Diff of the two buildlogs: -- --- b1/build.log 2025-09-04 01:13:16.141804971 +0000 +++ b2/build.log 2025-09-04 01:17:39.838119010 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Sep 3 13:10:26 -12 2025 -I: pbuilder-time-stamp: 1756948226 +I: Current time: Wed Oct 7 21:36:17 +14 2026 +I: pbuilder-time-stamp: 1791358577 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -26,53 +26,85 @@ dpkg-source: info: applying perl-5.42-precedence.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3437517/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/103686/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-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 Oct 7 07:36 /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/103686/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/103686/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]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(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='37d66d967aae4a219504b8838685f083' - 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='3437517' - PS1='# ' - PS2='> ' + INVOCATION_ID=d1922694b55c42b281c6d6ffc6f86ce4 + 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=103686 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.S2WHbgMX/pbuilderrc_albn --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.S2WHbgMX/b1 --logfile b1/build.log bioperl_1.7.8-2.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - 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.S2WHbgMX/pbuilderrc_qjDM --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.S2WHbgMX/b2 --logfile b2/build.log bioperl_1.7.8-2.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + 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 codethink04-arm64 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3437517/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/103686/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -460,7 +492,7 @@ Get: 252 http://deb.debian.org/debian unstable/main arm64 libxml-simple-perl all 2.25-2 [69.8 kB] Get: 253 http://deb.debian.org/debian unstable/main arm64 libyaml-perl all 1.31-1 [64.8 kB] Get: 254 http://deb.debian.org/debian unstable/main arm64 rename all 2.02-1 [21.8 kB] -Fetched 46.4 MB in 0s (109 MB/s) +Fetched 46.4 MB in 0s (127 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1: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 ... 20012 files and directories currently installed.) @@ -1523,7 +1555,11 @@ fakeroot is already the newest version (1.37.1.2-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/bioperl-1.7.8/ && 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 > ../bioperl_1.7.8-2_source.changes +I: user script /srv/workspace/pbuilder/103686/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/103686/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/bioperl-1.7.8/ && 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 > ../bioperl_1.7.8-2_source.changes dpkg-buildpackage: info: source package bioperl dpkg-buildpackage: info: source version 1.7.8-2 dpkg-buildpackage: info: source distribution unstable @@ -1550,517 +1586,517 @@ dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/bioperl-1.7.8' -cp lib/Bio/AlignIO/metafasta.pm blib/lib/Bio/AlignIO/metafasta.pm -cp lib/Bio/AnalysisI.pm blib/lib/Bio/AnalysisI.pm -cp lib/Bio/AlignIO/arp.pm blib/lib/Bio/AlignIO/arp.pm cp lib/Bio/Align/ProteinStatistics.pm blib/lib/Bio/Align/ProteinStatistics.pm -cp lib/Bio/Annotation/Relation.pm blib/lib/Bio/Annotation/Relation.pm +cp lib/Bio/AlignIO/largemultifasta.pm blib/lib/Bio/AlignIO/largemultifasta.pm +cp lib/Bio/AlignIO/proda.pm blib/lib/Bio/AlignIO/proda.pm +cp lib/Bio/Annotation/OntologyTerm.pm blib/lib/Bio/Annotation/OntologyTerm.pm +cp lib/Bio/Align/StatisticsI.pm blib/lib/Bio/Align/StatisticsI.pm cp lib/Bio/AlignIO/xmfa.pm blib/lib/Bio/AlignIO/xmfa.pm -cp lib/Bio/AnnotatableI.pm blib/lib/Bio/AnnotatableI.pm -cp lib/Bio/AlignIO/Handler/GenericAlignHandler.pm blib/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm -cp lib/Bio/AnalysisParserI.pm blib/lib/Bio/AnalysisParserI.pm -cp lib/Bio/AlignIO/phylip.pm blib/lib/Bio/AlignIO/phylip.pm -cp lib/Bio/AlignIO/clustalw.pm blib/lib/Bio/AlignIO/clustalw.pm -cp lib/Bio/Annotation/Reference.pm blib/lib/Bio/Annotation/Reference.pm cp lib/Bio/Annotation/AnnotationFactory.pm blib/lib/Bio/Annotation/AnnotationFactory.pm -cp lib/Bio/AlignIO/pfam.pm blib/lib/Bio/AlignIO/pfam.pm cp lib/Bio/Annotation/DBLink.pm blib/lib/Bio/Annotation/DBLink.pm -cp lib/Bio/AlignIO/emboss.pm blib/lib/Bio/AlignIO/emboss.pm -cp lib/Bio/Annotation/Collection.pm blib/lib/Bio/Annotation/Collection.pm +cp lib/Bio/AlignIO/maf.pm blib/lib/Bio/AlignIO/maf.pm +cp lib/Bio/AlignIO/fasta.pm blib/lib/Bio/AlignIO/fasta.pm cp lib/Bio/AlignIO/nexus.pm blib/lib/Bio/AlignIO/nexus.pm -cp lib/Bio/AlignIO/mega.pm blib/lib/Bio/AlignIO/mega.pm cp lib/Bio/AlignIO/prodom.pm blib/lib/Bio/AlignIO/prodom.pm -cp lib/Bio/Annotation/Comment.pm blib/lib/Bio/Annotation/Comment.pm -cp lib/Bio/AnalysisResultI.pm blib/lib/Bio/AnalysisResultI.pm +cp lib/Bio/AlignIO/arp.pm blib/lib/Bio/AlignIO/arp.pm +cp lib/Bio/Align/DNAStatistics.pm blib/lib/Bio/Align/DNAStatistics.pm +cp lib/Bio/AlignIO/selex.pm blib/lib/Bio/AlignIO/selex.pm cp lib/Bio/AlignIO.pm blib/lib/Bio/AlignIO.pm -cp lib/Bio/Align/StatisticsI.pm blib/lib/Bio/Align/StatisticsI.pm cp lib/Bio/Align/Utilities.pm blib/lib/Bio/Align/Utilities.pm -cp lib/Bio/AlignIO/meme.pm blib/lib/Bio/AlignIO/meme.pm -cp lib/Bio/AlignIO/proda.pm blib/lib/Bio/AlignIO/proda.pm -cp lib/Bio/Align/AlignI.pm blib/lib/Bio/Align/AlignI.pm -cp lib/Bio/AlignIO/bl2seq.pm blib/lib/Bio/AlignIO/bl2seq.pm -cp lib/Bio/AlignIO/msf.pm blib/lib/Bio/AlignIO/msf.pm cp lib/Bio/AlignIO/mase.pm blib/lib/Bio/AlignIO/mase.pm -cp lib/Bio/AlignIO/psi.pm blib/lib/Bio/AlignIO/psi.pm -cp lib/Bio/AlignIO/largemultifasta.pm blib/lib/Bio/AlignIO/largemultifasta.pm -cp lib/Bio/Align/DNAStatistics.pm blib/lib/Bio/Align/DNAStatistics.pm -cp lib/Bio/AlignIO/fasta.pm blib/lib/Bio/AlignIO/fasta.pm -cp lib/Bio/AlignIO/maf.pm blib/lib/Bio/AlignIO/maf.pm +cp lib/Bio/Annotation/Reference.pm blib/lib/Bio/Annotation/Reference.pm +cp lib/Bio/AnnotatableI.pm blib/lib/Bio/AnnotatableI.pm +cp lib/Bio/AnalysisResultI.pm blib/lib/Bio/AnalysisResultI.pm +cp lib/Bio/AlignIO/phylip.pm blib/lib/Bio/AlignIO/phylip.pm +cp lib/Bio/AnalysisParserI.pm blib/lib/Bio/AnalysisParserI.pm +cp lib/Bio/AlignIO/emboss.pm blib/lib/Bio/AlignIO/emboss.pm +cp lib/Bio/Annotation/Collection.pm blib/lib/Bio/Annotation/Collection.pm +cp lib/Bio/AlignIO/metafasta.pm blib/lib/Bio/AlignIO/metafasta.pm +cp lib/Bio/AlignIO/clustalw.pm blib/lib/Bio/AlignIO/clustalw.pm cp lib/Bio/Align/PairwiseStatistics.pm blib/lib/Bio/Align/PairwiseStatistics.pm +cp lib/Bio/AlignIO/psi.pm blib/lib/Bio/AlignIO/psi.pm +cp lib/Bio/Annotation/Relation.pm blib/lib/Bio/Annotation/Relation.pm +cp lib/Bio/AlignIO/Handler/GenericAlignHandler.pm blib/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm +cp lib/Bio/AlignIO/meme.pm blib/lib/Bio/AlignIO/meme.pm +cp lib/Bio/AlignIO/mega.pm blib/lib/Bio/AlignIO/mega.pm +cp lib/Bio/AlignIO/pfam.pm blib/lib/Bio/AlignIO/pfam.pm +cp lib/Bio/Annotation/Comment.pm blib/lib/Bio/Annotation/Comment.pm +cp lib/Bio/AnalysisI.pm blib/lib/Bio/AnalysisI.pm cp lib/Bio/AlignIO/po.pm blib/lib/Bio/AlignIO/po.pm -cp lib/Bio/Annotation/OntologyTerm.pm blib/lib/Bio/Annotation/OntologyTerm.pm -cp lib/Bio/AlignIO/selex.pm blib/lib/Bio/AlignIO/selex.pm -cp lib/Bio/Annotation/SimpleValue.pm blib/lib/Bio/Annotation/SimpleValue.pm -cp lib/Bio/DB/Flat/BDB/genbank.pm blib/lib/Bio/DB/Flat/BDB/genbank.pm -cp lib/Bio/CodonUsage/Table.pm blib/lib/Bio/CodonUsage/Table.pm +cp lib/Bio/AlignIO/bl2seq.pm blib/lib/Bio/AlignIO/bl2seq.pm +cp lib/Bio/AlignIO/msf.pm blib/lib/Bio/AlignIO/msf.pm +cp lib/Bio/Align/AlignI.pm blib/lib/Bio/Align/AlignI.pm +cp lib/Bio/DB/RandomAccessI.pm blib/lib/Bio/DB/RandomAccessI.pm +cp lib/Bio/DB/Failover.pm blib/lib/Bio/DB/Failover.pm +cp lib/Bio/DB/GFF/Util/Rearrange.pm blib/lib/Bio/DB/GFF/Util/Rearrange.pm cp lib/Bio/DB/Qual.pm blib/lib/Bio/DB/Qual.pm -cp lib/Bio/DB/Flat/BDB/embl.pm blib/lib/Bio/DB/Flat/BDB/embl.pm -cp lib/Bio/DB/Taxonomy/flatfile.pm blib/lib/Bio/DB/Taxonomy/flatfile.pm -cp lib/Bio/DB/Taxonomy.pm blib/lib/Bio/DB/Taxonomy.pm -cp lib/Bio/DB/GenericWebAgent.pm blib/lib/Bio/DB/GenericWebAgent.pm -cp lib/Bio/Annotation/Target.pm blib/lib/Bio/Annotation/Target.pm -cp lib/Bio/DB/Taxonomy/greengenes.pm blib/lib/Bio/DB/Taxonomy/greengenes.pm -cp lib/Bio/DB/Flat/BDB.pm blib/lib/Bio/DB/Flat/BDB.pm -cp lib/Bio/DB/IndexedBase.pm blib/lib/Bio/DB/IndexedBase.pm -cp lib/Bio/DB/QueryI.pm blib/lib/Bio/DB/QueryI.pm -cp lib/Bio/DB/Taxonomy/silva.pm blib/lib/Bio/DB/Taxonomy/silva.pm +cp lib/Bio/DB/Taxonomy/list.pm blib/lib/Bio/DB/Taxonomy/list.pm cp lib/Bio/DB/ReferenceI.pm blib/lib/Bio/DB/ReferenceI.pm -cp lib/Bio/DB/UpdateableSeqI.pm blib/lib/Bio/DB/UpdateableSeqI.pm -cp lib/Bio/Annotation/TagTree.pm blib/lib/Bio/Annotation/TagTree.pm -cp lib/Bio/DB/Flat/BinarySearch.pm blib/lib/Bio/DB/Flat/BinarySearch.pm -cp lib/Bio/DB/RandomAccessI.pm blib/lib/Bio/DB/RandomAccessI.pm -cp lib/Bio/DB/DBFetch.pm blib/lib/Bio/DB/DBFetch.pm -cp lib/Bio/DB/Fasta.pm blib/lib/Bio/DB/Fasta.pm -cp lib/Bio/CodonUsage/IO.pm blib/lib/Bio/CodonUsage/IO.pm cp lib/Bio/AnnotationCollectionI.pm blib/lib/Bio/AnnotationCollectionI.pm -cp lib/Bio/DB/Taxonomy/list.pm blib/lib/Bio/DB/Taxonomy/list.pm -cp lib/Bio/DB/FileCache.pm blib/lib/Bio/DB/FileCache.pm -cp lib/Bio/Annotation/StructuredValue.pm blib/lib/Bio/Annotation/StructuredValue.pm cp lib/Bio/DB/Query/WebQuery.pm blib/lib/Bio/DB/Query/WebQuery.pm +cp lib/Bio/DB/Flat/BinarySearch.pm blib/lib/Bio/DB/Flat/BinarySearch.pm +cp lib/Bio/DB/Flat/BDB/genbank.pm blib/lib/Bio/DB/Flat/BDB/genbank.pm cp lib/Bio/DB/LocationI.pm blib/lib/Bio/DB/LocationI.pm -cp lib/Bio/DB/Registry.pm blib/lib/Bio/DB/Registry.pm cp lib/Bio/DB/Flat/BDB/fasta.pm blib/lib/Bio/DB/Flat/BDB/fasta.pm -cp lib/Bio/Annotation/Tree.pm blib/lib/Bio/Annotation/Tree.pm +cp lib/Bio/DB/Taxonomy.pm blib/lib/Bio/DB/Taxonomy.pm +cp lib/Bio/DB/Taxonomy/flatfile.pm blib/lib/Bio/DB/Taxonomy/flatfile.pm +cp lib/Bio/Annotation/TagTree.pm blib/lib/Bio/Annotation/TagTree.pm +cp lib/Bio/DB/Taxonomy/silva.pm blib/lib/Bio/DB/Taxonomy/silva.pm +cp lib/Bio/DB/Taxonomy/greengenes.pm blib/lib/Bio/DB/Taxonomy/greengenes.pm +cp lib/Bio/DB/Flat/BDB/embl.pm blib/lib/Bio/DB/Flat/BDB/embl.pm +cp lib/Bio/DB/GenericWebAgent.pm blib/lib/Bio/DB/GenericWebAgent.pm +cp lib/Bio/DB/Flat.pm blib/lib/Bio/DB/Flat.pm +cp lib/Bio/Annotation/TypeManager.pm blib/lib/Bio/Annotation/TypeManager.pm +cp lib/Bio/Annotation/Target.pm blib/lib/Bio/Annotation/Target.pm +cp lib/Bio/DB/QueryI.pm blib/lib/Bio/DB/QueryI.pm +cp lib/Bio/Annotation/SimpleValue.pm blib/lib/Bio/Annotation/SimpleValue.pm +cp lib/Bio/Annotation/StructuredValue.pm blib/lib/Bio/Annotation/StructuredValue.pm cp lib/Bio/AnnotationI.pm blib/lib/Bio/AnnotationI.pm -cp lib/Bio/DB/Failover.pm blib/lib/Bio/DB/Failover.pm +cp lib/Bio/DB/IndexedBase.pm blib/lib/Bio/DB/IndexedBase.pm +cp lib/Bio/DB/Fasta.pm blib/lib/Bio/DB/Fasta.pm +cp lib/Bio/Annotation/Tree.pm blib/lib/Bio/Annotation/Tree.pm +cp lib/Bio/DB/FileCache.pm blib/lib/Bio/DB/FileCache.pm +cp lib/Bio/DB/UpdateableSeqI.pm blib/lib/Bio/DB/UpdateableSeqI.pm +cp lib/Bio/DB/GFF/Util/Binning.pm blib/lib/Bio/DB/GFF/Util/Binning.pm cp lib/Bio/DB/SeqI.pm blib/lib/Bio/DB/SeqI.pm -cp lib/Bio/Annotation/TypeManager.pm blib/lib/Bio/Annotation/TypeManager.pm +cp lib/Bio/DB/DBFetch.pm blib/lib/Bio/DB/DBFetch.pm +cp lib/Bio/DB/Flat/BDB.pm blib/lib/Bio/DB/Flat/BDB.pm cp lib/Bio/DB/Flat/BDB/swiss.pm blib/lib/Bio/DB/Flat/BDB/swiss.pm -cp lib/Bio/DB/Flat.pm blib/lib/Bio/DB/Flat.pm -cp lib/Bio/DB/GFF/Util/Rearrange.pm blib/lib/Bio/DB/GFF/Util/Rearrange.pm +cp lib/Bio/CodonUsage/Table.pm blib/lib/Bio/CodonUsage/Table.pm +cp lib/Bio/DB/Registry.pm blib/lib/Bio/DB/Registry.pm +cp lib/Bio/CodonUsage/IO.pm blib/lib/Bio/CodonUsage/IO.pm cp lib/Bio/DB/InMemoryCache.pm blib/lib/Bio/DB/InMemoryCache.pm -cp lib/Bio/DB/GFF/Util/Binning.pm blib/lib/Bio/DB/GFF/Util/Binning.pm -cp lib/Bio/Factory/ObjectFactory.pm blib/lib/Bio/Factory/ObjectFactory.pm -cp lib/Bio/Factory/AnalysisI.pm blib/lib/Bio/Factory/AnalysisI.pm -cp lib/Bio/Event/EventHandlerI.pm blib/lib/Bio/Event/EventHandlerI.pm -cp lib/Bio/LocatableSeq.pm blib/lib/Bio/LocatableSeq.pm -cp lib/Bio/Factory/SequenceProcessorI.pm blib/lib/Bio/Factory/SequenceProcessorI.pm -cp lib/Bio/IdentifiableI.pm blib/lib/Bio/IdentifiableI.pm -cp lib/Bio/Factory/LocationFactoryI.pm blib/lib/Bio/Factory/LocationFactoryI.pm -cp lib/Bio/Index/Blast.pm blib/lib/Bio/Index/Blast.pm -cp lib/Bio/Factory/SequenceStreamI.pm blib/lib/Bio/Factory/SequenceStreamI.pm -cp lib/Bio/Factory/ObjectBuilderI.pm blib/lib/Bio/Factory/ObjectBuilderI.pm cp lib/Bio/Index/Swissprot.pm blib/lib/Bio/Index/Swissprot.pm -cp lib/Bio/Index/GenBank.pm blib/lib/Bio/Index/GenBank.pm -cp lib/Bio/Factory/ApplicationFactoryI.pm blib/lib/Bio/Factory/ApplicationFactoryI.pm -cp lib/Bio/Das/SegmentI.pm blib/lib/Bio/Das/SegmentI.pm +cp lib/Bio/HandlerBaseI.pm blib/lib/Bio/HandlerBaseI.pm cp lib/Bio/DescribableI.pm blib/lib/Bio/DescribableI.pm -cp lib/Bio/Event/EventGeneratorI.pm blib/lib/Bio/Event/EventGeneratorI.pm +cp lib/Bio/Factory/SequenceFactoryI.pm blib/lib/Bio/Factory/SequenceFactoryI.pm +cp lib/Bio/Index/EMBL.pm blib/lib/Bio/Index/EMBL.pm +cp lib/Bio/IdentifiableI.pm blib/lib/Bio/IdentifiableI.pm +cp lib/Bio/Event/EventHandlerI.pm blib/lib/Bio/Event/EventHandlerI.pm cp lib/Bio/DasI.pm blib/lib/Bio/DasI.pm -cp lib/Bio/Factory/SeqAnalysisParserFactory.pm blib/lib/Bio/Factory/SeqAnalysisParserFactory.pm -cp lib/Bio/Factory/SeqAnalysisParserFactoryI.pm blib/lib/Bio/Factory/SeqAnalysisParserFactoryI.pm -cp lib/Bio/Index/Fasta.pm blib/lib/Bio/Index/Fasta.pm -cp lib/Bio/Factory/ObjectFactoryI.pm blib/lib/Bio/Factory/ObjectFactoryI.pm -cp lib/Bio/Das/FeatureTypeI.pm blib/lib/Bio/Das/FeatureTypeI.pm -cp lib/Bio/Index/AbstractSeq.pm blib/lib/Bio/Index/AbstractSeq.pm cp lib/Bio/Factory/DriverFactory.pm blib/lib/Bio/Factory/DriverFactory.pm -cp lib/Bio/Factory/FTLocationFactory.pm blib/lib/Bio/Factory/FTLocationFactory.pm +cp lib/Bio/Das/FeatureTypeI.pm blib/lib/Bio/Das/FeatureTypeI.pm cp lib/Bio/Index/Qual.pm blib/lib/Bio/Index/Qual.pm -cp lib/Bio/DBLinkContainerI.pm blib/lib/Bio/DBLinkContainerI.pm cp lib/Bio/Index/Abstract.pm blib/lib/Bio/Index/Abstract.pm +cp lib/Bio/Factory/ObjectFactory.pm blib/lib/Bio/Factory/ObjectFactory.pm +cp lib/Bio/Factory/AnalysisI.pm blib/lib/Bio/Factory/AnalysisI.pm +cp lib/Bio/Index/GenBank.pm blib/lib/Bio/Index/GenBank.pm cp lib/Bio/DB/WebDBSeqI.pm blib/lib/Bio/DB/WebDBSeqI.pm +cp lib/Bio/Event/EventGeneratorI.pm blib/lib/Bio/Event/EventGeneratorI.pm +cp lib/Bio/Factory/ObjectBuilderI.pm blib/lib/Bio/Factory/ObjectBuilderI.pm cp lib/Bio/Index/Fastq.pm blib/lib/Bio/Index/Fastq.pm +cp lib/Bio/Index/BlastTable.pm blib/lib/Bio/Index/BlastTable.pm +cp lib/Bio/Factory/SequenceStreamI.pm blib/lib/Bio/Factory/SequenceStreamI.pm +cp lib/Bio/DBLinkContainerI.pm blib/lib/Bio/DBLinkContainerI.pm +cp lib/Bio/Index/AbstractSeq.pm blib/lib/Bio/Index/AbstractSeq.pm +cp lib/Bio/Factory/ApplicationFactoryI.pm blib/lib/Bio/Factory/ApplicationFactoryI.pm +cp lib/Bio/LocatableSeq.pm blib/lib/Bio/LocatableSeq.pm +cp lib/Bio/Factory/SeqAnalysisParserFactoryI.pm blib/lib/Bio/Factory/SeqAnalysisParserFactoryI.pm cp lib/Bio/Factory/TreeFactoryI.pm blib/lib/Bio/Factory/TreeFactoryI.pm +cp lib/Bio/Index/Blast.pm blib/lib/Bio/Index/Blast.pm cp lib/Bio/Index/SwissPfam.pm