HmmerIO.hmmer3_tab.rst. +Creating file /tmp/tmpxou5smmy/Bio.SearchIO.HmmerIO.hmmer3_text.rst. +Creating file /tmp/tmpxou5smmy/Bio.SearchIO.InterproscanIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SearchIO.InterproscanIO.interproscan_xml.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.AbiIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.AceIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.FastaIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.GckIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.GfaIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.IgIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.InsdcIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.Interfaces.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.NibIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.PdbIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.PhdIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.PirIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.QualityIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.SeqXmlIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.SffIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.SnapGeneIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.SwissIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.TabIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.TwoBitIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.UniprotIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqIO.XdnaIO.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqUtils.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqUtils.CheckSum.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqUtils.IsoelectricPoint.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqUtils.MeltingTemp.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqUtils.ProtParam.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqUtils.ProtParamData.rst. +Creating file /tmp/tmpxou5smmy/Bio.SeqUtils.lcc.rst. +Creating file /tmp/tmpxou5smmy/Bio.Sequencing.rst. +Creating file /tmp/tmpxou5smmy/Bio.Sequencing.Ace.rst. +Creating file /tmp/tmpxou5smmy/Bio.Sequencing.Phd.rst. +Creating file /tmp/tmpxou5smmy/Bio.Sequencing.Applications.rst. +Creating file /tmp/tmpxou5smmy/Bio.SwissProt.rst. +Creating file /tmp/tmpxou5smmy/Bio.SwissProt.KeyWList.rst. +Creating file /tmp/tmpxou5smmy/Bio.TogoWS.rst. +Creating file /tmp/tmpxou5smmy/Bio.UniGene.rst. +Creating file /tmp/tmpxou5smmy/Bio.UniProt.rst. +Creating file /tmp/tmpxou5smmy/Bio.UniProt.GOA.rst. +Creating file /tmp/tmpxou5smmy/Bio.codonalign.rst. +Creating file /tmp/tmpxou5smmy/Bio.codonalign.codonalignment.rst. +Creating file /tmp/tmpxou5smmy/Bio.codonalign.codonseq.rst. +Creating file /tmp/tmpxou5smmy/Bio.motifs.rst. +Creating file /tmp/tmpxou5smmy/Bio.motifs.alignace.rst. +Creating file /tmp/tmpxou5smmy/Bio.motifs.clusterbuster.rst. +Creating file /tmp/tmpxou5smmy/Bio.motifs.mast.rst. +Creating file /tmp/tmpxou5smmy/Bio.motifs.matrix.rst. +Creating file /tmp/tmpxou5smmy/Bio.motifs.meme.rst. +Creating file /tmp/tmpxou5smmy/Bio.motifs.minimal.rst. +Creating file /tmp/tmpxou5smmy/Bio.motifs.pfm.rst. +Creating file /tmp/tmpxou5smmy/Bio.motifs.thresholds.rst. +Creating file /tmp/tmpxou5smmy/Bio.motifs.transfac.rst. +Creating file /tmp/tmpxou5smmy/Bio.motifs.xms.rst. +Creating file /tmp/tmpxou5smmy/Bio.motifs.applications.rst. +Creating file /tmp/tmpxou5smmy/Bio.motifs.jaspar.rst. +Creating file /tmp/tmpxou5smmy/Bio.motifs.jaspar.db.rst. +Creating file /tmp/tmpxou5smmy/Bio.phenotype.rst. +Creating file /tmp/tmpxou5smmy/Bio.phenotype.phen_micro.rst. +Creating file /tmp/tmpxou5smmy/Bio.phenotype.pm_fitting.rst. +File /tmp/tmpxou5smmy/conf.py already exists, skipping. +File /tmp/tmpxou5smmy/index.rst already exists, skipping. +File /tmp/tmpxou5smmy/Makefile already exists, skipping. +File /tmp/tmpxou5smmy/make.bat already exists, skipping. building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 29 source files that are out of date @@ -4047,7 +4083,7 @@ test_MarkovModel ... ok test_Medline ... ok test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. -test_NCBIXML ... Exception ignored in: +test_NCBIXML ... Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/python-biopython-1.85+dfsg/.pybuild/cpython3_3.13/build/Bio/Blast/NCBIXML.py", line 1319, in parse expat_parser.Parse(NULL, True) @@ -4535,12 +4571,12 @@ BioSQL.DBUtils docstring test ... ok BioSQL.Loader docstring test ... ok ---------------------------------------------------------------------- -Ran 551 tests in 680.522 seconds +Ran 551 tests in 1831.379 seconds Skipping any tests requiring internet access Python version: 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0] Operating system: posix linux - rm -fr -- /tmp/dh-xdg-rundir-QIJi9dlh + rm -fr -- /tmp/dh-xdg-rundir-BXWYcrrt # Cleanup steps after tests. set -e \ ; if [ -d Tests_avoid ] \ @@ -4724,8 +4760,8 @@ copying /build/reproducible-path/python-biopython-1.85+dfsg/.pybuild/cpython3_3.13/build/other_trees.xml -> /build/reproducible-path/python-biopython-1.85+dfsg/debian/tmp/usr/lib/python3.13/dist-packages copying /build/reproducible-path/python-biopython-1.85+dfsg/.pybuild/cpython3_3.13/build/tree1.nwk -> /build/reproducible-path/python-biopython-1.85+dfsg/debian/tmp/usr/lib/python3.13/dist-packages creating /build/reproducible-path/python-biopython-1.85+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/Tests -creating /build/reproducible-path/python-biopython-1.85+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/Tests/tmpdirprankmsasinN8A -creating /build/reproducible-path/python-biopython-1.85+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/Tests/tmpdirprankmsaTB9bqm +creating /build/reproducible-path/python-biopython-1.85+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/Tests/tmpdirprankmsaYoilpK +creating /build/reproducible-path/python-biopython-1.85+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/Tests/tmpdirprankmsaKS1whZ copying /build/reproducible-path/python-biopython-1.85+dfsg/.pybuild/cpython3_3.13/build/Tests/output.best.nex -> /build/reproducible-path/python-biopython-1.85+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/Tests copying /build/reproducible-path/python-biopython-1.85+dfsg/.pybuild/cpython3_3.13/build/Tests/output.best.fas -> /build/reproducible-path/python-biopython-1.85+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/Tests creating /build/reproducible-path/python-biopython-1.85+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/Tests/__pycache__ @@ -8584,15 +8620,15 @@ install -p -m0644 debian/TODO debian/python3-biopython/usr/share/doc/python3-biopython/TODO.Debian install -p -m0644 debian/copyright debian/python3-biopython/usr/share/doc/python3-biopython/copyright dh_installchangelogs -O--buildsystem=pybuild - install -m0755 -d debian/python-biopython-doc/usr/share/doc/python-biopython-doc - install -p -m0644 debian/.debhelper/generated/python-biopython-doc/dh_installchangelogs.dch.trimmed debian/python-biopython-doc/usr/share/doc/python-biopython-doc/changelog.Debian - install -p -m0644 debian/.debhelper/generated/python-biopython-doc/dh_installchangelogs.news.trimmed debian/python-biopython-doc/usr/share/doc/python-biopython-doc/NEWS.Debian install -m0755 -d debian/python3-biopython/usr/share/doc/python3-biopython install -p -m0644 debian/.debhelper/generated/python3-biopython/dh_installchangelogs.dch.trimmed debian/python3-biopython/usr/share/doc/python3-biopython/changelog.Debian install -p -m0644 debian/.debhelper/generated/python3-biopython/dh_installchangelogs.news.trimmed debian/python3-biopython/usr/share/doc/python3-biopython/NEWS.Debian install -m0755 -d debian/python3-biopython-sql/usr/share/doc/python3-biopython-sql install -p -m0644 debian/.debhelper/generated/python3-biopython-sql/dh_installchangelogs.dch.trimmed debian/python3-biopython-sql/usr/share/doc/python3-biopython-sql/changelog.Debian install -p -m0644 debian/.debhelper/generated/python3-biopython-sql/dh_installchangelogs.news.trimmed debian/python3-biopython-sql/usr/share/doc/python3-biopython-sql/NEWS.Debian + install -m0755 -d debian/python-biopython-doc/usr/share/doc/python-biopython-doc + install -p -m0644 debian/.debhelper/generated/python-biopython-doc/dh_installchangelogs.dch.trimmed debian/python-biopython-doc/usr/share/doc/python-biopython-doc/changelog.Debian + install -p -m0644 debian/.debhelper/generated/python-biopython-doc/dh_installchangelogs.news.trimmed debian/python-biopython-doc/usr/share/doc/python-biopython-doc/NEWS.Debian dh_installexamples -O--buildsystem=pybuild dh_installexamples: warning: Cannot auto-detect main package for