Diff of the two buildlogs: -- --- b1/build.log 2024-12-06 03:18:32.638374826 +0000 +++ b2/build.log 2024-12-06 03:26:21.285342237 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Dec 5 15:09:07 -12 2024 -I: pbuilder-time-stamp: 1733454547 +I: Current time: Fri Dec 6 17:18:44 +14 2024 +I: pbuilder-time-stamp: 1733455124 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 new-bioperl-require.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/14743/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/12475/tmp/hooks/D01_modify_environment starting +debug: Running on virt64b. +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 Dec 6 03:19 /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/12475/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/12475/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + 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]="32" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='e695eacd9b6744ee8384f32da2ad0aba' - 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='14743' - PS1='# ' - PS2='> ' + INVOCATION_ID=ea12eedbf99f47bb8f872759607d2b90 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=12475 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.CvqafaTV/pbuilderrc_Xz8C --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.CvqafaTV/b1 --logfile b1/build.log roary_3.13.0+dfsg-2.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.CvqafaTV/pbuilderrc_mi9Y --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.CvqafaTV/b2 --logfile b2/build.log roary_3.13.0+dfsg-2.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux wbq0 6.1.0-28-armmp #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/14743/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/12475/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -486,7 +518,7 @@ Get: 313 http://deb.debian.org/debian trixie/main armhf unzip armhf 6.0-28 [152 kB] Get: 314 http://deb.debian.org/debian trixie/main armhf xdg-utils all 1.2.1-2 [75.8 kB] Get: 315 http://deb.debian.org/debian trixie/main armhf r-base-core armhf 4.4.2-1 [28.0 MB] -Fetched 109 MB in 11s (9627 kB/s) +Fetched 109 MB in 5s (22.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:armhf. (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 ... 19684 files and directories currently installed.) @@ -1531,8 +1563,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Dec 6 03:12:44 UTC 2024. -Universal Time is now: Fri Dec 6 03:12:44 UTC 2024. +Local time is now: Fri Dec 6 03:21:35 UTC 2024. +Universal Time is now: Fri Dec 6 03:21:35 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libjson-maybexs-perl (1.004008-1) ... @@ -1799,7 +1831,11 @@ Building tag database... -> Finished parsing the build-deps 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-2_source.changes +I: user script /srv/workspace/pbuilder/12475/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/12475/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-2_source.changes dpkg-buildpackage: info: source package roary dpkg-buildpackage: info: source version 3.13.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -1832,98 +1868,98 @@ Writing Makefile for Bio::Roary Writing MYMETA.yml and MYMETA.json dh_auto_build -D .build/debian-build - cd .build/debian-build && make -j3 + cd .build/debian-build && make -j4 make[1]: Entering directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' -cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm -cp lib/Bio/Roary/AccessoryBinaryFasta.pm blib/lib/Bio/Roary/AccessoryBinaryFasta.pm -cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm -cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm -cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm -cp lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm blib/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm -cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.pm +cp lib/Bio/Roary/AnnotateGroups.pm blib/lib/Bio/Roary/AnnotateGroups.pm cp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm +cp lib/Bio/Roary/AssemblyStatistics.pm blib/lib/Bio/Roary/AssemblyStatistics.pm +cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm +cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.pm +cp lib/Bio/Roary/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm +cp lib/Bio/Roary/AccessoryClustering.pm blib/lib/Bio/Roary/AccessoryClustering.pm +cp lib/Bio/Roary/CommandLine/AssemblyStatistics.pm blib/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm +cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.pm cp lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm blib/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm +cp lib/Bio/Roary/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.pm +cp lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm blib/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm +cp lib/Bio/Roary/External/CheckTools.pm blib/lib/Bio/Roary/External/CheckTools.pm +cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm +cp lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm +cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm +cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm +cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm +cp lib/Bio/Roary/CommandLine/IterativeCdhit.pm blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pm +cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm cp lib/Bio/Roary/CommandLine/Common.pm blib/lib/Bio/Roary/CommandLine/Common.pm -cp lib/Bio/Roary/AccessoryClustering.pm blib/lib/Bio/Roary/AccessoryClustering.pm cp lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm blib/lib/Bio/Roary/CommandLine/UniqueGenesPerSample.pm -cp lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm +cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.pm +cp lib/Bio/Roary/AccessoryBinaryFasta.pm blib/lib/Bio/Roary/AccessoryBinaryFasta.pm cp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm -cp lib/Bio/Roary/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.pm -cp lib/Bio/Roary/AssemblyStatistics.pm blib/lib/Bio/Roary/AssemblyStatistics.pm cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm cp lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm blib/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm -cp lib/Bio/Roary/CommandLine/AssemblyStatistics.pm blib/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm -cp lib/Bio/Roary/External/CheckTools.pm blib/lib/Bio/Roary/External/CheckTools.pm -cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm -cp lib/Bio/Roary/AnnotateGroups.pm blib/lib/Bio/Roary/AnnotateGroups.pm -cp lib/Bio/Roary/CommandLine/IterativeCdhit.pm blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pm -cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm -cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.pm -cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm -cp lib/Bio/Roary/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm -cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.pm -cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm -cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm -cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm +cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm +cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm cp lib/Bio/Roary/MergeMultifastaAlignments.pm blib/lib/Bio/Roary/MergeMultifastaAlignments.pm -cp lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/External/GeneAlignmentFromNucleotides.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/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm -cp lib/Bio/Roary/Output/GroupMultifasta.pm blib/lib/Bio/Roary/Output/GroupMultifasta.pm -cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm +cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm +cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm cp lib/Bio/Roary/External/Mcl.pm blib/lib/Bio/Roary/External/Mcl.pm -cp lib/Bio/Roary/Output/EmblGroups.pm blib/lib/Bio/Roary/Output/EmblGroups.pm -cp lib/Bio/Roary/JobRunner/Parallel.pm blib/lib/Bio/Roary/JobRunner/Parallel.pm -cp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm -cp lib/Bio/Roary/ExtractProteomeFromGFFs.pm blib/lib/Bio/Roary/ExtractProteomeFromGFFs.