Diff of the two buildlogs: -- --- b1/build.log 2024-06-16 09:35:20.098317725 +0000 +++ b2/build.log 2024-06-16 09:37:19.013258347 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jul 19 03:57:04 -12 2025 -I: pbuilder-time-stamp: 1752940624 +I: Current time: Sun Jul 20 05:58:22 +14 2025 +I: pbuilder-time-stamp: 1752940702 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying new-bioperl-require.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2879416/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1666928/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-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 Jul 19 15:58 /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/1666928/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1666928/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]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.21(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='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='91ca338e675142638f5ebb51fd2f2e91' - 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='2879416' - PS1='# ' - PS2='> ' + INVOCATION_ID=4cce98749e724bcfa0548d5a9defd42f + 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=1666928 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.FxSYKciw/pbuilderrc_8gIL --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.FxSYKciw/b1 --logfile b1/build.log roary_3.13.0+dfsg-1.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.FxSYKciw/pbuilderrc_q2sH --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.FxSYKciw/b2 --logfile b2/build.log roary_3.13.0+dfsg-1.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 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 5 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2879416/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/1666928/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -487,7 +519,7 @@ Get: 314 http://deb.debian.org/debian unstable/main arm64 unzip arm64 6.0-28 [157 kB] Get: 315 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 316 http://deb.debian.org/debian unstable/main arm64 r-base-core arm64 4.4.1-1 [28.0 MB] -Fetched 109 MB in 1s (127 MB/s) +Fetched 109 MB in 1s (109 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (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 ... 19700 files and directories currently installed.) @@ -1533,8 +1565,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Jul 19 15:57:40 UTC 2025. -Universal Time is now: Sat Jul 19 15:57:40 UTC 2025. +Local time is now: Sat Jul 19 15:59:29 UTC 2025. +Universal Time is now: Sat Jul 19 15:59:29 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libjson-maybexs-perl (1.004005-1) ... @@ -1809,7 +1841,11 @@ fakeroot is already the newest version (1.35-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/roary-3.13.0+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 > ../roary_3.13.0+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/1666928/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1666928/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/roary-3.13.0+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 > ../roary_3.13.0+dfsg-1_source.changes dpkg-buildpackage: info: source package roary dpkg-buildpackage: info: source version 3.13.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -1843,112 +1879,112 @@ dh_auto_build -D .build/debian-build cd .build/debian-build && make -j12 make[1]: Entering directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' -cp lib/Bio/Roary/CommandLine/IterativeCdhit.pm blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pm -cp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm -cp lib/Bio/Roary/External/CheckTools.pm blib/lib/Bio/Roary/External/CheckTools.pm -cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm -cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.pm -cp lib/Bio/Roary/AnnotateGroups.pm blib/lib/Bio/Roary/AnnotateGroups.pm -cp lib/Bio/Roary/CommandLine/Common.pm blib/lib/Bio/Roary/CommandLine/Common.pm -cp lib/Bio/Roary/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.pm -cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm -cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm -cp lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm blib/lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm +cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.pm +cp lib/Bio/Roary/CommandLine/IterativeCdhit.pm blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pm cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm -cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.pm -cp lib/Bio/Roary/AccessoryClustering.pm blib/lib/Bio/Roary/AccessoryClustering.pm -cp lib/Bio/Roary/AssemblyStatistics.pm blib/lib/Bio/Roary/AssemblyStatistics.pm cp lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm blib/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm -cp lib/Bio/Roary/AccessoryBinaryFasta.pm blib/lib/Bio/Roary/AccessoryBinaryFasta.pm -cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.pm -cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm +cp lib/Bio/Roary/External/CheckTools.pm blib/lib/Bio/Roary/External/CheckTools.pm cp lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm blib/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm +cp lib/Bio/Roary/AssemblyStatistics.pm blib/lib/Bio/Roary/AssemblyStatistics.pm +cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.pm +cp lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm +cp lib/Bio/Roary/AccessoryBinaryFasta.pm blib/lib/Bio/Roary/AccessoryBinaryFasta.pm +cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm cp lib/Bio/Roary/CommandLine/AssemblyStatistics.pm blib/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm -cp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm +cp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm +cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm +cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.pm +cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm cp lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm blib/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm +cp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm +cp lib/Bio/Roary/AnnotateGroups.pm blib/lib/Bio/Roary/AnnotateGroups.pm cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm +cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm +cp lib/Bio/Roary/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.pm cp lib/Bio/Roary/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm -cp lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm -cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm -cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.pm -cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.pm -cp lib/Bio/Roary/External/IterativeCdhit.pm blib/lib/Bio/Roary/External/IterativeCdhit.pm -cp lib/Bio/Roary/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm +cp lib/Bio/Roary/CommandLine/Common.pm blib/lib/Bio/Roary/CommandLine/Common.pm +cp lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm blib/lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm +cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm +cp lib/Bio/Roary/AccessoryClustering.pm blib/lib/Bio/Roary/AccessoryClustering.pm cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.pm -cp lib/Bio/Roary/Output/EMBLHeaderCommon.pm blib/lib/Bio/Roary/Output/EMBLHeaderCommon.pm -cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm -cp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm -cp lib/Bio/Roary/MergeMultifastaAlignments.pm blib/lib/Bio/Roary/MergeMultifastaAlignments.pm -cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm -cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm -cp lib/Bio/Roary/External/Fasttree.pm blib/lib/Bio/Roary/External/Fasttree.pm -cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm cp lib/Bio/Roary/JobRunner/Parallel.pm blib/lib/Bio/Roary/JobRunner/Parallel.pm -cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm -cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm cp lib/Bio/Roary/Output/EmblGroups.pm blib/lib/Bio/Roary/Output/EmblGroups.pm -cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm -cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm -cp lib/Bio/Roary/GeneNamesFromGFF.pm blib/lib/Bio/Roary/GeneNamesFromGFF.pm -cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.pm cp lib/Bio/Roary/Output/GroupMultifasta.pm blib/lib/Bio/Roary/Output/GroupMultifasta.pm -cp lib/Bio/Roary/ExtractProteomeFromGFFs.pm blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pm -cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm cp lib/Bio/Roary/External/Mcl.pm blib/lib/Bio/Roary/External/Mcl.pm -cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm -cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm -cp lib/Bio/Roary/External/Mafft.pm blib/lib/Bio/Roary/External/Mafft.pm +cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm +cp lib/Bio/Roary/ExtractProteomeFromGFFs.pm blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pm +cp lib/Bio/Roary/External/Fasttree.pm blib/lib/Bio/Roary/External/Fasttree.pm +cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.pm +cp lib/Bio/Roary/Output/EMBLHeaderCommon.pm blib/lib/Bio/Roary/Output/EMBLHeaderCommon.pm cp lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm +cp lib/Bio/Roary/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm +cp lib/Bio/Roary/GeneNamesFromGFF.pm blib/lib/Bio/Roary/GeneNamesFromGFF.pm cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm +cp lib/Bio/Roary/External/Mafft.pm blib/lib/Bio/Roary/External/Mafft.pm +cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm +cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm +cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.pm +cp lib/Bio/Roary/MergeMultifastaAlignments.pm blib/lib/Bio/Roary/MergeMultifastaAlignments.pm +cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm +cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm +cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm +cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.pm +cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm +cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm +cp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm +cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm +cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm +cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm +cp lib/Bio/Roary/External/IterativeCdhit.pm blib/lib/Bio/Roary/External/IterativeCdhit.pm +cp lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm +cp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm +cp lib/Bio/Roary/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm +cp lib/Bio/Roary/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm +cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm cp lib/Bio/Roary/UniqueGenesPerSample.pm blib/lib/Bio/Roary/UniqueGenesPerSample.pm +cp lib/Bio/Roary/PresenceAbsenceMatrix.pm blib/lib/Bio/Roary/PresenceAbsenceMatrix.pm cp lib/Bio/Roary/SplitGroups.pm blib/lib/Bio/Roary/SplitGroups.pm -cp lib/Bio/Roary/SampleOrder.pm blib/lib/Bio/Roary/SampleOrder.pm -cp lib/Bio/Roary/SequenceLengths.pm blib/lib/Bio/Roary/SequenceLengths.pm cp lib/Bio/Roary/Output/QueryGroups.pm blib/lib/Bio/Roary/Output/QueryGroups.pm -cp lib/Bio/Roary/SpreadsheetRole.pm blib/lib/Bio/Roary/SpreadsheetRole.pm -cp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm -cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm -cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm -cp lib/Bio/Roary/PresenceAbsenceMatrix.pm blib/lib/Bio/Roary/PresenceAbsenceMatrix.pm -cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm -cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm cp lib/Bio/Roary/QC/Report.pm blib/lib/Bio/Roary/QC/Report.pm -cp lib/Bio/Roary/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm +cp lib/Bio/Roary/SampleOrder.pm blib/lib/Bio/Roary/SampleOrder.pm cp lib/Bio/Roary/ReorderSpreadsheet.pm blib/lib/Bio/Roary/ReorderSpreadsheet.pm -cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm -cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm -cp lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm -cp lib/Bio/Roary/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm +cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm +cp lib/Bio/Roary/SpreadsheetRole.pm blib/lib/Bio/Roary/SpreadsheetRole.pm +cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm +cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm +cp lib/Bio/Roary/SequenceLengths.pm blib/lib/Bio/Roary/SequenceLengths.pm +cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm +cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm cp bin/create_pan_genome blib/script/create_pan_genome cp bin/create_pan_genome_plots blib/script/create_pan_genome_plots cp bin/extract_proteome_from_gff blib/script/extract_proteome_from_gff -cp bin/iterative_cdhit blib/script/iterative_cdhit -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome_plots +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome +cp bin/iterative_cdhit blib/script/iterative_cdhit "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/extract_proteome_from_gff -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/iterative_cdhit cp bin/pan_genome_assembly_statistics blib/script/pan_genome_assembly_statistics +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/iterative_cdhit "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_assembly_statistics cp bin/pan_genome_core_alignment blib/script/pan_genome_core_alignment cp bin/pan_genome_post_analysis blib/script/pan_genome_post_analysis +cp bin/pan_genome_reorder_spreadsheet blib/script/pan_genome_reorder_spreadsheet +cp bin/parallel_all_against_all_blastp blib/script/parallel_all_against_all_blastp "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_core_alignment "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_post_analysis -cp bin/pan_genome_reorder_spreadsheet blib/script/pan_genome_reorder_spreadsheet "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_reorder_spreadsheet -cp bin/parallel_all_against_all_blastp blib/script/parallel_all_against_all_blastp "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/parallel_all_against_all_blastp cp bin/protein_alignment_from_nucleotides blib/script/protein_alignment_from_nucleotides -cp bin/query_pan_genome blib/script/query_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/protein_alignment_from_nucleotides +cp bin/query_pan_genome blib/script/query_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/query_pan_genome cp bin/roary blib/script/roary "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary cp bin/roary-create_pan_genome_plots.R blib/script/roary-create_pan_genome_plots.R -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-create_pan_genome_plots.R cp bin/roary-pan_genome_reorder_spreadsheet blib/script/roary-pan_genome_reorder_spreadsheet +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-create_pan_genome_plots.R "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-pan_genome_reorder_spreadsheet cp bin/roary-query_pan_genome blib/script/roary-query_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary-query_pan_genome @@ -1979,84 +2015,84 @@ Manifying 28 pod documents Manifying 25 pod documents Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParallelAllAgainstAllBlast.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SortFasta.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReorderSpreadsheet.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParseGFFAnnotationRole.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PresenceAbsenceMatrix.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReformatInputGFFs.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PrepareInputFiles.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PostAnalysis.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SpreadsheetRole.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SequenceLengths.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SortFasta.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SpreadsheetRole.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PrepareInputFiles.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ParallelAllAgainstAllBlast.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ReorderSpreadsheet.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SampleOrder.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/SplitGroups.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PresenceAbsenceMatrix.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/UniqueGenesPerSample.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/IterativeCdhit.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFFs.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterUnknownsFromFasta.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GeneNamesFromGFF.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/InflateClusters.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/OrderGenes.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterFullClusters.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/PostAnalysis.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupStatistics.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/MergeMultifastaAlignments.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterFullClusters.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/LookupGeneFiles.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/IterativeCdhit.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/OrderGenes.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GroupLabels.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/MergeMultifastaAlignments.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/FilterUnknownsFromFasta.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/InflateClusters.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/GeneNamesFromGFF.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFF.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ExtractProteomeFromGFFs.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryClustering.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/BedFromGFFRole.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ClustersRole.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CombinedProteome.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ChunkFastaFile.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnnotateGroups.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnalyseGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryBinaryFasta.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AssemblyStatistics.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AccessoryClustering.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/ContigsToGeneIDsFromGFF.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CombinedProteome.