python-biopython-doc. If the default is wrong, please use --doc-main-package install -m0755 -d debian/python-biopython-doc/usr/share/doc/python-biopython-doc/examples @@ -8635,7 +8671,7 @@ D: dh_python3 pydist:175: trying to find dependency for numpy (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed D: dh_python3 pydist:284: dependency: included in build-deps -D: dh_python3 depends:253: D={'python3-numpy', 'python3 (>= 3.13~)', 'python3 (<< 3.14)', 'python3:any'}; R=[]; S=[]; E=[], B=[]; RT=[] +D: dh_python3 depends:253: D={'python3 (<< 3.14)', 'python3:any', 'python3 (>= 3.13~)', 'python3-numpy'}; R=[]; S=[]; E=[], B=[]; RT=[] D: dh_python3 dh_python3:205: processing package python3-biopython-sql... D: dh_python3 fs:50: moving files from debian/python3-biopython-sql/usr/lib/python3.13/dist-packages to debian/python3-biopython-sql/usr/lib/python3/dist-packages/ D: dh_python3 fs:338: package python3-biopython-sql details = {'requires.txt': set(), 'egg-info': set(), 'dist-info': set(), 'nsp.txt': set(), 'shebangs': set(), 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': set(), 'ext_no_version': set()} @@ -8662,56 +8698,56 @@ ln -s ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_static/searchtools.js dh_strip_nondeterminism -O--buildsystem=pybuild Using 1738853069 as canonical time + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/GD_sigils.png using File::StripNondeterminism::handlers::png + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/GD_sigil_labels.png using File::StripNondeterminism::handlers::png + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/GD_sigil_arrow_shafts.png using File::StripNondeterminism::handlers::png + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/GD_sigil_arrow_heads.png using File::StripNondeterminism::handlers::png + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/three_track_cl2a.png using File::StripNondeterminism::handlers::png + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/three_track_cl.png using File::StripNondeterminism::handlers::png + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/tRNA_chrom.png using File::StripNondeterminism::handlers::png + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/smcra.png using File::StripNondeterminism::handlers::png + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/plasmid_circular.png using File::StripNondeterminism::handlers::png + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/phylo-simple-draw.png using File::StripNondeterminism::handlers::png + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/phylo-draw-example.png using File::StripNondeterminism::handlers::png + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/phylo-color-draw.png using File::StripNondeterminism::handlers::png Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/simple_chrom.png using File::StripNondeterminism::handlers::png Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/plasmid_linear_nice.png using File::StripNondeterminism::handlers::png Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/plasmid_linear.png using File::StripNondeterminism::handlers::png Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/plasmid_circular_nice.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/phe-pairs-3pbl.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/hist_plot.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/gc_plot.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/dot_plot_scatter.png using File::StripNondeterminism::handlers::png + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_static/plus.png using File::StripNondeterminism::handlers::png + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_static/minus.png using File::StripNondeterminism::handlers::png + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_static/file.png using File::StripNondeterminism::handlers::png + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/three_track_simple.png using File::StripNondeterminism::handlers::png Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/dot_plot.png using File::StripNondeterminism::handlers::png Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/biopython_logo_m.png using File::StripNondeterminism::handlers::png Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/SRR001666.png using File::StripNondeterminism::handlers::png Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/PSIBlastRecord.