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/Fasttree.pm blib/lib/Bio/Roary/External/Fasttree.pm cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm +cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm +cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.pm cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm -cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm -cp lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm blib/lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.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/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm +cp lib/Bio/Roary/ExtractProteomeFromGFFs.pm blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pm +cp lib/Bio/Roary/Output/EmblGroups.pm blib/lib/Bio/Roary/Output/EmblGroups.pm cp lib/Bio/Roary/External/Mafft.pm blib/lib/Bio/Roary/External/Mafft.pm -cp lib/Bio/Roary/External/IterativeCdhit.pm blib/lib/Bio/Roary/External/IterativeCdhit.pm -cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.pm -cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm -cp lib/Bio/Roary/GeneNamesFromGFF.pm blib/lib/Bio/Roary/GeneNamesFromGFF.pm +cp lib/Bio/Roary/JobRunner/Parallel.pm blib/lib/Bio/Roary/JobRunner/Parallel.pm +cp lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm blib/lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm +cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.pm +cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm +cp lib/Bio/Roary/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm +cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.pm +cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.pm +cp lib/Bio/Roary/Output/GroupMultifasta.pm blib/lib/Bio/Roary/Output/GroupMultifasta.pm +cp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm +cp lib/Bio/Roary/Output/EMBLHeaderCommon.pm blib/lib/Bio/Roary/Output/EMBLHeaderCommon.pm +cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm +cp lib/Bio/Roary/GeneNamesFromGFF.pm blib/lib/Bio/Roary/GeneNamesFromGFF.pm cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm -cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm -cp lib/Bio/Roary/PresenceAbsenceMatrix.pm blib/lib/Bio/Roary/PresenceAbsenceMatrix.pm +cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm +cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.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/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/SampleOrder.pm blib/lib/Bio/Roary/SampleOrder.pm +cp lib/Bio/Roary/QC/Report.pm blib/lib/Bio/Roary/QC/Report.pm +cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm cp lib/Bio/Roary/UniqueGenesPerSample.pm blib/lib/Bio/Roary/UniqueGenesPerSample.pm -cp lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm -cp lib/Bio/Roary/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm -cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm -cp lib/Bio/Roary/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm -cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm -cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm -cp lib/Bio/Roary/ReorderSpreadsheet.pm blib/lib/Bio/Roary/ReorderSpreadsheet.pm -cp lib/Bio/Roary/SplitGroups.pm blib/lib/Bio/Roary/SplitGroups.pm cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm -cp lib/Bio/Roary/QC/Report.pm blib/lib/Bio/Roary/QC/Report.pm -cp lib/Bio/Roary/SpreadsheetRole.pm blib/lib/Bio/Roary/SpreadsheetRole.pm -cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm +cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm +cp lib/Bio/Roary/SplitGroups.pm blib/lib/Bio/Roary/SplitGroups.pm +cp lib/Bio/Roary/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm +cp lib/Bio/Roary/PresenceAbsenceMatrix.pm blib/lib/Bio/Roary/PresenceAbsenceMatrix.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/SpreadsheetRole.pm blib/lib/Bio/Roary/SpreadsheetRole.pm +cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm +cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm +cp lib/Bio/Roary/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm cp bin/create_pan_genome blib/script/create_pan_genome -cp bin/create_pan_genome_plots blib/script/create_pan_genome_plots "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome +cp bin/create_pan_genome_plots blib/script/create_pan_genome_plots "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome_plots cp bin/extract_proteome_from_gff blib/script/extract_proteome_from_gff "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- 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/iterative_cdhit cp bin/pan_genome_assembly_statistics blib/script/pan_genome_assembly_statistics -cp bin/pan_genome_core_alignment blib/script/pan_genome_core_alignment "/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 "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_core_alignment cp bin/pan_genome_post_analysis blib/script/pan_genome_post_analysis "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_post_analysis @@ -1960,203 +1996,203 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install -D .build/debian-build --destdir=debian/roary/ - cd .build/debian-build && make -j3 install DESTDIR=/build/reproducible-path/roary-3.13.0\+dfsg/debian/roary AM_UPDATE_INFO_DIR=no PREFIX=/usr + cd .build/debian-build && make -j4 install DESTDIR=/build/reproducible-path/roary-3.13.0\+dfsg/debian/roary AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' Manifying 16 pod documents Manifying 26 pod documents 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/GeneNamesFromGFF.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/BedFromGFFRole.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/AnalyseGroups.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/LookupGeneFiles.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/Exceptions.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/ReorderSpreadsheet.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/AccessoryClustering.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/ParseGFFAnnotationRole.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/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/ExtractProteomeFromGFF.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/AssemblyStatistics.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/ParallelAllAgainstAllBlast.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/InflateClusters.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/SampleOrder.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/ReformatInputGFFs.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/PostAnalysis.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/ParseGFFAnnotationRole.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/UniqueGenesPerSample.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/SequenceLengths.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/AnnotateGroups.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/ContigsToGeneIDsFromGFF.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/OrderGenes.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/CombinedProteome.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/SpreadsheetRole.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/AccessoryClustering.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/GroupLabels.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/ReorderSpreadsheet.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/FilterFullClusters.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/IterativeCdhit.