blib/lib/Bio/Index/SwissPfam.pm -cp lib/Bio/HandlerBaseI.pm blib/lib/Bio/HandlerBaseI.pm -cp lib/Bio/Index/BlastTable.pm blib/lib/Bio/Index/BlastTable.pm -cp lib/Bio/Index/EMBL.pm blib/lib/Bio/Index/EMBL.pm -cp lib/Bio/Factory/SequenceFactoryI.pm blib/lib/Bio/Factory/SequenceFactoryI.pm -cp lib/Bio/IdCollectionI.pm blib/lib/Bio/IdCollectionI.pm +cp lib/Bio/Factory/LocationFactoryI.pm blib/lib/Bio/Factory/LocationFactoryI.pm +cp lib/Bio/Das/SegmentI.pm blib/lib/Bio/Das/SegmentI.pm cp lib/Bio/FeatureHolderI.pm blib/lib/Bio/FeatureHolderI.pm -cp lib/Bio/Ontology/DocumentRegistry.pm blib/lib/Bio/Ontology/DocumentRegistry.pm -cp lib/Bio/Location/Atomic.pm blib/lib/Bio/Location/Atomic.pm -cp lib/Bio/Matrix/PSM/IO/masta.pm blib/lib/Bio/Matrix/PSM/IO/masta.pm +cp lib/Bio/Factory/FTLocationFactory.pm blib/lib/Bio/Factory/FTLocationFactory.pm +cp lib/Bio/Index/Fasta.pm blib/lib/Bio/Index/Fasta.pm +cp lib/Bio/Factory/SequenceProcessorI.pm blib/lib/Bio/Factory/SequenceProcessorI.pm +cp lib/Bio/IdCollectionI.pm blib/lib/Bio/IdCollectionI.pm +cp lib/Bio/Factory/ObjectFactoryI.pm blib/lib/Bio/Factory/ObjectFactoryI.pm +cp lib/Bio/Factory/SeqAnalysisParserFactory.pm blib/lib/Bio/Factory/SeqAnalysisParserFactory.pm +cp lib/Bio/Location/WidestCoordPolicy.pm blib/lib/Bio/Location/WidestCoordPolicy.pm cp lib/Bio/Matrix/PhylipDist.pm blib/lib/Bio/Matrix/PhylipDist.pm -cp lib/Bio/Matrix/PSM/InstanceSiteI.pm blib/lib/Bio/Matrix/PSM/InstanceSiteI.pm +cp lib/Bio/Matrix/PSM/Psm.pm blib/lib/Bio/Matrix/PSM/Psm.pm +cp lib/Bio/Matrix/PSM/ProtMatrix.pm blib/lib/Bio/Matrix/PSM/ProtMatrix.pm +cp lib/Bio/Location/AvWithinCoordPolicy.pm blib/lib/Bio/Location/AvWithinCoordPolicy.pm +cp lib/Bio/Matrix/PSM/IO/masta.pm blib/lib/Bio/Matrix/PSM/IO/masta.pm cp lib/Bio/Location/CoordinatePolicyI.pm blib/lib/Bio/Location/CoordinatePolicyI.pm -cp lib/Bio/Matrix/PSM/SiteMatrixI.pm blib/lib/Bio/Matrix/PSM/SiteMatrixI.pm -cp lib/Bio/Matrix/PSM/ProtPsm.pm blib/lib/Bio/Matrix/PSM/ProtPsm.pm +cp lib/Bio/Location/FuzzyLocationI.pm blib/lib/Bio/Location/FuzzyLocationI.pm +cp lib/Bio/Matrix/PSM/IO.pm blib/lib/Bio/Matrix/PSM/IO.pm cp lib/Bio/Matrix/PSM/PsmHeaderI.pm blib/lib/Bio/Matrix/PSM/PsmHeaderI.pm -cp lib/Bio/Matrix/Mlagan.pm blib/lib/Bio/Matrix/Mlagan.pm -cp lib/Bio/Matrix/PSM/IO/psiblast.pm blib/lib/Bio/Matrix/PSM/IO/psiblast.pm -cp lib/Bio/Location/WidestCoordPolicy.pm blib/lib/Bio/Location/WidestCoordPolicy.pm +cp lib/Bio/Matrix/PSM/InstanceSite.pm blib/lib/Bio/Matrix/PSM/InstanceSite.pm cp lib/Bio/Matrix/IO.pm blib/lib/Bio/Matrix/IO.pm -cp lib/Bio/Matrix/PSM/IO/transfac.pm blib/lib/Bio/Matrix/PSM/IO/transfac.pm -cp lib/Bio/Matrix/IO/scoring.pm blib/lib/Bio/Matrix/IO/scoring.pm -cp lib/Bio/Location/Fuzzy.pm blib/lib/Bio/Location/Fuzzy.pm -cp lib/Bio/Matrix/PSM/IO/meme.pm blib/lib/Bio/Matrix/PSM/IO/meme.pm -cp lib/Bio/LocationI.pm blib/lib/Bio/LocationI.pm cp lib/Bio/Matrix/PSM/PsmHeader.pm blib/lib/Bio/Matrix/PSM/PsmHeader.pm -cp lib/Bio/Location/SplitLocationI.pm blib/lib/Bio/Location/SplitLocationI.pm +cp lib/Bio/LocationI.pm blib/lib/Bio/LocationI.pm +cp lib/Bio/Matrix/PSM/IO/psiblast.pm blib/lib/Bio/Matrix/PSM/IO/psiblast.pm +cp lib/Bio/Matrix/IO/mlagan.pm blib/lib/Bio/Matrix/IO/mlagan.pm +cp lib/Bio/Location/NarrowestCoordPolicy.pm blib/lib/Bio/Location/NarrowestCoordPolicy.pm cp lib/Bio/Matrix/IO/phylip.pm blib/lib/Bio/Matrix/IO/phylip.pm -cp lib/Bio/Matrix/PSM/InstanceSite.pm blib/lib/Bio/Matrix/PSM/InstanceSite.pm -cp lib/Bio/Location/AvWithinCoordPolicy.pm blib/lib/Bio/Location/AvWithinCoordPolicy.pm -cp lib/Bio/Location/Split.pm blib/lib/Bio/Location/Split.pm -cp lib/Bio/Matrix/Generic.pm blib/lib/Bio/Matrix/Generic.pm -cp lib/Bio/Matrix/PSM/ProtMatrix.pm blib/lib/Bio/Matrix/PSM/ProtMatrix.pm -cp lib/Bio/Matrix/PSM/PsmI.pm blib/lib/Bio/Matrix/PSM/PsmI.pm -cp lib/Bio/Matrix/PSM/Psm.pm blib/lib/Bio/Matrix/PSM/Psm.pm -cp lib/Bio/Matrix/PSM/IO.pm blib/lib/Bio/Matrix/PSM/IO.pm -cp lib/Bio/Matrix/PSM/IO/mast.pm blib/lib/Bio/Matrix/PSM/IO/mast.pm +cp lib/Bio/Matrix/PSM/SiteMatrixI.pm blib/lib/Bio/Matrix/PSM/SiteMatrixI.pm cp lib/Bio/Location/Simple.pm blib/lib/Bio/Location/Simple.pm +cp lib/Bio/Matrix/IO/scoring.pm blib/lib/Bio/Matrix/IO/scoring.pm +cp lib/Bio/Matrix/PSM/SiteMatrix.pm blib/lib/Bio/Matrix/PSM/SiteMatrix.pm +cp lib/Bio/Matrix/Generic.pm blib/lib/Bio/Matrix/Generic.pm +cp lib/Bio/Location/Split.pm blib/lib/Bio/Location/Split.pm +cp lib/Bio/Matrix/PSM/IO/meme.pm blib/lib/Bio/Matrix/PSM/IO/meme.pm cp lib/Bio/Matrix/MatrixI.pm blib/lib/Bio/Matrix/MatrixI.pm -cp lib/Bio/Matrix/IO/mlagan.pm blib/lib/Bio/Matrix/IO/mlagan.pm +cp lib/Bio/Location/Atomic.pm blib/lib/Bio/Location/Atomic.pm +cp lib/Bio/Matrix/PSM/PsmI.pm blib/lib/Bio/Matrix/PSM/PsmI.pm +cp lib/Bio/Matrix/Mlagan.pm blib/lib/Bio/Matrix/Mlagan.pm +cp lib/Bio/Location/Fuzzy.pm blib/lib/Bio/Location/Fuzzy.pm cp lib/Bio/Matrix/Scoring.pm blib/lib/Bio/Matrix/Scoring.pm -cp lib/Bio/Matrix/PSM/SiteMatrix.pm blib/lib/Bio/Matrix/PSM/SiteMatrix.pm -cp lib/Bio/Location/NarrowestCoordPolicy.pm blib/lib/Bio/Location/NarrowestCoordPolicy.pm -cp lib/Bio/Location/FuzzyLocationI.pm blib/lib/Bio/Location/FuzzyLocationI.pm -cp lib/Bio/OntologyIO/simplehierarchy.pm blib/lib/Bio/OntologyIO/simplehierarchy.pm -cp lib/Bio/OntologyIO/InterProParser.pm blib/lib/Bio/OntologyIO/InterProParser.pm -cp lib/Bio/OntologyIO.pm blib/lib/Bio/OntologyIO.pm -cp lib/Bio/OntologyIO/dagflat.pm blib/lib/Bio/OntologyIO/dagflat.pm -cp lib/Bio/Root/Exception.pm blib/lib/Bio/Root/Exception.pm +cp lib/Bio/Ontology/DocumentRegistry.pm blib/lib/Bio/Ontology/DocumentRegistry.pm +cp lib/Bio/Matrix/PSM/ProtPsm.pm blib/lib/Bio/Matrix/PSM/ProtPsm.pm +cp lib/Bio/Matrix/PSM/InstanceSiteI.pm blib/lib/Bio/Matrix/PSM/InstanceSiteI.pm +cp lib/Bio/Matrix/PSM/IO/mast.pm blib/lib/Bio/Matrix/PSM/IO/mast.pm +cp lib/Bio/Location/SplitLocationI.pm blib/lib/Bio/Location/SplitLocationI.pm +cp lib/Bio/Matrix/PSM/IO/transfac.pm blib/lib/Bio/Matrix/PSM/IO/transfac.pm +cp lib/Bio/Ontology/TermFactory.pm blib/lib/Bio/Ontology/TermFactory.pm +cp lib/Bio/Ontology/Term.pm blib/lib/Bio/Ontology/Term.pm +cp lib/Bio/Ontology/OBOterm.pm blib/lib/Bio/Ontology/OBOterm.pm +cp lib/Bio/OntologyIO/soflat.pm blib/lib/Bio/OntologyIO/soflat.pm +cp lib/Bio/Ontology/PathI.pm blib/lib/Bio/Ontology/PathI.pm cp lib/Bio/Ontology/GOterm.pm blib/lib/Bio/Ontology/GOterm.pm +cp lib/Bio/Ontology/Path.pm blib/lib/Bio/Ontology/Path.pm +cp lib/Bio/Ontology/OntologyStore.pm blib/lib/Bio/Ontology/OntologyStore.pm cp lib/Bio/Ontology/Relationship.pm blib/lib/Bio/Ontology/Relationship.pm -cp lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm +cp lib/Bio/Ontology/TermI.pm blib/lib/Bio/Ontology/TermI.pm cp lib/Bio/Ontology/InterProTerm.pm blib/lib/Bio/Ontology/InterProTerm.pm -cp lib/Bio/Range.pm blib/lib/Bio/Range.pm +cp lib/Bio/OntologyIO.pm blib/lib/Bio/OntologyIO.pm cp lib/Bio/Ontology/RelationshipType.pm blib/lib/Bio/Ontology/RelationshipType.pm -cp lib/Bio/Ontology/Ontology.pm blib/lib/Bio/Ontology/Ontology.pm +cp lib/Bio/Ontology/OntologyI.pm blib/lib/Bio/Ontology/OntologyI.pm +cp lib/Bio/OntologyIO/simplehierarchy.pm blib/lib/Bio/OntologyIO/simplehierarchy.pm +cp lib/Bio/Range.pm blib/lib/Bio/Range.pm +cp lib/Bio/Ontology/RelationshipI.pm blib/lib/Bio/Ontology/RelationshipI.pm cp lib/Bio/PrimarySeqI.pm blib/lib/Bio/PrimarySeqI.pm -cp lib/Bio/Ontology/PathI.pm blib/lib/Bio/Ontology/PathI.pm -cp lib/Bio/OntologyIO/Handlers/InterProHandler.pm blib/lib/Bio/OntologyIO/Handlers/InterProHandler.pm -cp lib/Bio/OntologyIO/goflat.pm blib/lib/Bio/OntologyIO/goflat.pm -cp lib/Bio/PrimarySeq.pm blib/lib/Bio/PrimarySeq.pm cp lib/Bio/OntologyIO/obo.pm blib/lib/Bio/OntologyIO/obo.pm cp lib/Bio/ParameterBaseI.pm blib/lib/Bio/ParameterBaseI.pm -cp lib/Bio/Ontology/OBOterm.pm blib/lib/Bio/Ontology/OBOterm.pm -cp lib/Bio/Ontology/OntologyEngineI.pm blib/lib/Bio/Ontology/OntologyEngineI.pm -cp lib/Bio/Ontology/Term.pm blib/lib/Bio/Ontology/Term.pm -cp lib/Bio/OntologyIO/soflat.pm blib/lib/Bio/OntologyIO/soflat.pm -cp lib/Bio/Ontology/TermFactory.pm blib/lib/Bio/Ontology/TermFactory.pm -cp lib/Bio/Ontology/RelationshipI.pm blib/lib/Bio/Ontology/RelationshipI.pm -cp lib/Bio/RangeI.pm blib/lib/Bio/RangeI.pm cp lib/Bio/Ontology/SimpleOntologyEngine.pm blib/lib/Bio/Ontology/SimpleOntologyEngine.pm -cp lib/Bio/Ontology/OntologyStore.pm blib/lib/Bio/Ontology/OntologyStore.pm -cp lib/Bio/Ontology/Path.pm blib/lib/Bio/Ontology/Path.pm -cp lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm blib/lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm cp lib/Bio/Ontology/RelationshipFactory.pm blib/lib/Bio/Ontology/RelationshipFactory.pm -cp lib/Bio/Ontology/OBOEngine.pm blib/lib/Bio/Ontology/OBOEngine.pm +cp lib/Bio/Ontology/OntologyEngineI.pm blib/lib/Bio/Ontology/OntologyEngineI.pm +cp lib/Bio/RangeI.pm blib/lib/Bio/RangeI.pm cp lib/Bio/PullParserI.pm blib/lib/Bio/PullParserI.pm -cp lib/Bio/Ontology/OntologyI.pm blib/lib/Bio/Ontology/OntologyI.pm -cp lib/Bio/Ontology/TermI.pm blib/lib/Bio/Ontology/TermI.pm +cp lib/Bio/OntologyIO/Handlers/InterProHandler.pm blib/lib/Bio/OntologyIO/Handlers/InterProHandler.pm cp lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm blib/lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm -cp lib/Bio/Search/DatabaseI.pm blib/lib/Bio/Search/DatabaseI.pm -cp lib/Bio/Search/BlastUtils.pm blib/lib/Bio/Search/BlastUtils.pm -cp lib/Bio/Search/Hit/HitI.pm blib/lib/Bio/Search/Hit/HitI.pm -cp lib/Bio/Search/HSP/BlastHSP.pm blib/lib/Bio/Search/HSP/BlastHSP.pm -cp lib/Bio/Root/HTTPget.pm blib/lib/Bio/Root/HTTPget.pm +cp lib/Bio/OntologyIO/goflat.pm blib/lib/Bio/OntologyIO/goflat.pm +cp lib/Bio/OntologyIO/dagflat.pm blib/lib/Bio/OntologyIO/dagflat.pm +cp lib/Bio/Ontology/OBOEngine.pm blib/lib/Bio/Ontology/OBOEngine.pm +cp lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm +cp lib/Bio/PrimarySeq.pm blib/lib/Bio/PrimarySeq.pm +cp lib/Bio/Ontology/Ontology.pm blib/lib/Bio/Ontology/Ontology.pm +cp lib/Bio/Root/Exception.pm blib/lib/Bio/Root/Exception.pm +cp lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm blib/lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm +cp lib/Bio/OntologyIO/InterProParser.pm blib/lib/Bio/OntologyIO/InterProParser.pm cp lib/Bio/Search/HSP/GenericHSP.pm blib/lib/Bio/Search/HSP/GenericHSP.pm -cp lib/Bio/Root/RootI.pm blib/lib/Bio/Root/RootI.pm -cp lib/Bio/Root/TestObject.pm blib/lib/Bio/Root/TestObject.pm -cp lib/Bio/Search/HSP/FastaHSP.pm blib/lib/Bio/Search/HSP/FastaHSP.pm -cp lib/Bio/Search/Hit/ModelHit.pm blib/lib/Bio/Search/Hit/ModelHit.pm -cp lib/Bio/Root/Root.pm blib/lib/Bio/Root/Root.pm -cp lib/Bio/Search/HSP/HSPI.pm blib/lib/Bio/Search/HSP/HSPI.pm -cp lib/Bio/Search/Hit/GenericHit.pm blib/lib/Bio/Search/Hit/GenericHit.pm -cp lib/Bio/Root/IO.pm blib/lib/Bio/Root/IO.pm -cp lib/Bio/Search/Hit/BlastHit.pm blib/lib/Bio/Search/Hit/BlastHit.pm +cp lib/Bio/Search/Hit/Fasta.pm blib/lib/Bio/Search/Hit/Fasta.pm +cp lib/Bio/Search/Hit/PsiBlastHit.pm blib/lib/Bio/Search/Hit/PsiBlastHit.pm cp lib/Bio/Search/BlastStatistics.pm blib/lib/Bio/Search/BlastStatistics.pm cp lib/Bio/Search/Processor.pm blib/lib/Bio/Search/Processor.pm +cp lib/Bio/Root/IO.pm blib/lib/Bio/Root/IO.pm +cp lib/Bio/Search/HSP/ModelHSP.pm blib/lib/Bio/Search/HSP/ModelHSP.pm +cp lib/Bio/Search/HSP/FastaHSP.pm blib/lib/Bio/Search/HSP/FastaHSP.pm +cp lib/Bio/Search/Iteration/IterationI.pm blib/lib/Bio/Search/Iteration/IterationI.pm +cp lib/Bio/Search/Hit/PullHitI.pm blib/lib/Bio/Search/Hit/PullHitI.pm +cp lib/Bio/Search/Iteration/GenericIteration.pm blib/lib/Bio/Search/Iteration/GenericIteration.pm +cp lib/Bio/Root/RootI.pm blib/lib/Bio/Root/RootI.pm +cp lib/Bio/Search/HSP/HSPI.pm blib/lib/Bio/Search/HSP/HSPI.pm +cp lib/Bio/Root/HTTPget.pm blib/lib/Bio/Root/HTTPget.pm +cp lib/Bio/Search/BlastUtils.pm blib/lib/Bio/Search/BlastUtils.pm +cp lib/Bio/Search/DatabaseI.pm blib/lib/Bio/Search/DatabaseI.pm +cp lib/Bio/Search/Hit/ModelHit.pm blib/lib/Bio/Search/Hit/ModelHit.pm +cp lib/Bio/Search/HSP/HSPFactory.pm blib/lib/Bio/Search/HSP/HSPFactory.pm cp lib/Bio/Root/Version.pm blib/lib/Bio/Root/Version.pm -cp lib/Bio/Search/GenericDatabase.pm blib/lib/Bio/Search/GenericDatabase.pm -cp lib/Bio/Search/HSP/WABAHSP.pm blib/lib/Bio/Search/HSP/WABAHSP.pm cp lib/Bio/Root/Test.pm blib/lib/Bio/Root/Test.pm -cp lib/Bio/Search/GenericStatistics.pm blib/lib/Bio/Search/GenericStatistics.pm -cp lib/Bio/Search/HSP/ModelHSP.pm blib/lib/Bio/Search/HSP/ModelHSP.pm -cp lib/Bio/Search/HSP/PullHSPI.pm blib/lib/Bio/Search/HSP/PullHSPI.pm cp lib/Bio/Search/Hit/BlastPullHit.pm blib/lib/Bio/Search/Hit/BlastPullHit.pm -cp lib/Bio/Search/Hit/Fasta.pm blib/lib/Bio/Search/Hit/Fasta.pm -cp lib/Bio/Search/Hit/PsiBlastHit.pm blib/lib/Bio/Search/Hit/PsiBlastHit.pm -cp lib/Bio/Search/HSP/HSPFactory.pm blib/lib/Bio/Search/HSP/HSPFactory.pm -cp lib/Bio/Search/Iteration/IterationI.pm blib/lib/Bio/Search/Iteration/IterationI.pm +cp lib/Bio/Search/HSP/PullHSPI.pm blib/lib/Bio/Search/HSP/PullHSPI.pm +cp lib/Bio/Root/Utilities.pm blib/lib/Bio/Root/Utilities.pm +cp lib/Bio/Search/GenericStatistics.pm blib/lib/Bio/Search/GenericStatistics.pm +cp lib/Bio/Search/HSP/PSLHSP.pm blib/lib/Bio/Search/HSP/PSLHSP.pm +cp lib/Bio/Search/Hit/BlastHit.pm blib/lib/Bio/Search/Hit/BlastHit.pm +cp lib/Bio/Root/TestObject.pm blib/lib/Bio/Root/TestObject.pm +cp lib/Bio/Search/GenericDatabase.pm blib/lib/Bio/Search/GenericDatabase.pm +cp lib/Bio/Search/Hit/HitFactory.pm blib/lib/Bio/Search/Hit/HitFactory.pm +cp lib/Bio/Search/HSP/BlastHSP.pm blib/lib/Bio/Search/HSP/BlastHSP.pm +cp lib/Bio/Search/Hit/GenericHit.pm blib/lib/Bio/Search/Hit/GenericHit.pm cp lib/Bio/Root/Storable.pm blib/lib/Bio/Root/Storable.pm +cp lib/Bio/Search/HSP/WABAHSP.pm blib/lib/Bio/Search/HSP/WABAHSP.pm cp lib/Bio/Search/HSP/BlastPullHSP.pm blib/lib/Bio/Search/HSP/BlastPullHSP.pm -cp lib/Bio/Search/Hit/HitFactory.pm blib/lib/Bio/Search/Hit/HitFactory.pm +cp lib/Bio/Root/Root.pm blib/lib/Bio/Root/Root.pm cp lib/Bio/Search/HSP/PsiBlastHSP.pm blib/lib/Bio/Search/HSP/PsiBlastHSP.pm -cp lib/Bio/Search/Hit/PullHitI.pm blib/lib/Bio/Search/Hit/PullHitI.pm -cp lib/Bio/Search/HSP/PSLHSP.pm blib/lib/Bio/Search/HSP/PSLHSP.pm -cp lib/Bio/Root/Utilities.pm blib/lib/Bio/Root/Utilities.pm -cp lib/Bio/Search/Iteration/GenericIteration.pm blib/lib/Bio/Search/Iteration/GenericIteration.pm -cp lib/Bio/SearchIO.pm blib/lib/Bio/SearchIO.pm -cp lib/Bio/SearchIO/blast.pm blib/lib/Bio/SearchIO/blast.pm -cp lib/Bio/SearchIO/blast_pull.pm blib/lib/Bio/SearchIO/blast_pull.pm -cp lib/Bio/SearchIO/Writer/TextResultWriter.pm blib/lib/Bio/SearchIO/Writer/TextResultWriter.pm -cp lib/Bio/Search/Result/BlastResult.pm blib/lib/Bio/Search/Result/BlastResult.pm -cp lib/Bio/SearchIO/Writer/GbrowseGFF.pm blib/lib/Bio/SearchIO/Writer/GbrowseGFF.pm -cp lib/Bio/SearchIO/EventHandlerI.pm blib/lib/Bio/SearchIO/EventHandlerI.pm -cp lib/Bio/Search/SearchUtils.pm blib/lib/Bio/Search/SearchUtils.pm -cp lib/Bio/Search/Result/INFERNALResult.pm blib/lib/Bio/Search/Result/INFERNALResult.pm -cp lib/Bio/SearchIO/Writer/HTMLResultWriter.pm blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm +cp lib/Bio/Search/Hit/HitI.pm blib/lib/Bio/Search/Hit/HitI.pm cp lib/Bio/SearchIO/FastHitEventBuilder.pm blib/lib/Bio/SearchIO/FastHitEventBuilder.pm +cp lib/Bio/SearchIO/Writer/HTMLResultWriter.pm blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm cp lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm blib/lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm -cp lib/Bio/Search/Result/ResultFactory.pm blib/lib/Bio/Search/Result/ResultFactory.pm -cp lib/Bio/Search/Tiling/TilingI.pm blib/lib/Bio/Search/Tiling/TilingI.pm -cp lib/Bio/SearchIO/blasttable.pm blib/lib/Bio/SearchIO/blasttable.pm -cp lib/Bio/SearchIO/SearchResultEventBuilder.pm blib/lib/Bio/SearchIO/SearchResultEventBuilder.pm -cp lib/Bio/Search/Result/ResultI.pm blib/lib/Bio/Search/Result/ResultI.pm -cp lib/Bio/SearchIO/Writer/HitTableWriter.pm blib/lib/Bio/SearchIO/Writer/HitTableWriter.pm -cp lib/Bio/SearchIO/cross_match.pm blib/lib/Bio/SearchIO/cross_match.pm -cp lib/Bio/SearchIO/SearchWriterI.pm blib/lib/Bio/SearchIO/SearchWriterI.pm -cp lib/Bio/Search/Result/CrossMatchResult.pm blib/lib/Bio/Search/Result/CrossMatchResult.pm -cp lib/Bio/Search/Result/GenericResult.pm blib/lib/Bio/Search/Result/GenericResult.pm +cp lib/Bio/Search/Result/INFERNALResult.pm blib/lib/Bio/Search/Result/INFERNALResult.pm cp lib/Bio/SearchIO/axt.pm blib/lib/Bio/SearchIO/axt.pm +cp lib/Bio/Search/SearchUtils.pm blib/lib/Bio/Search/SearchUtils.pm cp lib/Bio/SearchIO/erpin.pm blib/lib/Bio/SearchIO/erpin.pm cp lib/Bio/Search/Tiling/MapTileUtils.pm blib/lib/Bio/Search/Tiling/MapTileUtils.pm -cp lib/Bio/Search/Result/BlastPullResult.pm blib/lib/Bio/Search/Result/BlastPullResult.pm +cp lib/Bio/SearchIO.pm blib/lib/Bio/SearchIO.pm +cp lib/Bio/Search/Result/ResultI.pm blib/lib/Bio/Search/Result/ResultI.pm +cp lib/Bio/Search/Result/GenericResult.pm blib/lib/Bio/Search/Result/GenericResult.pm cp lib/Bio/SearchIO/Writer/HSPTableWriter.pm blib/lib/Bio/SearchIO/Writer/HSPTableWriter.pm -cp lib/Bio/Search/Tiling/MapTiling.pm blib/lib/Bio/Search/Tiling/MapTiling.pm +cp lib/Bio/Search/Result/BlastPullResult.pm blib/lib/Bio/Search/Result/BlastPullResult.pm +cp lib/Bio/Search/Result/CrossMatchResult.pm blib/lib/Bio/Search/Result/CrossMatchResult.pm +cp lib/Bio/SearchIO/cross_match.pm blib/lib/Bio/SearchIO/cross_match.pm +cp lib/Bio/Search/Tiling/TilingI.pm blib/lib/Bio/Search/Tiling/TilingI.pm +cp lib/Bio/SearchIO/Writer/GbrowseGFF.pm blib/lib/Bio/SearchIO/Writer/GbrowseGFF.pm cp lib/Bio/Search/Result/PullResultI.pm blib/lib/Bio/Search/Result/PullResultI.pm +cp lib/Bio/Search/Tiling/MapTiling.pm blib/lib/Bio/Search/Tiling/MapTiling.pm +cp lib/Bio/SearchIO/SearchWriterI.pm blib/lib/Bio/SearchIO/SearchWriterI.pm +cp lib/Bio/SearchIO/EventHandlerI.pm blib/lib/Bio/SearchIO/EventHandlerI.pm cp lib/Bio/Search/Result/WABAResult.pm blib/lib/Bio/Search/Result/WABAResult.pm +cp lib/Bio/SearchIO/blasttable.pm blib/lib/Bio/SearchIO/blasttable.pm +cp lib/Bio/SearchIO/blast_pull.pm blib/lib/Bio/SearchIO/blast_pull.pm +cp lib/Bio/Search/Result/BlastResult.pm blib/lib/Bio/Search/Result/BlastResult.pm +cp lib/Bio/SearchIO/Writer/TextResultWriter.pm blib/lib/Bio/SearchIO/Writer/TextResultWriter.pm +cp lib/Bio/SearchIO/blast.pm blib/lib/Bio/SearchIO/blast.pm +cp lib/Bio/Search/Result/ResultFactory.pm blib/lib/Bio/Search/Result/ResultFactory.pm cp lib/Bio/SearchIO/Writer/ResultTableWriter.pm blib/lib/Bio/SearchIO/Writer/ResultTableWriter.pm cp lib/Bio/Search/StatisticsI.pm blib/lib/Bio/Search/StatisticsI.pm -cp lib/Bio/Seq/LargePrimarySeq.pm blib/lib/Bio/Seq/LargePrimarySeq.pm -cp lib/Bio/Seq/RichSeqI.pm blib/lib/Bio/Seq/RichSeqI.pm -cp lib/Bio/SearchIO/waba.pm blib/lib/Bio/SearchIO/waba.pm -cp lib/Bio/Seq/Meta.pm blib/lib/Bio/Seq/Meta.pm -cp lib/Bio/SeqFeature/Amplicon.pm blib/lib/Bio/SeqFeature/Amplicon.pm -cp lib/Bio/SeqFeature/Computation.pm blib/lib/Bio/SeqFeature/Computation.pm -cp lib/Bio/Seq/SeqBuilder.pm blib/lib/Bio/Seq/SeqBuilder.pm -cp lib/Bio/Seq/TraceI.pm blib/lib/Bio/Seq/TraceI.pm -cp lib/Bio/Seq/PrimedSeq.pm blib/lib/Bio/Seq/PrimedSeq.pm -cp lib/Bio/Seq/BaseSeqProcessor.pm blib/lib/Bio/Seq/BaseSeqProcessor.pm -cp lib/Bio/SearchIO/gmap_f9.pm blib/lib/Bio/SearchIO/gmap_f9.pm -cp lib/Bio/Seq/SeqFactory.pm blib/lib/Bio/Seq/SeqFactory.pm -cp lib/Bio/SearchIO/fasta.pm blib/lib/Bio/SearchIO/fasta.pm -cp lib/Bio/SearchIO/rnamotif.pm blib/lib/Bio/SearchIO/rnamotif.pm +cp lib/Bio/SearchIO/Writer/HitTableWriter.pm blib/lib/Bio/SearchIO/Writer/HitTableWriter.pm +cp lib/Bio/SearchIO/SearchResultEventBuilder.pm blib/lib/Bio/SearchIO/SearchResultEventBuilder.pm +cp lib/Bio/Seq/SeqFastaSpeedFactory.pm blib/lib/Bio/Seq/SeqFastaSpeedFactory.pm cp lib/Bio/SearchIO/sim4.pm blib/lib/Bio/SearchIO/sim4.pm -cp lib/Bio/Seq.pm blib/lib/Bio/Seq.pm -cp lib/Bio/Seq/LargeLocatableSeq.pm blib/lib/Bio/Seq/LargeLocatableSeq.pm -cp lib/Bio/SeqFeature/AnnotationAdaptor.pm blib/lib/Bio/SeqFeature/AnnotationAdaptor.pm +cp lib/Bio/Seq/MetaI.pm blib/lib/Bio/Seq/MetaI.pm +cp lib/Bio/SeqFeature/FeaturePair.pm blib/lib/Bio/SeqFeature/FeaturePair.pm +cp lib/Bio/Seq/PrimedSeq.pm blib/lib/Bio/Seq/PrimedSeq.pm +cp lib/Bio/SearchIO/wise.pm blib/lib/Bio/SearchIO/wise.pm cp lib/Bio/Seq/LargeSeqI.pm blib/lib/Bio/Seq/LargeSeqI.pm -cp lib/Bio/Seq/SeqFastaSpeedFactory.pm blib/lib/Bio/Seq/SeqFastaSpeedFactory.pm cp lib/Bio/SearchIO/psl.pm blib/lib/Bio/SearchIO/psl.pm -cp lib/Bio/SearchIO/wise.pm blib/lib/Bio/SearchIO/wise.pm -cp lib/Bio/Seq/SequenceTrace.pm blib/lib/Bio/Seq/SequenceTrace.pm -cp lib/Bio/SearchIO/megablast.pm blib/lib/Bio/SearchIO/megablast.pm +cp lib/Bio/Seq.pm blib/lib/Bio/Seq.pm cp lib/Bio/SeqAnalysisParserI.pm blib/lib/Bio/SeqAnalysisParserI.pm -cp lib/Bio/SeqFeature/Gene/Exon.pm blib/lib/Bio/SeqFeature/Gene/Exon.pm -cp lib/Bio/SeqFeature/FeaturePair.pm blib/lib/Bio/SeqFeature/FeaturePair.pm -cp lib/Bio/Seq/SimulatedRead.pm blib/lib/Bio/Seq/SimulatedRead.pm -cp lib/Bio/SeqFeature/CollectionI.pm blib/lib/Bio/SeqFeature/CollectionI.pm -cp lib/Bio/Seq/RichSeq.pm blib/lib/Bio/Seq/RichSeq.pm -cp lib/Bio/SearchIO/exonerate.pm blib/lib/Bio/SearchIO/exonerate.pm +cp lib/Bio/Seq/BaseSeqProcessor.pm blib/lib/Bio/Seq/BaseSeqProcessor.pm +cp lib/Bio/SeqFeature/Collection.pm blib/lib/Bio/SeqFeature/Collection.pm +cp lib/Bio/SeqFeature/Computation.pm blib/lib/Bio/SeqFeature/Computation.pm cp lib/Bio/SearchIO/infernal.pm blib/lib/Bio/SearchIO/infernal.pm -cp lib/Bio/Seq/MetaI.pm blib/lib/Bio/Seq/MetaI.pm -cp lib/Bio/Seq/PrimaryQual.pm blib/lib/Bio/Seq/PrimaryQual.pm -cp lib/Bio/Seq/Quality.pm blib/lib/Bio/Seq/Quality.pm +cp lib/Bio/Seq/LargeLocatableSeq.pm blib/lib/Bio/Seq/LargeLocatableSeq.pm cp lib/Bio/Seq/LargeSeq.pm blib/lib/Bio/Seq/LargeSeq.pm -cp lib/Bio/Seq/Meta/Array.pm blib/lib/Bio/Seq/Meta/Array.pm -cp lib/Bio/SeqFeature/Collection.pm blib/lib/Bio/SeqFeature/Collection.pm +cp lib/Bio/Seq/PrimaryQual.pm blib/lib/Bio/Seq/PrimaryQual.pm +cp lib/Bio/Seq/SeqBuilder.pm blib/lib/Bio/Seq/SeqBuilder.pm +cp lib/Bio/SearchIO/waba.pm blib/lib/Bio/SearchIO/waba.pm +cp lib/Bio/SearchIO/exonerate.pm blib/lib/Bio/SearchIO/exonerate.pm cp lib/Bio/Seq/EncodedSeq.pm blib/lib/Bio/Seq/EncodedSeq.pm +cp lib/Bio/Seq/SimulatedRead.pm blib/lib/Bio/Seq/SimulatedRead.pm +cp lib/Bio/SearchIO/fasta.pm blib/lib/Bio/SearchIO/fasta.pm +cp lib/Bio/SeqFeature/Gene/Exon.pm blib/lib/Bio/SeqFeature/Gene/Exon.pm +cp lib/Bio/Seq/RichSeq.pm blib/lib/Bio/Seq/RichSeq.pm +cp lib/Bio/Seq/SequenceTrace.pm blib/lib/Bio/Seq/SequenceTrace.pm +cp lib/Bio/SearchIO/megablast.pm blib/lib/Bio/SearchIO/megablast.pm +cp lib/Bio/SeqFeature/CollectionI.pm blib/lib/Bio/SeqFeature/CollectionI.pm +cp lib/Bio/Seq/SeqFactory.pm blib/lib/Bio/Seq/SeqFactory.pm cp lib/Bio/Seq/QualI.pm blib/lib/Bio/Seq/QualI.pm -cp lib/Bio/SeqFeature/Tools/FeatureNamer.pm blib/lib/Bio/SeqFeature/Tools/FeatureNamer.pm -cp lib/Bio/SeqIO/FTHelper.pm blib/lib/Bio/SeqIO/FTHelper.pm +cp lib/Bio/Seq/LargePrimarySeq.pm blib/lib/Bio/Seq/LargePrimarySeq.pm +cp lib/Bio/Seq/Quality.pm blib/lib/Bio/Seq/Quality.pm +cp lib/Bio/SeqFeature/AnnotationAdaptor.pm blib/lib/Bio/SeqFeature/AnnotationAdaptor.pm +cp lib/Bio/Seq/Meta/Array.pm blib/lib/Bio/Seq/Meta/Array.pm +cp lib/Bio/SearchIO/rnamotif.pm blib/lib/Bio/SearchIO/rnamotif.pm +cp lib/Bio/Seq/Meta.pm blib/lib/Bio/Seq/Meta.pm +cp lib/Bio/SearchIO/gmap_f9.pm blib/lib/Bio/SearchIO/gmap_f9.pm +cp lib/Bio/Seq/RichSeqI.pm blib/lib/Bio/Seq/RichSeqI.pm +cp lib/Bio/Seq/TraceI.pm blib/lib/Bio/Seq/TraceI.pm +cp lib/Bio/SeqFeature/Amplicon.pm blib/lib/Bio/SeqFeature/Amplicon.pm +cp lib/Bio/SeqFeature/Gene/Promoter.pm blib/lib/Bio/SeqFeature/Gene/Promoter.pm +cp lib/Bio/SeqIO/asciitree.pm blib/lib/Bio/SeqIO/asciitree.pm +cp lib/Bio/SeqFeature/PositionProxy.pm blib/lib/Bio/SeqFeature/PositionProxy.pm +cp lib/Bio/SeqFeature/Lite.pm blib/lib/Bio/SeqFeature/Lite.pm +cp lib/Bio/SeqIO/embldriver.pm blib/lib/Bio/SeqIO/embldriver.pm +cp lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm blib/lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm cp lib/Bio/SeqFeature/Gene/Poly_A_site.pm blib/lib/Bio/SeqFeature/Gene/Poly_A_site.pm -cp lib/Bio/SeqFeature/Gene/UTR.pm blib/lib/Bio/SeqFeature/Gene/UTR.pm -cp lib/Bio/SeqIO/fastq.pm blib/lib/Bio/SeqIO/fastq.pm cp lib/Bio/SeqIO/bsml_sax.pm blib/lib/Bio/SeqIO/bsml_sax.pm -cp lib/Bio/SeqFeature/SimilarityPair.pm blib/lib/Bio/SeqFeature/SimilarityPair.pm -cp lib/Bio/SeqIO/fasta.pm blib/lib/Bio/SeqIO/fasta.pm -cp lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm blib/lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm -cp lib/Bio/SeqFeature/Gene/Intron.pm blib/lib/Bio/SeqFeature/Gene/Intron.pm -cp lib/Bio/SeqIO/MultiFile.pm blib/lib/Bio/SeqIO/MultiFile.pm -cp lib/Bio/SeqFeature/Gene/Promoter.pm blib/lib/Bio/SeqFeature/Gene/Promoter.pm +cp lib/Bio/SeqFeature/Gene/GeneStructure.pm blib/lib/Bio/SeqFeature/Gene/GeneStructure.pm +cp lib/Bio/SeqFeature/Gene/GeneStructureI.pm blib/lib/Bio/SeqFeature/Gene/GeneStructureI.pm +cp lib/Bio/SeqIO/embl.pm blib/lib/Bio/SeqIO/embl.pm +cp lib/Bio/SeqFeature/Tools/FeatureNamer.pm blib/lib/Bio/SeqFeature/Tools/FeatureNamer.pm cp lib/Bio/SeqFeature/Gene/NC_Feature.pm blib/lib/Bio/SeqFeature/Gene/NC_Feature.pm -cp lib/Bio/SeqFeature/PositionProxy.pm blib/lib/Bio/SeqFeature/PositionProxy.pm +cp lib/Bio/SeqFeature/Similarity.pm blib/lib/Bio/SeqFeature/Similarity.pm +cp lib/Bio/SeqIO/bsml.pm blib/lib/Bio/SeqIO/bsml.pm +cp lib/Bio/SeqFeature/Gene/UTR.pm blib/lib/Bio/SeqFeature/Gene/UTR.pm +cp lib/Bio/SeqFeatureI.pm blib/lib/Bio/SeqFeatureI.pm +cp lib/Bio/SeqIO/MultiFile.pm blib/lib/Bio/SeqIO/MultiFile.pm +cp lib/Bio/SeqFeature/TypedSeqFeatureI.pm blib/lib/Bio/SeqFeature/TypedSeqFeatureI.pm cp lib/Bio/SeqFeature/Gene/Transcript.pm blib/lib/Bio/SeqFeature/Gene/Transcript.pm -cp lib/Bio/SeqIO/embl.pm blib/lib/Bio/SeqIO/embl.pm -cp lib/Bio/SeqFeature/Gene/GeneStructure.pm blib/lib/Bio/SeqFeature/Gene/GeneStructure.pm cp lib/Bio/SeqFeature/Generic.pm blib/lib/Bio/SeqFeature/Generic.pm -cp lib/Bio/SeqFeatureI.pm blib/lib/Bio/SeqFeatureI.pm -cp lib/Bio/SeqFeature/Similarity.pm blib/lib/Bio/SeqFeature/Similarity.pm +cp lib/Bio/SeqIO/FTHelper.pm blib/lib/Bio/SeqIO/FTHelper.pm +cp lib/Bio/SeqFeature/Gene/ExonI.pm blib/lib/Bio/SeqFeature/Gene/ExonI.pm cp lib/Bio/SeqFeature/SubSeq.pm blib/lib/Bio/SeqFeature/SubSeq.pm +cp lib/Bio/SeqIO/ace.pm blib/lib/Bio/SeqIO/ace.pm +cp lib/Bio/SeqIO/fastq.pm blib/lib/Bio/SeqIO/fastq.pm cp lib/Bio/SeqFeature/Tools/TypeMapper.pm blib/lib/Bio/SeqFeature/Tools/TypeMapper.pm -cp lib/Bio/SeqFeature/Tools/Unflattener.pm blib/lib/Bio/SeqFeature/Tools/Unflattener.pm cp lib/Bio/SeqFeature/Gene/TranscriptI.pm blib/lib/Bio/SeqFeature/Gene/TranscriptI.pm -cp lib/Bio/SeqFeature/TypedSeqFeatureI.pm blib/lib/Bio/SeqFeature/TypedSeqFeatureI.pm -cp lib/Bio/SeqFeature/Gene/ExonI.pm blib/lib/Bio/SeqFeature/Gene/ExonI.pm -cp lib/Bio/SeqFeature/Gene/GeneStructureI.pm blib/lib/Bio/SeqFeature/Gene/GeneStructureI.pm +cp lib/Bio/SeqFeature/Gene/Intron.pm blib/lib/Bio/SeqFeature/Gene/Intron.pm +cp lib/Bio/SeqFeature/Tools/IDHandler.pm blib/lib/Bio/SeqFeature/Tools/IDHandler.pm +cp lib/Bio/SeqFeature/SimilarityPair.pm blib/lib/Bio/SeqFeature/SimilarityPair.pm cp lib/Bio/SeqIO.pm blib/lib/Bio/SeqIO.pm +cp lib/Bio/SeqFeature/Tools/Unflattener.pm blib/lib/Bio/SeqFeature/Tools/Unflattener.pm cp lib/Bio/SeqI.pm blib/lib/Bio/SeqI.pm -cp lib/Bio/SeqIO/bsml.pm blib/lib/Bio/SeqIO/bsml.pm -cp lib/Bio/SeqFeature/Lite.pm blib/lib/Bio/SeqFeature/Lite.pm -cp lib/Bio/SeqFeature/Tools/IDHandler.pm blib/lib/Bio/SeqFeature/Tools/IDHandler.pm -cp lib/Bio/SeqIO/embldriver.pm blib/lib/Bio/SeqIO/embldriver.pm -cp lib/Bio/SeqIO/ace.pm blib/lib/Bio/SeqIO/ace.pm cp lib/Bio/SeqFeature/Primer.pm blib/lib/Bio/SeqFeature/Primer.pm -cp lib/Bio/SeqIO/asciitree.pm blib/lib/Bio/SeqIO/asciitree.pm -cp lib/Bio/SeqIO/pir.pm blib/lib/Bio/SeqIO/pir.pm -cp lib/Bio/SeqIO/kegg.pm blib/lib/Bio/SeqIO/kegg.pm -cp lib/Bio/SeqIO/swissdriver.pm blib/lib/Bio/SeqIO/swissdriver.pm -cp lib/Bio/SeqIO/locuslink.pm blib/lib/Bio/SeqIO/locuslink.pm -cp lib/Bio/SimpleAnalysisI.pm blib/lib/Bio/SimpleAnalysisI.pm -cp lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm blib/lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm -cp lib/Bio/SeqIO/tab.pm blib/lib/Bio/SeqIO/tab.pm -cp lib/Bio/SeqIO/swiss.pm blib/lib/Bio/SeqIO/swiss.pm -cp lib/Bio/Taxon.pm blib/lib/Bio/Taxon.pm -cp lib/Bio/SeqIO/largefasta.pm blib/lib/Bio/SeqIO/largefasta.pm -cp lib/Bio/SeqIO/mbsout.pm blib/lib/Bio/SeqIO/mbsout.pm -cp lib/Bio/SeqIO/tigr.pm blib/lib/Bio/SeqIO/tigr.pm -cp lib/Bio/SimpleAlign.pm blib/lib/Bio/SimpleAlign.pm +cp lib/Bio/SeqIO/fasta.pm blib/lib/Bio/SeqIO/fasta.pm +cp lib/Bio/Tools/AmpliconSearch.pm blib/lib/Bio/Tools/AmpliconSearch.pm +cp lib/Bio/SeqIO/gcg.pm blib/lib/Bio/SeqIO/gcg.pm +cp lib/Bio/Tools/AnalysisResult.pm blib/lib/Bio/Tools/AnalysisResult.pm +cp lib/Bio/Tools/Alignment/Trim.pm blib/lib/Bio/Tools/Alignment/Trim.pm cp lib/Bio/SeqUtils.pm blib/lib/Bio/SeqUtils.pm -cp lib/Bio/SeqIO/table.pm blib/lib/Bio/SeqIO/table.pm -cp lib/Bio/SeqIO/raw.pm blib/lib/Bio/SeqIO/raw.pm -cp lib/Bio/SeqIO/game/gameSubs.pm blib/lib/Bio/SeqIO/game/gameSubs.pm -cp lib/Bio/Tools/Alignment/Consed.pm blib/lib/Bio/Tools/Alignment/Consed.pm -cp lib/Bio/SeqIO/msout.pm blib/lib/Bio/SeqIO/msout.pm -cp lib/Bio/SeqIO/game/featHandler.pm blib/lib/Bio/SeqIO/game/featHandler.pm -cp lib/Bio/SeqIO/gbdriver.pm blib/lib/Bio/SeqIO/gbdriver.pm -cp lib/Bio/Tools/Blat.pm blib/lib/Bio/Tools/Blat.pm -cp lib/Bio/SeqIO/game.pm blib/lib/Bio/SeqIO/game.pm -cp lib/Bio/SeqIO/genbank.pm blib/lib/Bio/SeqIO/genbank.pm cp lib/Bio/SeqIO/seqxml.pm blib/lib/Bio/SeqIO/seqxml.pm +cp lib/Bio/SeqIO/largefasta.pm blib/lib/Bio/SeqIO/largefasta.pm +cp lib/Bio/SeqIO/metafasta.pm blib/lib/Bio/SeqIO/metafasta.pm cp lib/Bio/SeqIO/tigrxml.pm blib/lib/Bio/SeqIO/tigrxml.pm -cp lib/Bio/Tools/AnalysisResult.pm blib/lib/Bio/Tools/AnalysisResult.pm -cp lib/Bio/SeqIO/game/seqHandler.pm blib/lib/Bio/SeqIO/game/seqHandler.pm -cp lib/Bio/SeqIO/scf.pm blib/lib/Bio/SeqIO/scf.pm +cp lib/Bio/SeqIO/game/featHandler.pm blib/lib/Bio/SeqIO/game/featHandler.pm +cp lib/Bio/SeqIO/gbxml.pm blib/lib/Bio/SeqIO/gbxml.pm cp lib/Bio/SeqIO/qual.pm blib/lib/Bio/SeqIO/qual.pm -cp lib/Bio/SeqIO/metafasta.pm blib/lib/Bio/SeqIO/metafasta.pm -cp lib/Bio/Tools/AmpliconSearch.pm blib/lib/Bio/Tools/AmpliconSearch.pm +cp lib/Bio/SeqIO/gbdriver.pm blib/lib/Bio/SeqIO/gbdriver.pm +cp lib/Bio/SeqIO/scf.pm blib/lib/Bio/SeqIO/scf.pm +cp lib/Bio/SeqIO/swissdriver.pm blib/lib/Bio/SeqIO/swissdriver.pm +cp lib/Bio/SeqIO/kegg.pm blib/lib/Bio/SeqIO/kegg.pm +cp lib/Bio/SeqIO/tab.pm blib/lib/Bio/SeqIO/tab.pm +cp lib/Bio/SeqIO/pir.pm blib/lib/Bio/SeqIO/pir.pm +cp lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm blib/lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm +cp lib/Bio/SeqIO/tigr.pm blib/lib/Bio/SeqIO/tigr.pm +cp lib/Bio/SeqIO/game/gameHandler.pm blib/lib/Bio/SeqIO/game/gameHandler.pm cp lib/Bio/SeqIO/phd.pm blib/lib/Bio/SeqIO/phd.pm -cp lib/Bio/SeqIO/game/gameWriter.pm blib/lib/Bio/SeqIO/game/gameWriter.pm +cp lib/Bio/Tools/Blat.pm blib/lib/Bio/Tools/Blat.pm +cp lib/Bio/Taxon.pm blib/lib/Bio/Taxon.pm +cp lib/Bio/Tools/Alignment/Consed.pm blib/lib/Bio/Tools/Alignment/Consed.pm +cp lib/Bio/SeqIO/swiss.pm blib/lib/Bio/SeqIO/swiss.pm +cp lib/Bio/SeqIO/game/seqHandler.pm blib/lib/Bio/SeqIO/game/seqHandler.pm cp lib/Bio/Species.pm blib/lib/Bio/Species.pm -cp lib/Bio/SeqIO/gbxml.pm blib/lib/Bio/SeqIO/gbxml.pm +cp lib/Bio/SimpleAnalysisI.pm blib/lib/Bio/SimpleAnalysisI.pm +cp lib/Bio/SeqIO/game/gameWriter.pm blib/lib/Bio/SeqIO/game/gameWriter.pm +cp lib/Bio/SeqIO/locuslink.pm blib/lib/Bio/SeqIO/locuslink.pm +cp lib/Bio/SeqIO/table.pm blib/lib/Bio/SeqIO/table.pm +cp lib/Bio/SeqIO/game/gameSubs.pm blib/lib/Bio/SeqIO/game/gameSubs.pm +cp lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm blib/lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm +cp lib/Bio/SeqIO/msout.pm blib/lib/Bio/SeqIO/msout.pm +cp lib/Bio/SeqIO/mbsout.pm blib/lib/Bio/SeqIO/mbsout.pm +cp lib/Bio/SeqIO/raw.pm blib/lib/Bio/SeqIO/raw.pm cp lib/Bio/SeqIO/tinyseq.pm blib/lib/Bio/SeqIO/tinyseq.pm -cp lib/Bio/SeqIO/gcg.pm blib/lib/Bio/SeqIO/gcg.pm -cp lib/Bio/Tools/Alignment/Trim.pm blib/lib/Bio/Tools/Alignment/Trim.pm -cp lib/Bio/SeqIO/game/gameHandler.pm blib/lib/Bio/SeqIO/game/gameHandler.pm -cp lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm blib/lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm -cp lib/Bio/Tools/Genscan.pm blib/lib/Bio/Tools/Genscan.pm -cp lib/Bio/Tools/Coil.pm blib/lib/Bio/Tools/Coil.pm +cp lib/Bio/SeqIO/genbank.pm blib/lib/Bio/SeqIO/genbank.pm +cp lib/Bio/SimpleAlign.pm blib/lib/Bio/SimpleAlign.pm +cp lib/Bio/SeqIO/game.pm blib/lib/Bio/SeqIO/game.pm +cp lib/Bio/Tools/CodonTable.pm blib/lib/Bio/Tools/CodonTable.pm +cp lib/Bio/Tools/EMBOSS/Palindrome.pm blib/lib/Bio/Tools/EMBOSS/Palindrome.pm +cp lib/Bio/Tools/Genomewise.pm blib/lib/Bio/Tools/Genomewise.pm +cp lib/Bio/Tools/Est2Genome.pm blib/lib/Bio/Tools/Est2Genome.pm +cp lib/Bio/Tools/Eponine.pm blib/lib/Bio/Tools/Eponine.pm +cp lib/Bio/Tools/PrositeScan.pm blib/lib/Bio/Tools/PrositeScan.pm cp lib/Bio/Tools/OddCodes.pm blib/lib/Bio/Tools/OddCodes.pm -cp lib/Bio/Tools/Genemark.pm blib/lib/Bio/Tools/Genemark.pm -cp lib/Bio/Tools/Geneid.pm blib/lib/Bio/Tools/Geneid.pm +cp lib/Bio/Tools/Lucy.pm blib/lib/Bio/Tools/Lucy.pm +cp lib/Bio/Tools/Fgenesh.pm blib/lib/Bio/Tools/Fgenesh.pm +cp lib/Bio/Tools/Grail.pm blib/lib/Bio/Tools/Grail.pm +cp lib/Bio/Tools/Phylo/Molphy.pm blib/lib/Bio/Tools/Phylo/Molphy.pm +cp lib/Bio/Tools/Primer/Pair.pm blib/lib/Bio/Tools/Primer/Pair.pm +cp lib/Bio/Tools/Phylo/Molphy/Result.pm blib/lib/Bio/Tools/Phylo/Molphy/Result.pm +cp lib/Bio/Tools/Promoterwise.pm blib/lib/Bio/Tools/Promoterwise.pm +cp lib/Bio/Tools/EPCR.pm blib/lib/Bio/Tools/EPCR.pm +cp lib/Bio/Tools/Primer/Feature.pm blib/lib/Bio/Tools/Primer/Feature.pm +cp lib/Bio/Tools/Primer3.pm blib/lib/Bio/Tools/Primer3.pm cp lib/Bio/Tools/Phylo/Gerp.pm blib/lib/Bio/Tools/Phylo/Gerp.pm -cp lib/Bio/Tools/GuessSeqFormat.pm blib/lib/Bio/Tools/GuessSeqFormat.pm -cp lib/Bio/Tools/Prints.pm blib/lib/Bio/Tools/Prints.pm +cp lib/Bio/Tools/Prediction/Gene.pm blib/lib/Bio/Tools/Prediction/Gene.pm +cp lib/Bio/Tools/Primer/Assessor/Base.pm blib/lib/Bio/Tools/Primer/Assessor/Base.pm +cp lib/Bio/Tools/Genscan.pm blib/lib/Bio/Tools/Genscan.pm cp lib/Bio/Tools/MZEF.pm blib/lib/Bio/Tools/MZEF.pm -cp lib/Bio/Tools/Match.pm blib/lib/Bio/Tools/Match.pm -cp lib/Bio/Tools/Genomewise.pm blib/lib/Bio/Tools/Genomewise.pm cp lib/Bio/Tools/Pseudowise.pm blib/lib/Bio/Tools/Pseudowise.pm -cp lib/Bio/Tools/Promoterwise.pm blib/lib/Bio/Tools/Promoterwise.pm -cp lib/Bio/Tools/Phylo/Phylip/ProtDist.pm blib/lib/Bio/Tools/Phylo/Phylip/ProtDist.pm cp lib/Bio/Tools/Glimmer.pm blib/lib/Bio/Tools/Glimmer.pm -cp lib/Bio/Tools/EPCR.pm blib/lib/Bio/Tools/EPCR.pm -cp lib/Bio/Tools/Eponine.pm blib/lib/Bio/Tools/Eponine.pm +cp lib/Bio/Tools/Prints.pm blib/lib/Bio/Tools/Prints.pm +cp lib/Bio/Tools/Prediction/Exon.pm blib/lib/Bio/Tools/Prediction/Exon.pm +cp lib/Bio/Tools/Genewise.pm blib/lib/Bio/Tools/Genewise.pm +cp lib/Bio/Tools/Genemark.pm blib/lib/Bio/Tools/Genemark.pm +cp lib/Bio/Tools/Phylo/Phylip/ProtDist.pm blib/lib/Bio/Tools/Phylo/Phylip/ProtDist.pm cp lib/Bio/Tools/FootPrinter.pm blib/lib/Bio/Tools/FootPrinter.pm -cp lib/Bio/Tools/Phylo/Molphy/Result.pm blib/lib/Bio/Tools/Phylo/Molphy/Result.pm +cp lib/Bio/Tools/Primer/AssessorI.pm blib/lib/Bio/Tools/Primer/AssessorI.pm cp lib/Bio/Tools/ESTScan.pm blib/lib/Bio/Tools/ESTScan.pm +cp lib/Bio/Tools/Coil.pm blib/lib/Bio/Tools/Coil.pm +cp lib/Bio/Tools/Geneid.pm blib/lib/Bio/Tools/Geneid.pm cp lib/Bio/Tools/GFF.pm blib/lib/Bio/Tools/GFF.pm -cp lib/Bio/Tools/Prediction/Exon.pm blib/lib/Bio/Tools/Prediction/Exon.pm -cp lib/Bio/Tools/Primer/Feature.pm blib/lib/Bio/Tools/Primer/Feature.pm -cp lib/Bio/Tools/Est2Genome.pm blib/lib/Bio/Tools/Est2Genome.pm -cp lib/Bio/Tools/IUPAC.pm blib/lib/Bio/Tools/IUPAC.pm -cp lib/Bio/Tools/Genewise.pm blib/lib/Bio/Tools/Genewise.pm -cp lib/Bio/Tools/Primer3.pm blib/lib/Bio/Tools/Primer3.pm +cp lib/Bio/Tools/GuessSeqFormat.pm blib/lib/Bio/Tools/GuessSeqFormat.pm cp lib/Bio/Tools/ECnumber.pm blib/lib/Bio/Tools/ECnumber.pm -cp lib/Bio/Tools/Prediction/Gene.pm blib/lib/Bio/Tools/Prediction/Gene.pm +cp lib/Bio/Tools/IUPAC.pm blib/lib/Bio/Tools/IUPAC.pm +cp lib/Bio/Tools/Match.pm blib/lib/Bio/Tools/Match.pm cp lib/Bio/Tools/Profile.pm blib/lib/Bio/Tools/Profile.pm -cp lib/Bio/Tools/CodonTable.pm blib/lib/Bio/Tools/CodonTable.pm -cp lib/Bio/Tools/Primer/AssessorI.pm blib/lib/Bio/Tools/Primer/AssessorI.pm -cp lib/Bio/Tools/PrositeScan.pm blib/lib/Bio/Tools/PrositeScan.pm -cp lib/Bio/Tools/Grail.pm blib/lib/Bio/Tools/Grail.pm -cp lib/Bio/Tools/Phylo/Molphy.pm blib/lib/Bio/Tools/Phylo/Molphy.pm -cp lib/Bio/Tools/Primer/Pair.pm blib/lib/Bio/Tools/Primer/Pair.pm -cp lib/Bio/Tools/Lucy.pm blib/lib/Bio/Tools/Lucy.pm -cp lib/Bio/Tools/EMBOSS/Palindrome.pm blib/lib/Bio/Tools/EMBOSS/Palindrome.pm -cp lib/Bio/Tools/Fgenesh.pm blib/lib/Bio/Tools/Fgenesh.pm -cp lib/Bio/Tools/Primer/Assessor/Base.pm blib/lib/Bio/Tools/Primer/Assessor/Base.pm +cp lib/Bio/Tools/Spidey/Exon.pm blib/lib/Bio/Tools/Spidey/Exon.pm cp lib/Bio/Tree/NodeI.pm blib/lib/Bio/Tree/NodeI.pm +cp lib/Bio/Tools/Signalp/ExtendedSignalp.pm blib/lib/Bio/Tools/Signalp/ExtendedSignalp.pm +cp lib/Bio/Tools/Run/WrapperBase/CommandExts.pm blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm +cp lib/Bio/Tree/Node.pm blib/lib/Bio/Tree/Node.pm +cp lib/Bio/Tools/Spidey/Results.pm blib/lib/Bio/Tools/Spidey/Results.pm +cp lib/Bio/Tools/Run/WrapperBase.pm blib/lib/Bio/Tools/Run/WrapperBase.pm +cp lib/Bio/Tools/TargetP.pm blib/lib/Bio/Tools/TargetP.pm +cp lib/Bio/Tools/SeqPattern/Backtranslate.pm blib/lib/Bio/Tools/SeqPattern/Backtranslate.pm +cp lib/Bio/Tools/tRNAscanSE.pm blib/lib/Bio/Tools/tRNAscanSE.pm +cp lib/Bio/Tree/AnnotatableNode.pm blib/lib/Bio/Tree/AnnotatableNode.pm +cp lib/Bio/Tools/Run/AnalysisFactory.pm blib/lib/Bio/Tools/Run/AnalysisFactory.pm cp lib/Bio/Tools/SeqPattern.pm blib/lib/Bio/Tools/SeqPattern.pm cp lib/Bio/Tree/Statistics.pm blib/lib/Bio/Tree/Statistics.pm -cp lib/Bio/Tools/RepeatMasker.pm blib/lib/Bio/Tools/RepeatMasker.pm -cp lib/Bio/Tree/AnnotatableNode.pm blib/lib/Bio/Tree/AnnotatableNode.pm -cp lib/Bio/Tools/isPcr.pm blib/lib/Bio/Tools/isPcr.pm +cp lib/Bio/Tools/Run/ParametersI.pm blib/lib/Bio/Tools/Run/ParametersI.pm +cp lib/Bio/Tools/Sigcleave.pm blib/lib/Bio/Tools/Sigcleave.pm cp lib/Bio/Tree/Compatible.pm blib/lib/Bio/Tree/Compatible.pm -cp lib/Bio/Tools/TargetP.pm blib/lib/Bio/Tools/TargetP.pm +cp lib/Bio/Tools/isPcr.pm blib/lib/Bio/Tools/isPcr.pm cp lib/Bio/Tools/pICalculator.pm blib/lib/Bio/Tools/pICalculator.pm -cp lib/Bio/Tools/Run/ParametersI.pm blib/lib/Bio/Tools/Run/ParametersI.pm -cp lib/Bio/Tools/Spidey/Results.pm blib/lib/Bio/Tools/Spidey/Results.pm -cp lib/Bio/Tools/SeqPattern/Backtranslate.pm blib/lib/Bio/Tools/SeqPattern/Backtranslate.pm -cp lib/Bio/Tools/Run/Analysis.pm blib/lib/Bio/Tools/Run/Analysis.pm -cp lib/Bio/Tree/Tree.pm blib/lib/Bio/Tree/Tree.pm -cp lib/Bio/Tools/TandemRepeatsFinder.pm blib/lib/Bio/Tools/TandemRepeatsFinder.pm -cp lib/Bio/Tools/Spidey/Exon.pm blib/lib/Bio/Tools/Spidey/Exon.pm -cp lib/Bio/Tree/Node.pm blib/lib/Bio/Tree/Node.pm -cp lib/Bio/Tools/Run/GenericParameters.pm blib/lib/Bio/Tools/Run/GenericParameters.pm -cp lib/Bio/Tools/Signalp.pm blib/lib/Bio/Tools/Signalp.pm -cp lib/Bio/Tools/RandomDistFunctions.pm blib/lib/Bio/Tools/RandomDistFunctions.pm -cp lib/Bio/Tools/tRNAscanSE.pm blib/lib/Bio/Tools/tRNAscanSE.pm -cp lib/Bio/Tools/SeqWords.pm blib/lib/Bio/Tools/SeqWords.pm +cp lib/Bio/Tools/QRNA.pm blib/lib/Bio/Tools/QRNA.pm cp lib/Bio/Tools/Tmhmm.pm blib/lib/Bio/Tools/Tmhmm.pm cp lib/Bio/Tree/RandomFactory.pm blib/lib/Bio/Tree/RandomFactory.pm -cp lib/Bio/Tools/ipcress.pm blib/lib/Bio/Tools/ipcress.pm -cp lib/Bio/Tools/Sim4/Exon.pm blib/lib/Bio/Tools/Sim4/Exon.pm -cp lib/Bio/Tools/Run/AnalysisFactory.pm blib/lib/Bio/Tools/Run/AnalysisFactory.pm +cp lib/Bio/Tree/NodeNHX.pm blib/lib/Bio/Tree/NodeNHX.pm +cp lib/Bio/Tools/TandemRepeatsFinder.pm blib/lib/Bio/Tools/TandemRepeatsFinder.pm +cp lib/Bio/Tools/RandomDistFunctions.pm blib/lib/Bio/Tools/RandomDistFunctions.pm cp lib/Bio/Tools/Run/Phylo/PhyloBase.pm blib/lib/Bio/Tools/Run/Phylo/PhyloBase.pm -cp lib/Bio/Tools/Run/WrapperBase.pm blib/lib/Bio/Tools/Run/WrapperBase.pm -cp lib/Bio/Tools/Run/WrapperBase/CommandExts.pm blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm -cp lib/Bio/Tools/Seg.pm blib/lib/Bio/Tools/Seg.pm -cp lib/Bio/Tools/Sigcleave.pm blib/lib/Bio/Tools/Sigcleave.pm -cp lib/Bio/Tools/Signalp/ExtendedSignalp.pm blib/lib/Bio/Tools/Signalp/ExtendedSignalp.pm -cp lib/Bio/Tools/QRNA.pm blib/lib/Bio/Tools/QRNA.pm +cp lib/Bio/Tools/ipcress.pm blib/lib/Bio/Tools/ipcress.pm +cp lib/Bio/Tools/SeqWords.pm blib/lib/Bio/Tools/SeqWords.pm cp lib/Bio/Tools/Sim4/Results.pm blib/lib/Bio/Tools/Sim4/Results.pm +cp lib/Bio/Tools/Run/GenericParameters.pm blib/lib/Bio/Tools/Run/GenericParameters.pm +cp lib/Bio/Tools/Run/Analysis.pm blib/lib/Bio/Tools/Run/Analysis.pm +cp lib/Bio/Tools/Signalp.pm blib/lib/Bio/Tools/Signalp.pm +cp lib/Bio/Tools/Sim4/Exon.pm blib/lib/Bio/Tools/Sim4/Exon.pm +cp lib/Bio/Tree/Tree.pm blib/lib/Bio/Tree/Tree.pm cp lib/Bio/Tools/SeqStats.pm blib/lib/Bio/Tools/SeqStats.pm +cp lib/Bio/Tools/Seg.pm blib/lib/Bio/Tools/Seg.pm cp lib/Bio/Tree/DistanceFactory.pm blib/lib/Bio/Tree/DistanceFactory.pm -cp lib/Bio/Tree/NodeNHX.pm blib/lib/Bio/Tree/NodeNHX.pm +cp lib/Bio/Tools/RepeatMasker.pm blib/lib/Bio/Tools/RepeatMasker.pm +cp lib/Bio/TreeIO/phyloxml.pm blib/lib/Bio/TreeIO/phyloxml.pm +cp lib/Bio/TreeIO/pag.pm blib/lib/Bio/TreeIO/pag.pm +cp lib/Bio/TreeIO/NewickParser.pm blib/lib/Bio/TreeIO/NewickParser.pm +cp lib/Bio/UpdateableSeqI.pm blib/lib/Bio/UpdateableSeqI.pm cp lib/Bio/TreeIO/tabtree.pm blib/lib/Bio/TreeIO/tabtree.pm -cp lib/Bio/Tree/TreeFunctionsI.pm blib/lib/Bio/Tree/TreeFunctionsI.pm +cp lib/Bio/TreeIO/lintree.pm blib/lib/Bio/TreeIO/lintree.pm +cp lib/Bio/WebAgent.pm blib/lib/Bio/WebAgent.pm cp lib/Bio/TreeIO/newick.pm blib/lib/Bio/TreeIO/newick.pm +cp lib/Bio/TreeIO/nexus.pm blib/lib/Bio/TreeIO/nexus.pm +cp lib/Bio/TreeIO.pm blib/lib/Bio/TreeIO.pm cp lib/Bio/TreeIO/cluster.pm blib/lib/Bio/TreeIO/cluster.pm +cp lib/Bio/TreeIO/TreeEventBuilder.pm blib/lib/Bio/TreeIO/TreeEventBuilder.pm cp lib/BioPerl.pm blib/lib/BioPerl.pm cp lib/Bio/Tree/TreeI.pm blib/lib/Bio/Tree/TreeI.pm -cp lib/Bio/TreeIO/TreeEventBuilder.pm blib/lib/Bio/TreeIO/TreeEventBuilder.pm -cp lib/Bio/TreeIO.pm blib/lib/Bio/TreeIO.pm -cp lib/Bio/TreeIO/NewickParser.pm blib/lib/Bio/TreeIO/NewickParser.pm -cp lib/Bio/WebAgent.pm blib/lib/Bio/WebAgent.pm cp lib/Bio/TreeIO/nhx.pm blib/lib/Bio/TreeIO/nhx.pm -cp lib/Bio/TreeIO/pag.pm blib/lib/Bio/TreeIO/pag.pm -cp lib/Bio/TreeIO/nexus.pm blib/lib/Bio/TreeIO/nexus.pm -cp lib/Bio/UpdateableSeqI.pm blib/lib/Bio/UpdateableSeqI.pm -cp lib/Bio/TreeIO/lintree.pm blib/lib/Bio/TreeIO/lintree.pm -cp lib/Bio/TreeIO/phyloxml.pm blib/lib/Bio/TreeIO/phyloxml.pm +cp lib/Bio/Tree/TreeFunctionsI.pm blib/lib/Bio/Tree/TreeFunctionsI.pm cp bin/bp_aacomp blib/script/bp_aacomp -cp bin/bp_bioflat_index blib/script/bp_bioflat_index "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_aacomp +cp bin/bp_bioflat_index blib/script/bp_bioflat_index +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_bioflat_index cp bin/bp_biogetseq blib/script/bp_biogetseq +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_biogetseq cp bin/bp_dbsplit blib/script/bp_dbsplit cp bin/bp_extract_feature_seq blib/script/bp_extract_feature_seq -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_bioflat_index -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_biogetseq "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_dbsplit -cp bin/bp_fastam9_to_table blib/script/bp_fastam9_to_table "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_extract_feature_seq -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_fastam9_to_table +cp bin/bp_fastam9_to_table blib/script/bp_fastam9_to_table cp bin/bp_fetch blib/script/bp_fetch +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_fastam9_to_table "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_fetch cp bin/bp_filter_search blib/script/bp_filter_search -cp bin/bp_find-blast-matches blib/script/bp_find-blast-matches "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_filter_search -cp bin/bp_gccalc blib/script/bp_gccalc +cp bin/bp_find-blast-matches blib/script/bp_find-blast-matches "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_find-blast-matches +cp bin/bp_gccalc blib/script/bp_gccalc "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_gccalc cp bin/bp_genbank2gff3 blib/script/bp_genbank2gff3 -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_genbank2gff3 cp bin/bp_index blib/script/bp_index +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_genbank2gff3 "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_index cp bin/bp_local_taxonomydb_query blib/script/bp_local_taxonomydb_query -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_local_taxonomydb_query cp bin/bp_make_mrna_protein blib/script/bp_make_mrna_protein +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_local_taxonomydb_query "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_make_mrna_protein cp bin/bp_mask_by_search blib/script/bp_mask_by_search -cp bin/bp_mrtrans blib/script/bp_mrtrans "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mask_by_search +cp bin/bp_mrtrans blib/script/bp_mrtrans "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mrtrans cp bin/bp_mutate blib/script/bp_mutate "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mutate cp bin/bp_nexus2nh blib/script/bp_nexus2nh "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_nexus2nh cp bin/bp_nrdb blib/script/bp_nrdb +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_nrdb cp bin/bp_oligo_count blib/script/bp_oligo_count cp bin/bp_process_gadfly blib/script/bp_process_gadfly -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_nrdb "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_oligo_count "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_process_gadfly cp bin/bp_process_sgd blib/script/bp_process_sgd @@ -2068,8 +2104,8 @@ cp bin/bp_revtrans-motif blib/script/bp_revtrans-motif "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_revtrans-motif cp bin/bp_search2alnblocks blib/script/bp_search2alnblocks -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2alnblocks cp bin/bp_search2gff blib/script/bp_search2gff +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2alnblocks "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2gff cp bin/bp_search2table blib/script/bp_search2table "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2table @@ -2082,22 +2118,22 @@ cp bin/bp_seqcut blib/script/bp_seqcut "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqcut cp bin/bp_seqpart blib/script/bp_seqpart -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqpart cp bin/bp_seqret blib/script/bp_seqret +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqpart "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqret cp bin/bp_seqretsplit blib/script/bp_seqretsplit "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqretsplit cp bin/bp_split_seq blib/script/bp_split_seq "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_split_seq cp bin/bp_sreformat blib/script/bp_sreformat -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_sreformat cp bin/bp_taxid4species blib/script/bp_taxid4species +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_sreformat "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_taxid4species cp bin/bp_taxonomy2tree blib/script/bp_taxonomy2tree -cp bin/bp_translate_seq blib/script/bp_translate_seq "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_taxonomy2tree -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_translate_seq +cp bin/bp_translate_seq blib/script/bp_translate_seq cp bin/bp_tree2pag blib/script/bp_tree2pag +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_translate_seq "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_tree2pag cp bin/bp_unflatten_seq blib/script/bp_unflatten_seq "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_unflatten_seq @@ -2980,31 +3016,31 @@ 1..27 ok 1 - use Bio::AlignIO; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::AnnotatableI' -ok 3 - input filehandle method test : psi +ok 3 - input filehandle method test : clustalw ok 4 - input filehandle method test : nexus -ok 5 - input filehandle method test : fasta -ok 6 - input filehandle method test : phylip -ok 7 - input filehandle method test : prodom -ok 8 - input filehandle method test : po -ok 9 - input filehandle method test : msf -ok 10 - input filehandle method test : metafasta -ok 11 - input filehandle method test : xmfa -ok 12 - input filehandle method test : selex -ok 13 - input filehandle method test : arp -ok 14 - input filehandle method test : mase +ok 5 - input filehandle method test : psi +ok 6 - input filehandle method test : msf +ok 7 - input filehandle method test : selex +ok 8 - input filehandle method test : metafasta +ok 9 - input filehandle method test : mase +ok 10 - input filehandle method test : fasta +ok 11 - input filehandle method test : arp +ok 12 - input filehandle method test : xmfa +ok 13 - input filehandle method test : phylip +ok 14 - input filehandle method test : po ok 15 - input filehandle method test : pfam -ok 16 - input filehandle method test : clustalw -ok 17 - filehandle output test : psi +ok 16 - input filehandle method test : prodom +ok 17 - filehandle output test : clustalw ok 18 - filehandle output test : nexus -ok 19 - filehandle output test : fasta -ok 20 - filehandle output test : phylip -ok 21 - filehandle output test : po -ok 22 - filehandle output test : msf -ok 23 - filehandle output test : metafasta +ok 19 - filehandle output test : psi +ok 20 - filehandle output test : msf +ok 21 - filehandle output test : selex +ok 22 - filehandle output test : metafasta +ok 23 - filehandle output test : fasta ok 24 - filehandle output test : xmfa -ok 25 - filehandle output test : selex -ok 26 - filehandle output test : pfam -ok 27 - filehandle output test : clustalw +ok 25 - filehandle output test : phylip +ok 26 - filehandle output test : po +ok 27 - filehandle output test : pfam ok t/AlignIO/arp.t ..................... 1..48 @@ -4422,25 +4458,25 @@ ok 17 - to_string looks reasonable ok 18 - There are 8 root InterPro terms ok 19 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 20 - term Kringle in ontology InterPro +ok 20 - term Region in ontology InterPro ok 21 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 22 - term Region in ontology InterPro +ok 22 - term Helix-turn-helix, AraC type in ontology InterPro ok 23 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 24 - term Conserved Site in ontology InterPro +ok 24 - term Repeat in ontology InterPro ok 25 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 26 - term Helix-turn-helix, AraC type in ontology InterPro +ok 26 - term post-translational modification in ontology InterPro ok 27 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 28 - term Repeat in ontology InterPro +ok 28 - term Conserved Site in ontology InterPro ok 29 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 30 - term Integrins alpha chain in ontology InterPro +ok 30 - term Binding Site in ontology InterPro ok 31 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 32 - term Binding Site in ontology InterPro +ok 32 - term Cdc20/Fizzy in ontology InterPro ok 33 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 34 - term Cdc20/Fizzy in ontology InterPro +ok 34 - term Integrins alpha chain in ontology InterPro ok 35 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 36 - term post-translational modification in ontology InterPro +ok 36 - term Active Site in ontology InterPro ok 37 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 38 - term Active Site in ontology InterPro +ok 38 - term Kringle in ontology InterPro ok 39 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 40 - term Active Site in ontology InterPro ok 41 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' @@ -4463,14 +4499,14 @@ ok 58 ok 59 ok 60 -ok 61 - Kringle term has one parent -ok 62 - Kringle term has one ancestor -ok 63 - Helix-turn-helix, AraC type term has one parent -ok 64 - Helix-turn-helix, AraC type term has one ancestor +ok 61 - Helix-turn-helix, AraC type term has one parent +ok 62 - Helix-turn-helix, AraC type term has one ancestor +ok 63 - Cdc20/Fizzy term has one parent +ok 64 - Cdc20/Fizzy term has one ancestor ok 65 - Integrins alpha chain term has one parent ok 66 - Integrins alpha chain term has one ancestor -ok 67 - Cdc20/Fizzy term has one parent -ok 68 - Cdc20/Fizzy term has one ancestor +ok 67 - Kringle term has one parent +ok 68 - Kringle term has one ancestor ok 69 - secondary accession map has 2 keys ok t/Ontology/IO/obo.t ................. @@ -6366,24 +6402,24 @@ ok 1080 ok 1081 ok 1082 -ok 1083 - blast for fast.bls -ok 1084 - exonerate for f.exon -ok 1085 - fasta for f.m9 -ok 1086 - fasta for f.fasta -ok 1087 - blastxml for f.xml -ok 1088 - blast for filename.bls -ok 1089 - blastxml for f.blastxml -ok 1090 - fasta for f.SSEARCH.m9 -ok 1091 - blast for f.tblx -ok 1092 - exonerate for f.exonerate -ok 1093 - fasta for f.osearch -ok 1094 - blast for filename.blast -ok 1095 - fasta for f.fa -ok 1096 - fasta for f.fx -ok 1097 - blast for f.blx -ok 1098 - fasta for f.psearch -ok 1099 - fasta for f.fy -ok 1100 - fasta for f.ssearch +ok 1083 - blastxml for f.blastxml +ok 1084 - fasta for f.SSEARCH.m9 +ok 1085 - exonerate for f.exon +ok 1086 - fasta for f.psearch +ok 1087 - blast for filename.bls +ok 1088 - fasta for f.fa +ok 1089 - blast for fast.bls +ok 1090 - fasta for f.ssearch +ok 1091 - fasta for f.fy +ok 1092 - fasta for f.m9 +ok 1093 - blast for f.tblx +ok 1094 - exonerate for f.exonerate +ok 1095 - fasta for f.fx +ok 1096 - blast for f.blx +ok 1097 - fasta for f.fasta +ok 1098 - fasta for f.osearch +ok 1099 - blastxml for f.xml +ok 1100 - blast for filename.blast ok 1101 ok 1102 ok 1103 @@ -8332,24 +8368,24 @@ t/SearchIO/SearchIO.t ............... 1..19 ok 1 - use Bio::SearchIO; -ok 2 - blast for filename.blast -ok 3 - blast for f.tblx -ok 4 - fasta for f.osearch -ok 5 - fasta for f.fx -ok 6 - blast for f.blx -ok 7 - fasta for f.fasta -ok 8 - blast for filename.bls -ok 9 - fasta for f.fa -ok 10 - exonerate for f.exonerate -ok 11 - fasta for f.ssearch -ok 12 - fasta for f.SSEARCH.m9 -ok 13 - exonerate for f.exon -ok 14 - fasta for f.fy -ok 15 - blastxml for f.xml -ok 16 - fasta for f.m9 -ok 17 - blastxml for f.blastxml -ok 18 - fasta for f.psearch -ok 19 - blast for fast.bls +ok 2 - blastxml for f.xml +ok 3 - exonerate for f.exonerate +ok 4 - blastxml for f.blastxml +ok 5 - fasta for f.fa +ok 6 - exonerate for f.exon +ok 7 - fasta for f.SSEARCH.m9 +ok 8 - blast for f.blx +ok 9 - fasta for f.psearch +ok 10 - blast for f.tblx +ok 11 - fasta for f.osearch +ok 12 - blast for filename.blast +ok 13 - fasta for f.fasta +ok 14 - fasta for f.fx +ok 15 - blast for fast.bls +ok 16 - fasta for f.fy +ok 17 - blast for filename.bls +ok 18 - fasta for f.m9 +ok 19 - fasta for f.ssearch ok t/SearchIO/sim4.t ................... 1..102 @@ -9385,14 +9421,14 @@ ok 910 - h cn: exact (0.92885) <= max (0.92885) ok 911 - bl2seq.blastx.out ok 912 - tile bl2seq.blastx.out hit 1 \#hsps 6 -ok 913 - q id: est (0.71429) = fast (0.71429) -ok 914 - q cn: est (1.00000) = fast (1.00000) -ok 915 - q id: est (0.35714) = fast (0.35714) -ok 916 - q cn: est (0.57143) = fast (0.57143) -ok 917 - q id: exact (0.70536) ~ est (0.70495) -ok 918 - q id: exact (0.70536) <= max (0.94286) -ok 919 - q cn: exact (0.78810) ~ est (0.78803) -ok 920 - q cn: exact (0.78810) <= max (0.96429) +ok 913 - q id: exact (0.70536) ~ est (0.70495) +ok 914 - q id: exact (0.70536) <= max (0.94286) +ok 915 - q cn: exact (0.78810) ~ est (0.78803) +ok 916 - q cn: exact (0.78810) <= max (0.96429) +ok 917 - q id: est (0.71429) = fast (0.71429) +ok 918 - q cn: est (1.00000) = fast (1.00000) +ok 919 - q id: est (0.35714) = fast (0.35714) +ok 920 - q cn: est (0.57143) = fast (0.57143) ok 921 - h id: exact (0.61923) ~ est (0.61955) ok 922 - h id: exact (0.61923) <= max (0.64231) ok 923 - h cn: exact (0.73077) ~ est (0.73077) @@ -9418,10 +9454,10 @@ ok 943 - q id: exact (0.68750) <= max (0.68750) ok 944 - q cn: exact (0.81250) ~ est (0.81250) ok 945 - q cn: exact (0.81250) <= max (0.81250) -ok 946 - h id: est (0.66667) = fast (0.66667) -ok 947 - h cn: est (0.77778) = fast (0.77778) -ok 948 - h id: est (0.71429) = fast (0.71429) -ok 949 - h cn: est (0.85714) = fast (0.85714) +ok 946 - h id: est (0.71429) = fast (0.71429) +ok 947 - h cn: est (0.85714) = fast (0.85714) +ok 948 - h id: est (0.66667) = fast (0.66667) +ok 949 - h cn: est (0.77778) = fast (0.77778) ok 950 - dnaEbsub_ecoli.wutblastn ok 951 - tile dnaEbsub_ecoli.wutblastn hit 1 \#hsps 1 ok 952 - q id: est (0.36386) = fast (0.36386) @@ -9535,37 +9571,37 @@ ok 1060 - h cn: est (0.60000) = fast (0.60000) ok 1061 - dnaEbsub_ecoli.wutblastx ok 1062 - tile dnaEbsub_ecoli.wutblastx hit 1 \#hsps 12 -ok 1063 - q id: exact (0.40224) ~ est (0.40912) -ok 1064 - q id: exact (0.40224) <= max (0.42628) -ok 1065 - q cn: exact (0.58494) ~ est (0.58968) -ok 1066 - q cn: exact (0.58494) <= max (0.62179) -ok 1067 - q id: exact (0.44118) ~ est (0.44118) -ok 1068 - q id: exact (0.44118) <= max (0.44118) -ok 1069 - q cn: exact (0.54412) ~ est (0.54412) -ok 1070 - q cn: exact (0.54412) <= max (0.54412) -ok 1071 - q id: est (0.25352) = fast (0.25352) -ok 1072 - q cn: est (0.47887) = fast (0.47887) -ok 1073 - q id: est (0.37500) = fast (0.37500) -ok 1074 - q cn: est (0.62500) = fast (0.62500) -ok 1075 - h id: exact (0.44118) ~ est (0.44118) -ok 1076 - h id: exact (0.44118) <= max (0.44118) -ok 1077 - h cn: exact (0.54412) ~ est (0.54412) -ok 1078 - h cn: exact (0.54412) <= max (0.54412) -ok 1079 - h id: est (0.25352) = fast (0.25352) -ok 1080 - h cn: est (0.47887) = fast (0.47887) -ok 1081 - h id: exact (0.39848) ~ est (0.40304) -ok 1082 - h id: exact (0.39848) <= max (0.40355) -ok 1083 - h cn: exact (0.58376) ~ est (0.58889) -ok 1084 - h cn: exact (0.58376) <= max (0.58883) +ok 1063 - q id: est (0.25352) = fast (0.25352) +ok 1064 - q cn: est (0.47887) = fast (0.47887) +ok 1065 - q id: est (0.37500) = fast (0.37500) +ok 1066 - q cn: est (0.62500) = fast (0.62500) +ok 1067 - q id: exact (0.40224) ~ est (0.40912) +ok 1068 - q id: exact (0.40224) <= max (0.42628) +ok 1069 - q cn: exact (0.58494) ~ est (0.58968) +ok 1070 - q cn: exact (0.58494) <= max (0.62179) +ok 1071 - q id: exact (0.44118) ~ est (0.44118) +ok 1072 - q id: exact (0.44118) <= max (0.44118) +ok 1073 - q cn: exact (0.54412) ~ est (0.54412) +ok 1074 - q cn: exact (0.54412) <= max (0.54412) +ok 1075 - h id: est (0.25352) = fast (0.25352) +ok 1076 - h cn: est (0.47887) = fast (0.47887) +ok 1077 - h id: exact (0.39848) ~ est (0.40304) +ok 1078 - h id: exact (0.39848) <= max (0.40355) +ok 1079 - h cn: exact (0.58376) ~ est (0.58889) +ok 1080 - h cn: exact (0.58376) <= max (0.58883) +ok 1081 - h id: exact (0.44118) ~ est (0.44118) +ok 1082 - h id: exact (0.44118) <= max (0.44118) +ok 1083 - h cn: exact (0.54412) ~ est (0.54412) +ok 1084 - h cn: exact (0.54412) <= max (0.54412) ok 1085 - tile dnaEbsub_ecoli.wutblastx hit 2 \#hsps 2 ok 1086 - q id: exact (0.41818) ~ est (0.41818) ok 1087 - q id: exact (0.41818) <= max (0.41818) ok 1088 - q cn: exact (0.52727) ~ est (0.52727) ok 1089 - q cn: exact (0.52727) <= max (0.52727) -ok 1090 - h id: est (0.53333) = fast (0.53333) -ok 1091 - h cn: est (0.66667) = fast (0.66667) -ok 1092 - h id: est (0.37500) = fast (0.37500) -ok 1093 - h cn: est (0.47500) = fast (0.47500) +ok 1090 - h id: est (0.37500) = fast (0.37500) +ok 1091 - h cn: est (0.47500) = fast (0.47500) +ok 1092 - h id: est (0.53333) = fast (0.53333) +ok 1093 - h cn: est (0.66667) = fast (0.66667) ok 1094 - bug2942: query m0: range correct ok 1095 - bug2942: query m1: range correct ok 1096 - bug2942: query m2: range correct @@ -9997,7 +10033,7 @@ ok 19 not ok 20 # TODO Need to fix columns before start of seq w/ start > 1 # Failed (TODO) test at t/Seq/LocatableSeq.t line 46. -# got: 'Bio::Location::Simple=HASH(0xaaaac806c4e8)' +# got: 'Bio::Location::Simple=HASH(0xaaaad4fdec30)' # expected: undef ok 21 ok 22 - An object of class 'Bio::AlignIO::pfam' isa 'Bio::AlignIO' @@ -11691,7 +11727,7 @@ ok 9 ok 10 ok 11 -ok 12 - Location String: ?..? +ok 12 - Location String: 145^177 ok 13 ok 14 - Bio::Location::Fuzzy ok 15 @@ -11702,9 +11738,9 @@ ok 20 ok 21 ok 22 -ok 23 - Location String: (122.133)..(204.221) +ok 23 - Location String: (23.45)..600 ok 24 -ok 25 - Bio::Location::Simple +ok 25 - Bio::Location::Fuzzy ok 26 ok 27 ok 28 @@ -11713,7 +11749,7 @@ ok 31 ok 32 ok 33 -ok 34 - Location String: J00194:100..202 +ok 34 - Location String: ?..? ok 35 ok 36 - Bio::Location::Fuzzy ok 37 @@ -11724,7 +11760,7 @@ ok 42 ok 43 ok 44 -ok 45 - Location String: <1..888 +ok 45 - Location String: 1..>888 ok 46 ok 47 - Bio::Location::Fuzzy ok 48 @@ -11735,9 +11771,9 @@ ok 53 ok 54 ok 55 -ok 56 - Location String: ?1..12 +ok 56 - Location String: (122.133)..(204.221) ok 57 -ok 58 - Bio::Location::Fuzzy +ok 58 - Bio::Location::Simple ok 59 ok 60 ok 61 @@ -11746,7 +11782,7 @@ ok 64 ok 65 ok 66 -ok 67 - Location String: ?22..?64 +ok 67 - Location String: 467 ok 68 ok 69 - Bio::Location::Fuzzy ok 70 @@ -11757,7 +11793,7 @@ ok 75 ok 76 ok 77 -ok 78 - Location String: (23.45)..600 +ok 78 - Location String: ?22..?64 ok 79 ok 80 - Bio::Location::Simple ok 81 @@ -11770,7 +11806,7 @@ ok 88 ok 89 - Location String: J00194:100..202 ok 90 -ok 91 - Bio::Location::Split +ok 91 - Bio::Location::Fuzzy ok 92 ok 93 ok 94 @@ -11779,7 +11815,7 @@ ok 97 ok 98 ok 99 -ok 100 - Location String: join(1..100,J00194.1:100..202) +ok 100 - Location String: 22..?64 ok 101 ok 102 - Bio::Location::Split ok 103 @@ -11792,7 +11828,7 @@ ok 110 ok 111 - Location String: join(AY016290.1:108..185,AY016291.1:1546..1599) ok 112 -ok 113 - Bio::Location::Fuzzy +ok 113 - Bio::Location::Split ok 114 ok 115 ok 116 @@ -11801,9 +11837,9 @@ ok 119 ok 120 ok 121 -ok 122 - Location String: complement(34..