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/plasmid_circular.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/phylo-simple-draw.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/phylo-draw-example.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/phylo-color-draw.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/GD_sigils.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/GD_sigil_labels.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/GD_sigil_arrow_shafts.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/GD_sigil_arrow_heads.png using File::StripNondeterminism::handlers::png + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Tests/PDB/1gbt.bcif.gz using File::StripNondeterminism::handlers::gzip + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Tests/KEGG/map03070.png using File::StripNondeterminism::handlers::png + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Tests/KEGG/map01100.png using File::StripNondeterminism::handlers::png + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Tests/Fasta/flowers.pro.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/examples/ls_orchid.gbk.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Tests/Roche/E3MFGYR02_random_10_reads.sff.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Tests/PDB/6wg6.bcif.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Tests/PDB/3jqh.bcif.gz using File::StripNondeterminism::handlers::gzip - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_static/plus.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_static/minus.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_static/file.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/three_track_simple.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/three_track_cl2a.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/three_track_cl.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/tRNA_chrom.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/smcra.png using File::StripNondeterminism::handlers::png Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/BlastRecord.png using File::StripNondeterminism::handlers::png Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/1a8o-ca-plot.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Tests/PDB/1gbt.bcif.gz using File::StripNondeterminism::handlers::gzip - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Tests/KEGG/map03070.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Tests/KEGG/map01100.png using File::StripNondeterminism::handlers::png - Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Tests/Fasta/flowers.pro.gz using File::StripNondeterminism::handlers::gzip + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/phe-pairs-3pbl.png using File::StripNondeterminism::handlers::png + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/hist_plot.png using File::StripNondeterminism::handlers::png + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/gc_plot.png using File::StripNondeterminism::handlers::png + Normalizing debian/python-biopython-doc/usr/share/doc/python-biopython-doc/html/_images/dot_plot_scatter.png using File::StripNondeterminism::handlers::png dh_compress -O--buildsystem=pybuild - cd debian/python3-biopython-sql cd debian/python3-biopython + cd debian/python3-biopython-sql cd debian/python-biopython-doc + chmod a-x usr/share/doc/python3-biopython/CONTRIB.rst usr/share/doc/python3-biopython/DEPRECATED.rst usr/share/doc/python3-biopython/NEWS.Debian usr/share/doc/python3-biopython/NEWS.rst usr/share/doc/python3-biopython/changelog.Debian chmod a-x usr/share/doc/python3-biopython-sql/NEWS.Debian usr/share/doc/python3-biopython-sql/changelog.Debian gzip -9nf usr/share/doc/python3-biopython-sql/NEWS.Debian usr/share/doc/python3-biopython-sql/changelog.Debian - chmod a-x usr/share/doc/python3-biopython/CONTRIB.rst usr/share/doc/python3-biopython/DEPRECATED.rst usr/share/doc/python3-biopython/NEWS.Debian usr/share/doc/python3-biopython/NEWS.rst usr/share/doc/python3-biopython/changelog.Debian gzip -9nf usr/share/doc/python3-biopython/CONTRIB.rst usr/share/doc/python3-biopython/DEPRECATED.rst usr/share/doc/python3-biopython/NEWS.Debian usr/share/doc/python3-biopython/NEWS.rst