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnnotateGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Exceptions.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/AnalyseGroups.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/QC/Report.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Parallel.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Local.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Role.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/NumberOfGroups.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastasNucleotide.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaNucleotide.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaProtein.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastas.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/QueryGroups.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/BlastIdentityFrequency.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastas.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/NumberOfGroups.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastaProtein.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupsMultifastasNucleotide.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/DifferenceBetweenSets.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/BlastIdentityFrequency.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EMBLHeaderCommon.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/GroupMultifasta.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EmblGroups.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/EMBLHeaderCommon.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/Output/DifferenceBetweenSets.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/GeneAlignmentFromNucleotides.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mafft.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Local.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Parallel.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/JobRunner/Role.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/IterativeCdhit.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/PostAnalysis.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mcl.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Fasttree.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Prank.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mafft.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Makeblastdb.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/IterativeCdhit.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/GeneAlignmentFromNucleotides.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Fasttree.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Mcl.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Blastp.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/Cdhit.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/External/CheckTools.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/QueryRoary.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/CreatePanGenome.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/UniqueGenesPerSample.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Common.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryCoreAlignment.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryPostAnalysis.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/QueryRoary.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/AssemblyStatistics.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Roary.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/UniqueGenesPerSample.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/RoaryPostAnalysis.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/CreatePanGenome.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Common.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/IterativeCdhit.pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/perl5/Bio/Roary/CommandLine/Roary.pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/transfer_annotation_to_groups.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-unique_genes_per_sample.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-query_pan_genome.1p @@ -2153,20 +2189,20 @@ Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AccessoryBinaryFasta.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/transfer_annotation_to_groups -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-unique_genes_per_sample Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-create_pan_genome_plots.R +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-unique_genes_per_sample Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-query_pan_genome Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary-pan_genome_reorder_spreadsheet -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/roary Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/query_pan_genome Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/protein_alignment_from_nucleotides -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_reorder_spreadsheet Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/parallel_all_against_all_blastp +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_reorder_spreadsheet Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_post_analysis -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/create_pan_genome -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_assembly_statistics Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/extract_proteome_from_gff +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_assembly_statistics Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/create_pan_genome_plots +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/create_pan_genome Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/iterative_cdhit Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_core_alignment make[1]: Leaving directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' @@ -2192,12 +2228,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1666928/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1666928/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/2879416 and its subdirectories -I: Current time: Sat Jul 19 03:58:17 -12 2025 -I: pbuilder-time-stamp: 1752940697 +I: removing directory /srv/workspace/pbuilder/1666928 and its subdirectories +I: Current time: Sun Jul 20 06:00:14 +14 2025 +I: pbuilder-time-stamp: 1752940814