(122.126)) +ok 122 - Location String: join(12..78,134..202) ok 123 -ok 124 - Bio::Location::Fuzzy +ok 124 - Bio::Location::Split ok 125 ok 126 ok 127 @@ -11812,9 +11848,9 @@ ok 130 ok 131 ok 132 -ok 133 - Location String: 1..? +ok 133 - Location String: join(1..100,J00194.1:100..202) ok 134 -ok 135 - Bio::Location::Fuzzy +ok 135 - Bio::Location::Split ok 136 ok 137 ok 138 @@ -11823,9 +11859,9 @@ ok 141 ok 142 ok 143 -ok 144 - Location String: (122.133)..(204.221) +ok 144 - Location String: complement(join(2691..4571,4918..5163)) ok 145 -ok 146 - Bio::Location::Simple +ok 146 - Bio::Location::Fuzzy ok 147 ok 148 ok 149 @@ -11834,9 +11870,9 @@ ok 152 ok 153 ok 154 -ok 155 - Location String: 467 +ok 155 - Location String: ?..>393 ok 156 -ok 157 - Bio::Location::Fuzzy +ok 157 - Bio::Location::Simple ok 158 ok 159 ok 160 @@ -11845,7 +11881,7 @@ ok 163 ok 164 ok 165 -ok 166 - Location String: <1..? +ok 166 - Location String: 123^124 ok 167 ok 168 - Bio::Location::Fuzzy ok 169 @@ -11856,9 +11892,9 @@ ok 174 ok 175 ok 176 -ok 177 - Location String: 22..?64 +ok 177 - Location String: ?2465..2774 ok 178 -ok 179 - Bio::Location::Split +ok 179 - Bio::Location::Fuzzy ok 180 ok 181 ok 182 @@ -11867,7 +11903,7 @@ ok 185 ok 186 ok 187 -ok 188 - Location String: join(12..78,134..202) +ok 188 - Location String: 1..? ok 189 ok 190 - Bio::Location::Fuzzy ok 191 @@ -11878,9 +11914,9 @@ ok 196 ok 197 ok 198 -ok 199 - Location String: (102.110) +ok 199 - Location String: <1..888 ok 200 -ok 201 - Bio::Location::Simple +ok 201 - Bio::Location::Fuzzy ok 202 ok 203 ok 204 @@ -11889,7 +11925,7 @@ ok 207 ok 208 ok 209 -ok 210 - Location String: 340..565 +ok 210 - Location String: ?1..12 ok 211 ok 212 - Bio::Location::Fuzzy ok 213 @@ -11900,7 +11936,7 @@ ok 218 ok 219 ok 220 -ok 221 - Location String: ?..536 +ok 221 - Location String: <345..500 ok 222 ok 223 - Bio::Location::Fuzzy ok 224 @@ -11911,9 +11947,9 @@ ok 229 ok 230 ok 231 -ok 232 - Location String: ?..>393 +ok 232 - Location String: (122.133)..(204.221) ok 233 -ok 234 - Bio::Location::Simple +ok 234 - Bio::Location::Fuzzy ok 235 ok 236 ok 237 @@ -11922,7 +11958,7 @@ ok 240 ok 241 ok 242 -ok 243 - Location String: 123^124 +ok 243 - Location String: complement(34..(122.126)) ok 244 ok 245 - Bio::Location::Fuzzy ok 246 @@ -11933,9 +11969,9 @@ ok 251 ok 252 ok 253 -ok 254 - Location String: 145^177 +ok 254 - Location String: ?..536 ok 255 -ok 256 - Bio::Location::Fuzzy +ok 256 - Bio::Location::Simple ok 257 ok 258 ok 259 @@ -11944,9 +11980,9 @@ ok 262 ok 263 ok 264 -ok 265 - Location String: <345..500 +ok 265 - Location String: J00194:100..202 ok 266 -ok 267 - Bio::Location::Fuzzy +ok 267 - Bio::Location::Split ok 268 ok 269 ok 270 @@ -11955,9 +11991,9 @@ ok 273 ok 274 ok 275 -ok 276 - Location String: 1..>888 +ok 276 - Location String: complement(join(94468..94578,94578..>94889)) ok 277 -ok 278 - Bio::Location::Split +ok 278 - Bio::Location::Simple ok 279 ok 280 ok 281 @@ -11966,9 +12002,9 @@ ok 284 ok 285 ok 286 -ok 287 - Location String: complement(join(2691..4571,4918..5163)) +ok 287 - Location String: 340..565 ok 288 -ok 289 - Bio::Location::Split +ok 289 - Bio::Location::Fuzzy ok 290 ok 291 ok 292 @@ -11977,7 +12013,7 @@ ok 295 ok 296 ok 297 -ok 298 - Location String: complement(join(94468..94578,94578..>94889)) +ok 298 - Location String: (102.110) ok 299 ok 300 - Bio::Location::Fuzzy ok 301 @@ -11988,7 +12024,7 @@ ok 306 ok 307 ok 308 -ok 309 - Location String: ?2465..2774 +ok 309 - Location String: <1..? ok 310 ok 311 - complement(join(2691..4571,4918..5163)) ok 312 - join(complement(4918..5163),complement(2691..4571)) @@ -12627,7 +12663,7 @@ not ok 9 - primary_id # TODO possible bug: RichSeq not setting primary_id? # Failed (TODO) test 'primary_id' # at t/SeqIO/gcg.t line 53. -# got: 'Bio::PrimarySeq=HASH(0xaaab12b96ce8)' +# got: 'Bio::PrimarySeq=HASH(0xaaab07c10a00)' # expected: 'roa1_drome' ok 10 - description ok 11 @@ -13584,21 +13620,21 @@ ok 2 - Bio::SeqIO::mbsout is at least api version 1.1.3 ok 3 - An object of class 'Bio::SeqIO::mbsout' isa 'Bio::SeqIO::mbsout' ok 4 - An object of class 'Bio::SeqIO::mbsout' isa 'Bio::SeqIO::mbsout' -ok 5 - Get POSITIONS -ok 6 - Get NEXT_RUN_NUM -ok 7 - Get SEGSITES -ok 8 - Get POP_MUT_PARAM_PER_SITE -ok 9 - Get LAST_READ_HAP_NUM -ok 10 - Get TOT_RUN_HAPS -ok 11 - Get NSITES -ok 12 - Get SELPOS -ok 13 - Get RUNS -ok 14 - Get CURRENT_RUN_SEGSITES +ok 5 - Get NEXT_RUN_NUM +ok 6 - Get TOT_RUN_HAPS +ok 7 - Get POP_MUT_PARAM_PER_SITE +ok 8 - Get POP_RECOMB_PARAM_PER_SITE +ok 9 - Get NFILES +ok 10 - Get CURRENT_RUN_SEGSITES +ok 11 - Get NREPS +ok 12 - Get MBS_INFO_LINE +ok 13 - Get SEGSITES +ok 14 - Get SELPOS ok 15 - Get TRAJ_FILENAME -ok 16 - Get MBS_INFO_LINE -ok 17 - Get NREPS -ok 18 - Get NFILES -ok 19 - Get POP_RECOMB_PARAM_PER_SITE +ok 16 - Get RUNS +ok 17 - Get POSITIONS +ok 18 - Get NSITES +ok 19 - Get LAST_READ_HAP_NUM ok 20 - Get next_hap at beginning of run ok 21 - Get next_hap after beginning of run ok 22 - Get next_pop after beginning of pop @@ -13609,21 +13645,21 @@ ok 27 - Get next_run at beginning of run ok 28 - have all lines been read? ok 29 - An object of class 'Bio::SeqIO::mbsout' isa 'Bio::SeqIO::mbsout' -ok 30 - Get NEXT_RUN_NUM -ok 31 - Get POSITIONS -ok 32 - Get NSITES -ok 33 - Get CURRENT_RUN_SEGSITES -ok 34 - Get RUNS -ok 35 - Get SELPOS -ok 36 - Get LAST_READ_HAP_NUM -ok 37 - Get POP_MUT_PARAM_PER_SITE +ok 30 - Get POP_RECOMB_PARAM_PER_SITE +ok 31 - Get NEXT_RUN_NUM +ok 32 - Get POP_MUT_PARAM_PER_SITE +ok 33 - Get TOT_RUN_HAPS +ok 34 - Get CURRENT_RUN_SEGSITES +ok 35 - Get NREPS +ok 36 - Get NFILES +ok 37 - Get MBS_INFO_LINE ok 38 - Get SEGSITES -ok 39 - Get TOT_RUN_HAPS -ok 40 - Get TRAJ_FILENAME -ok 41 - Get NFILES -ok 42 - Get POP_RECOMB_PARAM_PER_SITE -ok 43 - Get NREPS -ok 44 - Get MBS_INFO_LINE +ok 39 - Get SELPOS +ok 40 - Get NSITES +ok 41 - Get LAST_READ_HAP_NUM +ok 42 - Get TRAJ_FILENAME +ok 43 - Get RUNS +ok 44 - Get POSITIONS ok 45 - Get next_hap at beginning of run ok 46 - Get next_hap after beginning of run ok 47 - Testing mbsout::outgroup @@ -13634,21 +13670,21 @@ ok 52 - Get next_run after hap ok 53 - next run should be 5. ok 54 - An object of class 'Bio::SeqIO::mbsout' isa 'Bio::SeqIO::mbsout' -ok 55 - Get NREPS -ok 56 - Get POP_RECOMB_PARAM_PER_SITE -ok 57 - Get NFILES -ok 58 - Get MBS_INFO_LINE -ok 59 - Get TRAJ_FILENAME -ok 60 - Get NSITES -ok 61 - Get SELPOS -ok 62 - Get RUNS -ok 63 - Get CURRENT_RUN_SEGSITES -ok 64 - Get SEGSITES -ok 65 - Get POP_MUT_PARAM_PER_SITE -ok 66 - Get LAST_READ_HAP_NUM -ok 67 - Get TOT_RUN_HAPS -ok 68 - Get POSITIONS -ok 69 - Get NEXT_RUN_NUM +ok 55 - Get NEXT_RUN_NUM +ok 56 - Get POP_MUT_PARAM_PER_SITE +ok 57 - Get TOT_RUN_HAPS +ok 58 - Get POP_RECOMB_PARAM_PER_SITE +ok 59 - Get NFILES +ok 60 - Get CURRENT_RUN_SEGSITES +ok 61 - Get NREPS +ok 62 - Get MBS_INFO_LINE +ok 63 - Get SEGSITES +ok 64 - Get SELPOS +ok 65 - Get TRAJ_FILENAME +ok 66 - Get RUNS +ok 67 - Get POSITIONS +ok 68 - Get NSITES +ok 69 - Get LAST_READ_HAP_NUM ok 70 - Get next_run at end/beginning of run ok 71 - have all lines been read? ok 72 - Get next_run at eof @@ -13669,17 +13705,17 @@ ok 1 - use Bio::SeqIO::msout; ok 2 - Bio::SeqIO::msout is at least api version 1.1.5 ok 3 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 4 - Get CURRENT_RUN_SEGSITES -ok 5 - Get POSITIONS -ok 6 - Get POPS -ok 7 - Get TOT_RUN_HAPS -ok 8 - Get SEEDS -ok 9 - Get RUNS -ok 10 - Get LAST_READ_HAP_NUM -ok 11 - Get N_SITES -ok 12 - Get MS_INFO_LINE -ok 13 - Get SEGSITES -ok 14 - Get NEXT_RUN_NUM +ok 4 - Get N_SITES +ok 5 - Get POPS +ok 6 - Get SEGSITES +ok 7 - Get MS_INFO_LINE +ok 8 - Get NEXT_RUN_NUM +ok 9 - Get LAST_READ_HAP_NUM +ok 10 - Get TOT_RUN_HAPS +ok 11 - Get POSITIONS +ok 12 - Get RUNS +ok 13 - Get CURRENT_RUN_SEGSITES +ok 14 - Get SEEDS ok 15 - Get next_hap at beginning of run ok 16 - Get next_hap after beginning of run ok 17 - Testing msout::outgroup @@ -13692,17 +13728,17 @@ ok 24 - Get next_run at beginning of run ok 25 - have all lines been read? ok 26 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 27 - Get LAST_READ_HAP_NUM -ok 28 - Get RUNS -ok 29 - Get NEXT_RUN_NUM -ok 30 - Get SEGSITES -ok 31 - Get MS_INFO_LINE -ok 32 - Get N_SITES -ok 33 - Get CURRENT_RUN_SEGSITES -ok 34 - Get TOT_RUN_HAPS -ok 35 - Get SEEDS -ok 36 - Get POSITIONS -ok 37 - Get POPS +ok 27 - Get POSITIONS +ok 28 - Get TOT_RUN_HAPS +ok 29 - Get LAST_READ_HAP_NUM +ok 30 - Get SEEDS +ok 31 - Get RUNS +ok 32 - Get CURRENT_RUN_SEGSITES +ok 33 - Get POPS +ok 34 - Get N_SITES +ok 35 - Get NEXT_RUN_NUM +ok 36 - Get SEGSITES +ok 37 - Get MS_INFO_LINE ok 38 - Get next_hap at beginning of run ok 39 - Get next_hap after beginning of run ok 40 - Testing msout::outgroup @@ -13714,16 +13750,16 @@ ok 46 - next run should be 5. ok 47 - Get last hap through next_hap ok 48 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 49 - Get RUNS -ok 50 - Get LAST_READ_HAP_NUM -ok 51 - Get MS_INFO_LINE -ok 52 - Get SEGSITES -ok 53 - Get NEXT_RUN_NUM -ok 54 - Get CURRENT_RUN_SEGSITES -ok 55 - Get POSITIONS -ok 56 - Get POPS -ok 57 - Get TOT_RUN_HAPS -ok 58 - Get SEEDS +ok 49 - Get LAST_READ_HAP_NUM +ok 50 - Get POPS +ok 51 - Get TOT_RUN_HAPS +ok 52 - Get POSITIONS +ok 53 - Get SEGSITES +ok 54 - Get RUNS +ok 55 - Get CURRENT_RUN_SEGSITES +ok 56 - Get MS_INFO_LINE +ok 57 - Get SEEDS +ok 58 - Get NEXT_RUN_NUM ok 59 - Get next_pop at end of run ok 60 - have all lines been read? ok 61 - Get next_pop at eof @@ -13731,16 +13767,16 @@ ok 63 - Get next_hap at eof ok 64 - Get next_seq at eof ok 65 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 66 - Get TOT_RUN_HAPS -ok 67 - Get SEEDS -ok 68 - Get POSITIONS -ok 69 - Get POPS -ok 70 - Get CURRENT_RUN_SEGSITES -ok 71 - Get NEXT_RUN_NUM -ok 72 - Get N_SITES -ok 73 - Get MS_INFO_LINE -ok 74 - Get SEGSITES -ok 75 - Get LAST_READ_HAP_NUM +ok 66 - Get POPS +ok 67 - Get N_SITES +ok 68 - Get NEXT_RUN_NUM +ok 69 - Get MS_INFO_LINE +ok 70 - Get SEGSITES +ok 71 - Get POSITIONS +ok 72 - Get TOT_RUN_HAPS +ok 73 - Get LAST_READ_HAP_NUM +ok 74 - Get SEEDS +ok 75 - Get CURRENT_RUN_SEGSITES ok 76 - Get RUNS ok 77 - Get next_hap at beginning of run ok 78 - Get next_hap after beginning of run @@ -13758,17 +13794,17 @@ ok 90 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' ok 91 - Caught error in bad msout file 2 ok 92 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 93 - Get RUNS -ok 94 - Get LAST_READ_HAP_NUM -ok 95 - Get SEGSITES -ok 96 - Get MS_INFO_LINE -ok 97 - Get N_SITES -ok 98 - Get NEXT_RUN_NUM +ok 93 - Get SEGSITES +ok 94 - Get MS_INFO_LINE +ok 95 - Get NEXT_RUN_NUM +ok 96 - Get N_SITES +ok 97 - Get POPS +ok 98 - Get RUNS ok 99 - Get CURRENT_RUN_SEGSITES -ok 100 - Get POSITIONS -ok 101 - Get POPS +ok 100 - Get SEEDS +ok 101 - Get LAST_READ_HAP_NUM ok 102 - Get TOT_RUN_HAPS -ok 103 - Get SEEDS +ok 103 - Get POSITIONS ok 104 - Get next_hap at beginning of run ok 105 - Get next_hap after beginning of run ok 106 - Testing msout::outgroup @@ -13781,17 +13817,17 @@ ok 113 - Get next_run at beginning of run ok 114 - have all lines been read? ok 115 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 116 - Get LAST_READ_HAP_NUM -ok 117 - Get RUNS -ok 118 - Get NEXT_RUN_NUM -ok 119 - Get N_SITES -ok 120 - Get MS_INFO_LINE -ok 121 - Get SEGSITES -ok 122 - Get CURRENT_RUN_SEGSITES -ok 123 - Get SEEDS -ok 124 - Get TOT_RUN_HAPS -ok 125 - Get POPS -ok 126 - Get POSITIONS +ok 116 - Get N_SITES +ok 117 - Get POPS +ok 118 - Get MS_INFO_LINE +ok 119 - Get SEGSITES +ok 120 - Get NEXT_RUN_NUM +ok 121 - Get LAST_READ_HAP_NUM +ok 122 - Get POSITIONS +ok 123 - Get TOT_RUN_HAPS +ok 124 - Get CURRENT_RUN_SEGSITES +ok 125 - Get RUNS +ok 126 - Get SEEDS ok 127 - Get next_hap at beginning of run ok 128 - Get next_hap after beginning of run ok 129 - Testing msout::outgroup @@ -13803,17 +13839,17 @@ ok 135 - next run should be 5. ok 136 - Get last hap through next_hap ok 137 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 138 - Get MS_INFO_LINE -ok 139 - Get N_SITES -ok 140 - Get SEGSITES -ok 141 - Get NEXT_RUN_NUM -ok 142 - Get RUNS -ok 143 - Get LAST_READ_HAP_NUM -ok 144 - Get POPS -ok 145 - Get POSITIONS -ok 146 - Get SEEDS +ok 138 - Get SEGSITES +ok 139 - Get MS_INFO_LINE +ok 140 - Get NEXT_RUN_NUM +ok 141 - Get N_SITES +ok 142 - Get POPS +ok 143 - Get RUNS +ok 144 - Get CURRENT_RUN_SEGSITES +ok 145 - Get SEEDS +ok 146 - Get LAST_READ_HAP_NUM ok 147 - Get TOT_RUN_HAPS -ok 148 - Get CURRENT_RUN_SEGSITES +ok 148 - Get POSITIONS ok 149 - Get next_hap at beginning of run ok 150 - Get next_hap after beginning of run ok 151 - Testing msout::outgroup @@ -13973,7 +14009,7 @@ not ok 29 - accuracies # TODO documentation and code for accuracies() do not match # Failed (TODO) test 'accuracies' # at t/SeqIO/scf.t line 77. -# got: 'ARRAY(0xaaab19ccc5a0)' +# got: 'ARRAY(0xaaaac7b7cac0)' # expected: '482' ok 30 ok 31 - sub_peak_index @@ -14276,9 +14312,9 @@ ok 19 - dblink source ok 20 - dblink ID ok 21 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' -ok 22 - boolean property +ok 22 - property with value ok 23 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' -ok 24 - property with value +ok 24 - boolean property ok 25 - writer ok ok 26 - outfile is created ok 27 - seqXML version @@ -17697,7 +17733,7 @@ ------------------- t/Root/IO.t (Wstat: 0 Tests: 154 Failed: 0) TODO passed: 109, 112, 115, 118 -Files=211, Tests=14791, 96 wallclock secs ( 2.03 usr 0.60 sys + 81.84 cusr 12.96 csys = 97.43 CPU) +Files=211, Tests=14791, 174 wallclock secs ( 1.74 usr 0.55 sys + 70.22 cusr 11.39 csys = 83.90 CPU) Result: PASS make[1]: Leaving directory '/build/reproducible-path/bioperl-1.7.8' create-stamp debian/debhelper-build-stamp @@ -17722,476 +17758,476 @@ Manifying 33 pod documents Manifying 15 pod documents Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/BioPerl.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/UpdateableSeqI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/WebAgent.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Species.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqUtils.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/WebAgent.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/UpdateableSeqI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SimpleAlign.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Taxon.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SimpleAnalysisI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Species.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Taxon.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqUtils.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeatureI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqAnalysisParserI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/PrimarySeq.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/PullParserI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/RangeI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/ParameterBaseI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/PrimarySeq.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/PrimarySeqI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Range.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/LocationI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/FeatureHolderI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/IdCollectionI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/HandlerBaseI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/FeatureHolderI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/LocatableSeq.