usr/share/doc/python3-biopython/changelog.Debian - cd '/build/reproducible-path/python-biopython-1.85+dfsg' - cd '/build/reproducible-path/python-biopython-1.85+dfsg' - chmod a-x usr/share/doc/python-biopython-doc/NEWS.Debian usr/share/doc/python-biopython-doc/Tests/Abi/310.ab1 usr/share/doc/python-biopython-doc/Tests/Abi/3100.ab1 usr/share/doc/python-biopython-doc/Tests/Abi/3730.ab1 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usr/share/doc/python-biopython-doc/Tests/SwissProt/UniRef90_P99999.xml usr/share/doc/python-biopython-doc/Tests/SwissProt/multi_ex.gff usr/share/doc/python-biopython-doc/Tests/SwissProt/multi_ex.rdf usr/share/doc/python-biopython-doc/Tests/SwissProt/multi_ex.txt usr/share/doc/python-biopython-doc/Tests/SwissProt/multi_ex.xml usr/share/doc/python-biopython-doc/Tests/SwissProt/sp016 usr/share/doc/python-biopython-doc/Tests/SwissProt/uni001 usr/share/doc/python-biopython-doc/Tests/SwissProt/uni002 usr/share/doc/python-biopython-doc/Tests/SwissProt/uni003 usr/share/doc/python-biopython-doc/Tests/UniGene/Eca.1.2425.data usr/share/doc/python-biopython-doc/Tests/UniGene/Hs.2.data usr/share/doc/python-biopython-doc/Tests/UniProt/gene_association.goa_yeast.1.gaf usr/share/doc/python-biopython-doc/Tests/UniProt/goa_yeast.gaf usr/share/doc/python-biopython-doc/Tests/UniProt/goa_yeast.gpa.59.gpa usr/share/doc/python-biopython-doc/Tests/UniProt/gp_information.goa_yeast.28.gpi usr/share/doc/python-biopython-doc/Tests/codonalign/adh.aln usr/share/doc/python-biopython-doc/Tests/codonalign/drosophila.fasta usr/share/doc/python-biopython-doc/Tests/codonalign/egfr_nucl.fa usr/share/doc/python-biopython-doc/Tests/codonalign/egfr_pro.aln usr/share/doc/python-biopython-doc/Tests/codonalign/nucl2.fa usr/share/doc/python-biopython-doc/Tests/codonalign/nucl3.fa usr/share/doc/python-biopython-doc/Tests/codonalign/nucl4.fa usr/share/doc/python-biopython-doc/Tests/codonalign/pro2.aln usr/share/doc/python-biopython-doc/Tests/codonalign/pro3.aln usr/share/doc/python-biopython-doc/Tests/codonalign/pro4.aln usr/share/doc/python-biopython-doc/Tests/common_BioSQL.py usr/share/doc/python-biopython-doc/Tests/common_BioSQL_online.py usr/share/doc/python-biopython-doc/Tests/motifs/abdb.xms usr/share/doc/python-biopython-doc/Tests/motifs/alignace.out usr/share/doc/python-biopython-doc/Tests/motifs/mast.Klf1-200.cd.oops.xml.txt usr/share/doc/python-biopython-doc/Tests/motifs/mast.Klf1-200.cd.oops.xml.xml usr/share/doc/python-biopython-doc/Tests/motifs/mast.crp0.de.oops.txt.txt usr/share/doc/python-biopython-doc/Tests/motifs/mast.crp0.de.oops.txt.xml usr/share/doc/python-biopython-doc/Tests/motifs/meme.INO_up800.classic.oops.xml usr/share/doc/python-biopython-doc/Tests/motifs/meme.adh.classic.oops.xml usr/share/doc/python-biopython-doc/Tests/motifs/meme.farntrans5.classic.anr.xml usr/share/doc/python-biopython-doc/Tests/motifs/meme.out usr/share/doc/python-biopython-doc/Tests/motifs/meme.psp_test.classic.zoops.xml usr/share/doc/python-biopython-doc/Tests/msf/DOA_prot.msf usr/share/doc/python-biopython-doc/Tests/pairwise2_testCases.py usr/share/doc/python-biopython-doc/Tests/phenotype/BadPlate.json usr/share/doc/python-biopython-doc/Tests/phenotype/Plate.json usr/share/doc/python-biopython-doc/Tests/phenotype/Plate_2.json usr/share/doc/python-biopython-doc/Tests/phenotype/Plates.csv usr/share/doc/python-biopython-doc/Tests/phenotype/SmallPlate.json usr/share/doc/python-biopython-doc/Tests/phenotype/SmallPlate_2.json usr/share/doc/python-biopython-doc/Tests/phenotype/SmallPlates.csv usr/share/doc/python-biopython-doc/Tests/run_tests.py usr/share/doc/python-biopython-doc/Tests/search_tests_common.py usr/share/doc/python-biopython-doc/Tests/seq_tests_common.py usr/share/doc/python-biopython-doc/Tests/test_Ace.py usr/share/doc/python-biopython-doc/Tests/test_Affy.py usr/share/doc/python-biopython-doc/Tests/test_AlignIO.py usr/share/doc/python-biopython-doc/Tests/test_AlignIO_ClustalIO.py usr/share/doc/python-biopython-doc/Tests/test_AlignIO_FastaIO.py usr/share/doc/python-biopython-doc/Tests/test_AlignIO_MauveIO.py usr/share/doc/python-biopython-doc/Tests/test_AlignIO_PhylipIO.py usr/share/doc/python-biopython-doc/Tests/test_AlignInfo.py usr/share/doc/python-biopython-doc/Tests/test_Align_Alignment.py usr/share/doc/python-biopython-doc/Tests/test_Align_a2m.py usr/share/doc/python-biopython-doc/Tests/test_Align_bed.py