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/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/SpreadsheetRole.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/UniqueGenesPerSample.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/AccessoryBinaryFasta.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/CommandLine/RoaryPostAnalysis.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/RoaryCoreAlignment.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/GeneAlignmentFromNucleotides.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/perl5/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.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/QueryRoary.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/Common.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/TransferAnnotationToGroups.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/JobRunner/Local.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/External/Prank.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/PostAnalysis.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/Fasttree.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/Makeblastdb.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/Mcl.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/Output/QueryGroups.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/GroupsMultifastasNucleotide.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/GroupMultifasta.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/CoreGeneAlignmentCoordinatesEMBL.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/BlastIdentityFrequency.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/NumberOfGroups.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/GroupsMultifastaProtein.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/External/GeneAlignmentFromNucleotides.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/PostAnalysis.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/CheckTools.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/Blastp.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/IterativeCdhit.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/CommandLine/GeneAlignmentFromNucleotides.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/RoaryPostAnalysis.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/AssemblyStatistics.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/Roary.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/RoaryReorderSpreadsheet.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/QueryRoary.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/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/Output/GroupMultifasta.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/QC/Report.pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/protein_alignment_from_nucleotides.1p -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_assembly_statistics.1p -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/create_pan_genome_plots.1p -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/query_pan_genome.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/create_pan_genome.1p -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/extract_proteome_from_gff.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-query_pan_genome.1p +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/iterative_cdhit.1p +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/extract_proteome_from_gff.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary-pan_genome_reorder_spreadsheet.1p -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_reorder_spreadsheet.1p +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/pan_genome_post_analysis.1p -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/iterative_cdhit.1p -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary.1p +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/protein_alignment_from_nucleotides.1p +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_reorder_spreadsheet.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/parallel_all_against_all_blastp.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/create_pan_genome_plots.1p Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_core_alignment.1p -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::IterativeCdhit.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastaProtein.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::GeneAlignmentFromNucleotides.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::CheckTools.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PostAnalysis.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Mcl.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::EMBLHeaderCommon.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Common.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Local.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Blastp.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SampleOrder.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::QC::Report.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastaNucleotide.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::FilterFullClusters.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PrepareInputFiles.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::NumberOfGroups.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::InflateClusters.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/query_pan_genome.1p +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/create_pan_genome.1p +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/roary.1p +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man1/pan_genome_assembly_statistics.1p +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ExtractProteomeFromGff.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Makeblastdb.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::BedFromGFFRole.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AccessoryClustering.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PresenceAbsenceMatrix.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/share/man/man3/Bio::Roary::GeneNamesFromGFF.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::GeneAlignmentFromNucleotides.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GroupStatistics.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ParallelAllAgainstAllBlast.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::EmblGroups.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AssemblyStatistics.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::TransferAnnotationToGroups.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Role.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::OrderGenes.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::QueryGroups.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::LookupGeneFiles.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::IterativeCdhit.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::FilterUnknownsFromFasta.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastas.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ClustersRole.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::BlastIdentityFrequency.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastasNucleotide.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::CreatePanGenome.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SplitGroups.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Roary.3pm -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::UniqueGenesPerSample.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryReorderSpreadsheet.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::MergeMultifastaAlignments.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::PostAnalysis.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFFs.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::TransferAnnotationToGroups.