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DBLinkContainerI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DasI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DescribableI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/IdentifiableI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/LocatableSeq.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DescribableI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/HandlerBaseI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnnotationI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnnotationCollectionI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnalysisResultI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnalysisI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnalysisParserI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnalysisResultI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnnotatableI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnalysisI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/phyloxml.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/lintree.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/nexus.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/pag.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/nhx.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/NewickParser.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/TreeEventBuilder.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/cluster.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/nexus.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/newick.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/lintree.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/tabtree.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/TreeI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/NewickParser.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/pag.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/phyloxml.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/TreeFunctionsI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/NodeNHX.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/TreeI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/DistanceFactory.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/RandomFactory.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/Node.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/Tree.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/NodeNHX.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/RandomFactory.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/Compatible.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/AnnotatableNode.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/Statistics.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/AnnotatableNode.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/Node.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/NodeI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/SeqStats.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/QRNA.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Sigcleave.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/RepeatMasker.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Seg.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/ipcress.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Tmhmm.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/SeqStats.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Signalp.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/SeqWords.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/tRNAscanSE.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/ipcress.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/RandomDistFunctions.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Signalp.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/TandemRepeatsFinder.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Tmhmm.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/QRNA.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/pICalculator.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/TargetP.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/isPcr.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/RepeatMasker.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Sigcleave.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/SeqPattern.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Fgenesh.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Lucy.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Grail.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/PrositeScan.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/CodonTable.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/tRNAscanSE.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/TargetP.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Profile.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/ECnumber.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer3.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genewise.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Match.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/IUPAC.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Est2Genome.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/ECnumber.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/GuessSeqFormat.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/GFF.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Geneid.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Coil.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/ESTScan.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/FootPrinter.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Eponine.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/EPCR.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genemark.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genewise.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Prints.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Glimmer.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Promoterwise.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Pseudowise.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genomewise.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Match.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/MZEF.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Prints.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/GuessSeqFormat.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Geneid.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genemark.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/OddCodes.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Coil.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genscan.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/AmpliconSearch.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/AnalysisResult.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer3.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/EPCR.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Promoterwise.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Grail.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Fgenesh.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Lucy.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/OddCodes.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/PrositeScan.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Eponine.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Est2Genome.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genomewise.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/CodonTable.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Blat.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Signalp/ExtendedSignalp.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Sim4/Results.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/AnalysisResult.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/AmpliconSearch.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Sim4/Exon.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Sim4/Results.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/SeqPattern/Backtranslate.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Spidey/Exon.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Spidey/Results.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/WrapperBase.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/AnalysisFactory.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/GenericParameters.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/Analysis.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/GenericParameters.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/ParametersI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/WrapperBase/CommandExts.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/AnalysisFactory.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/WrapperBase.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/PhyloBase.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/EMBOSS/Palindrome.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer/Pair.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/WrapperBase/CommandExts.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Signalp/ExtendedSignalp.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Spidey/Results.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Spidey/Exon.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Prediction/Exon.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Prediction/Gene.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer/AssessorI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer/Feature.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer/Pair.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer/Assessor/Base.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Prediction/Gene.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Prediction/Exon.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Phylo/Molphy.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Phylo/Gerp.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Phylo/Molphy/Result.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Phylo/Molphy.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Phylo/Phylip/ProtDist.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Phylo/Molphy/Result.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/EMBOSS/Palindrome.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Analysis/SimpleAnalysisBase.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Alignment/Trim.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Alignment/Consed.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/gcg.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tinyseq.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/gbxml.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/phd.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/metafasta.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/qual.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/scf.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tigrxml.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/seqxml.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/genbank.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Alignment/Trim.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/gbdriver.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/msout.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/genbank.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tinyseq.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/raw.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/table.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tigr.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/mbsout.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/largefasta.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/msout.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/table.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/locuslink.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/swiss.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/phd.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tigr.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/pir.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tab.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/locuslink.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/swissdriver.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/kegg.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/pir.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/asciitree.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/swissdriver.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/scf.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/gbdriver.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/qual.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/gbxml.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tigrxml.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/metafasta.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/largefasta.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/seqxml.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/gcg.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/fasta.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/fastq.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/ace.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/embldriver.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/FTHelper.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/MultiFile.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/bsml.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/embl.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/MultiFile.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/fasta.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/bsml_sax.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/fastq.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/FTHelper.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/gameHandler.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/embldriver.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/asciitree.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tinyseq/tinyseqHandler.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/gameSubs.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/gameWriter.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/seqHandler.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/gameHandler.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/featHandler.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/gameSubs.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tinyseq/tinyseqHandler.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/Handler/GenericRichSeqHandler.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Primer.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Lite.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/TypedSeqFeatureI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/SimilarityPair.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/SubSeq.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Similarity.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Generic.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/TypedSeqFeatureI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Similarity.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Lite.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/PositionProxy.