usr/share/doc/python-biopython-doc/Tests/test_Align_bigbed.py usr/share/doc/python-biopython-doc/Tests/test_Align_bigmaf.py usr/share/doc/python-biopython-doc/Tests/test_Align_bigpsl.py usr/share/doc/python-biopython-doc/Tests/test_Align_chain.py usr/share/doc/python-biopython-doc/Tests/test_Align_clustal.py usr/share/doc/python-biopython-doc/Tests/test_Align_codonalign.py usr/share/doc/python-biopython-doc/Tests/test_Align_emboss.py usr/share/doc/python-biopython-doc/Tests/test_Align_exonerate.py usr/share/doc/python-biopython-doc/Tests/test_Align_fasta.py usr/share/doc/python-biopython-doc/Tests/test_Align_hhr.py usr/share/doc/python-biopython-doc/Tests/test_Align_maf.py usr/share/doc/python-biopython-doc/Tests/test_Align_mauve.py usr/share/doc/python-biopython-doc/Tests/test_Align_msf.py usr/share/doc/python-biopython-doc/Tests/test_Align_nexus.py usr/share/doc/python-biopython-doc/Tests/test_Align_phylip.py usr/share/doc/python-biopython-doc/Tests/test_Align_psl.py usr/share/doc/python-biopython-doc/Tests/test_Align_sam.py usr/share/doc/python-biopython-doc/Tests/test_Align_stockholm.py usr/share/doc/python-biopython-doc/Tests/test_Align_tabular.py usr/share/doc/python-biopython-doc/Tests/test_Application.py usr/share/doc/python-biopython-doc/Tests/test_BWA_tool.py @@ -8721,19 +8757,19 @@ debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/python-biopython-1.85+dfsg' dh_fixperms - find debian/python3-biopython-sql ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s - find debian/python-biopython-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python3-biopython ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s - find debian/python3-biopython-sql/usr/share/doc -type f -a -true -a ! -regex 'debian/python3-biopython-sql/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/python-biopython-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s + find debian/python3-biopython-sql ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python3-biopython/usr/share/doc -type f -a -true -a ! -regex 'debian/python3-biopython/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/python3-biopython-sql/usr/share/doc -type f -a -true -a ! -regex 'debian/python3-biopython-sql/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python-biopython-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/python-biopython-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-biopython/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/python3-biopython-sql/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/python3-biopython/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-biopython-sql -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python-biopython-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 - find debian/python3-biopython-sql/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/python3-biopython -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/python3-biopython-sql/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/python-biopython-doc/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-biopython/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/python-biopython-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 @@ -8840,41 +8876,41 @@ echo misc:Pre-Depends= >> debian/python3-biopython.substvars install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/DEBIAN dpkg-gencontrol -ppython3-biopython -ldebian/changelog -Tdebian/python3-biopython.substvars -cdebian/control -Pdebian/.debhelper/python3-biopython/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=python3-biopython-dbgsym "-DDepends=python3-biopython (= \${binary:Version})" "-DDescription=debug symbols for python3-biopython" "-DBuild-Ids=0f66c1ca2d2b6688c0906de123e7d733288ca568 13cf649d74e3104884bf97b4401236ae13d2b5ed 304402cc566f0fb89c2d9ab4ce4df86b8c7955e2 3469de8fc3f2121f74d0d4ecc027819133f6dfe1 38776cb4591aeac15d76fb364acdd8f328c51950 6f055a23fa7564abe889870e79cbcf963ff7c9ee aa4f0d3ef274507a19b1cb65b6a9b85f4e687697 b564ffec5e4e44716f551e904a93ffc5f7932247 cdd57a10bd1c31c7cfb33411aebb4a82ccbe1d57 d51e8d8906ea9835b5d39cccefef5a22b7b9d4df dca395788b35600d6b4f19f3b27eb6382ea2ef19" -DSection=debug -UMulti-Arch -UReplaces -UBreaks - install -m0755 -d debian/python-biopython-doc/DEBIAN - echo misc:Depends= >> debian/python-biopython-doc.substvars - echo misc:Pre-Depends= >> debian/python-biopython-doc.substvars - dpkg-gencontrol -ppython-biopython-doc -ldebian/changelog -Tdebian/python-biopython-doc.substvars -cdebian/control -Pdebian/python-biopython-doc install -m0755 -d debian/python3-biopython-sql/DEBIAN echo misc:Depends= >> debian/python3-biopython-sql.substvars echo misc:Pre-Depends= >> debian/python3-biopython-sql.substvars dpkg-gencontrol -ppython3-biopython-sql -ldebian/changelog -Tdebian/python3-biopython-sql.substvars -cdebian/control -Pdebian/python3-biopython-sql + install -m0755 -d debian/python-biopython-doc/DEBIAN + echo misc:Depends= >> debian/python-biopython-doc.substvars + echo misc:Pre-Depends= >> debian/python-biopython-doc.substvars + dpkg-gencontrol -ppython-biopython-doc -ldebian/changelog -Tdebian/python-biopython-doc.substvars -cdebian/control -Pdebian/python-biopython-doc +dpkg-gencontrol: warning: Provides field of package python3-biopython-sql: substitution variable ${python3:Provides} used, but is not defined + chmod 0644 -- debian/python3-biopython-sql/DEBIAN/control chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/DEBIAN/control dpkg-gencontrol -ppython3-biopython -ldebian/changelog -Tdebian/python3-biopython.substvars -cdebian/control -Pdebian/python3-biopython chmod 0644 -- debian/python-biopython-doc/DEBIAN/control -dpkg-gencontrol: warning: Provides field of package python3-biopython-sql: substitution variable ${python3:Provides} used, but is not defined - chmod 0644 -- debian/python3-biopython-sql/DEBIAN/control chmod 0644 -- debian/python3-biopython/DEBIAN/control dh_md5sums -O--buildsystem=pybuild - install -m0755 -d debian/python-biopython-doc/DEBIAN install -m0755 -d debian/python3-biopython/DEBIAN - cd debian/python-biopython-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums install -m0755 -d debian/python3-biopython-sql/DEBIAN cd debian/python3-biopython >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + install -m0755 -d debian/python-biopython-doc/DEBIAN cd debian/python3-biopython-sql >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + cd debian/python-biopython-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/python3-biopython-sql/DEBIAN/md5sums - chmod 0644 -- debian/python-biopython-doc/DEBIAN/md5sums chmod 0644 -- debian/python3-biopython/DEBIAN/md5sums install -m0755 -d debian/.debhelper/python3-biopython/dbgsym-root/DEBIAN cd debian/.debhelper/python3-biopython/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/python3-biopython/dbgsym-root/DEBIAN/md5sums + chmod 0644 -- debian/python-biopython-doc/DEBIAN/md5sums dh_builddeb -O--buildsystem=pybuild - dpkg-deb --root-owner-group --build debian/python3-biopython .. - dpkg-deb --root-owner-group --build debian/python-biopython-doc .. dpkg-deb --root-owner-group --build debian/.debhelper/python3-biopython/dbgsym-root .. + dpkg-deb --root-owner-group --build debian/python3-biopython .. dpkg-deb --root-owner-group --build debian/python3-biopython-sql .. -dpkg-deb: building package 'python-biopython-doc' in '../python-biopython-doc_1.85+dfsg-2_all.deb'. -dpkg-deb: building package 'python3-biopython-sql' in '../python3-biopython-sql_1.85+dfsg-2_all.deb'. + dpkg-deb --root-owner-group --build debian/python-biopython-doc .. dpkg-deb: building package 'python3-biopython-dbgsym' in '../python3-biopython-dbgsym_1.85+dfsg-2_arm64.deb'. +dpkg-deb: building package 'python3-biopython-sql' in '../python3-biopython-sql_1.85+dfsg-2_all.deb'. +dpkg-deb: building package 'python-biopython-doc' in '../python-biopython-doc_1.85+dfsg-2_all.deb'. dpkg-deb: building package 'python3-biopython' in '../python3-biopython_1.85+dfsg-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../python-biopython_1.85+dfsg-2_arm64.buildinfo dpkg-genchanges --build=binary -O../python-biopython_1.85+dfsg-2_arm64.changes @@ -8883,12 +8919,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3810273/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3810273/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/3075221 and its subdirectories -I: Current time: Wed Apr 1 14:36:02 -12 2026 -I: pbuilder-time-stamp: 1775097362 +I: removing directory /srv/workspace/pbuilder/3810273 and its subdirectories +I: Current time: Fri Feb 28 11:11:28 +14 2025 +I: pbuilder-time-stamp: 1740690688