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryCoreAlignment.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SortFasta.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Mafft.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ExtractProteomeFromGff.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFF.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Prank.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ChunkFastaFile.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractCoreGenesFromSpreadsheet.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ParallelAllAgainstAllBlast.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ContigsToGeneIDsFromGFF.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::LookupGeneFiles.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::BedFromGFFRole.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GroupStatistics.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GeneNamesFromGFF.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReformatInputGFFs.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnnotateGroups.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::FilterUnknownsFromFasta.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PrepareInputFiles.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/share/man/man3/Bio::Roary::External::Mcl.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Common.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CombinedProteome.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::IterativeCdhit.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GroupLabels.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastaProtein.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ParseGFFAnnotationRole.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::CheckTools.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::UniqueGenesPerSample.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReorderSpreadsheet.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Prank.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::BlastIdentityFrequency.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Parallel.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryCoreAlignment.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::AssemblyStatistics.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupMultifasta.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::IterativeCdhit.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SequenceLengths.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SpreadsheetRole.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::UniqueGenesPerSample.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::PostAnalysis.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractCoreGenesFromSpreadsheet.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Local.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::QueryGroups.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ExtractProteomeFromGFF.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryReorderSpreadsheet.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::UniqueGenesPerSample.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ClustersRole.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Blastp.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::EMBLHeaderCommon.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::IterativeCdhit.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::Roary.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Mafft.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::OrderGenes.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::DifferenceBetweenSets.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Exceptions.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastasNucleotide.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::GeneAlignmentFromNucleotides.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Fasttree.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ContigsToGeneIDsFromGFF.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnalyseGroups.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::GroupLabels.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::CreatePanGenome.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SplitGroups.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::NumberOfGroups.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::AssemblyStatistics.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SampleOrder.3pm +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::PostAnalysis.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::PresenceAbsenceMatrix.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AccessoryClustering.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::FilterFullClusters.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AssemblyStatistics.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::QueryRoary.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupMultifasta.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::DifferenceBetweenSets.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CombinedProteome.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::ReformatInputGFFs.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::CommandLine::RoaryPostAnalysis.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::SequenceLengths.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::QC::Report.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::AnalyseGroups.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::GeneAlignmentFromNucleotides.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::JobRunner::Role.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::MergeMultifastaAlignments.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastaNucleotide.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::Output::GroupsMultifastas.3pm +Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::InflateClusters.3pm Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::Cdhit.3pm -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/share/man/man3/Bio::Roary::External::IterativeCdhit.3pm -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/query_pan_genome -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/iterative_cdhit +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/create_pan_genome -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/pan_genome_core_alignment 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/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/pan_genome_reorder_spreadsheet 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_post_analysis +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/extract_proteome_from_gff -Installing /build/reproducible-path/roary-3.13.0+dfsg/debian/roary/usr/bin/pan_genome_core_alignment -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/parallel_all_against_all_blastp +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/pan_genome_assembly_statistics -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/iterative_cdhit -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/transfer_annotation_to_groups +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/roary-unique_genes_per_sample make[1]: Leaving directory '/build/reproducible-path/roary-3.13.0+dfsg/.build/debian-build' debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/roary-3.13.0+dfsg' @@ -2185,12 +2221,14 @@ 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/12475/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/12475/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/14743 and its subdirectories -I: Current time: Thu Dec 5 15:18:27 -12 2024 -I: pbuilder-time-stamp: 1733455107 +I: removing directory /srv/workspace/pbuilder/12475 and its subdirectories +I: Current time: Fri Dec 6 17:26:08 +14 2024 +I: pbuilder-time-stamp: 1733455568