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/SimilarityPair.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Collection.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/CollectionI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/FeaturePair.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Amplicon.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/AnnotationAdaptor.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/CollectionI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Computation.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Amplicon.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Tools/IDHandler.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Collection.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/FeaturePair.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Tools/Unflattener.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Tools/IDHandler.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Tools/TypeMapper.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Tools/FeatureNamer.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/GeneStructureI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/ExonI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Intron.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/TranscriptI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/GeneStructure.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/ExonI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Transcript.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/NC_Feature.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Promoter.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Intron.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/UTR.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/NC_Feature.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/GeneStructureI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/GeneStructure.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Poly_A_site.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Promoter.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Exon.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/QualI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/EncodedSeq.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/LargeSeq.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/TraceI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/RichSeqI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/Meta.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/Quality.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/PrimaryQual.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/MetaI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/LargePrimarySeq.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/QualI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SeqFactory.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SequenceTrace.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/RichSeq.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SimulatedRead.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SequenceTrace.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SeqFastaSpeedFactory.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/LargeSeqI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/EncodedSeq.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SeqBuilder.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/PrimaryQual.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/LargeSeq.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/LargeLocatableSeq.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SeqFactory.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/BaseSeqProcessor.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/LargeSeqI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/PrimedSeq.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/TraceI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SeqBuilder.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/Meta.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/RichSeqI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/LargePrimarySeq.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/MetaI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SeqFastaSpeedFactory.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/Meta/Array.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/infernal.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/exonerate.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/megablast.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/wise.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/psl.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/sim4.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/gmap_f9.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/rnamotif.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/megablast.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/fasta.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/gmap_f9.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/exonerate.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/waba.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/erpin.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/axt.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/SearchWriterI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/cross_match.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/infernal.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/psl.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/wise.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/sim4.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/SearchResultEventBuilder.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/blast.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/blast_pull.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/blasttable.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/EventHandlerI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/SearchWriterI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/cross_match.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/erpin.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/axt.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/IteratedSearchResultEventBuilder.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/FastHitEventBuilder.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/EventHandlerI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/blast_pull.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/blast.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/HitTableWriter.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/ResultTableWriter.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/TextResultWriter.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/GbrowseGFF.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/HSPTableWriter.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/HitTableWriter.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/HTMLResultWriter.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/GbrowseGFF.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/TextResultWriter.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/StatisticsI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/SearchUtils.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/GenericStatistics.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/GenericDatabase.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/GenericStatistics.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/DatabaseI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/BlastUtils.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Processor.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/BlastStatistics.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/BlastUtils.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/DatabaseI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Tiling/MapTiling.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Tiling/MapTileUtils.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Tiling/TilingI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Tiling/MapTileUtils.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/ResultFactory.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/BlastResult.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/WABAResult.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/PullResultI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/CrossMatchResult.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/BlastPullResult.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/GenericResult.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/CrossMatchResult.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/ResultI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/ResultFactory.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/INFERNALResult.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/BlastResult.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Iteration/GenericIteration.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Iteration/IterationI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/PSLHSP.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/HitI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/GenericHit.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/HitFactory.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/BlastHit.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/BlastPullHit.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/ModelHit.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/PullHitI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/PsiBlastHit.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/Fasta.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/PsiBlastHSP.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/BlastPullHSP.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/HSPFactory.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/PullHSPI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/ModelHSP.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/WABAHSP.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/BlastHSP.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/PSLHSP.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/PullHSPI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/HSPFactory.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/HSPI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/FastaHSP.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/ModelHSP.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/GenericHSP.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/BlastHSP.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/PullHitI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/HitFactory.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/PsiBlastHit.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/Fasta.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/BlastPullHit.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/BlastHit.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/GenericHit.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/ModelHit.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/HitI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Utilities.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Root.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Storable.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/TestObject.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Utilities.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Test.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Version.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/IO.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Root.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/TestObject.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/RootI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/HTTPget.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/RootI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/IO.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Exception.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/soflat.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/obo.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/goflat.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/dagflat.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/InterProParser.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/dagflat.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/goflat.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/obo.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/simplehierarchy.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/soflat.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/Handlers/BaseSAXHandler.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/Handlers/InterProHandler.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/Ontology.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OBOEngine.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OntologyEngineI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/RelationshipFactory.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/SimpleOntologyEngine.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/RelationshipI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OntologyI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/RelationshipType.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/InterProTerm.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/TermI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/Relationship.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OntologyStore.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/Path.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/GOterm.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/PathI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OBOterm.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/Term.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/TermFactory.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/DocumentRegistry.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/Scoring.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/Mlagan.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/MatrixI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/Generic.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/Mlagan.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PhylipDist.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO/mlagan.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO/phylip.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO/scoring.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/SiteMatrix.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/Psm.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO/phylip.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO/mlagan.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/InstanceSiteI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/ProtPsm.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/PsmI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/ProtMatrix.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/InstanceSite.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/SiteMatrix.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/SiteMatrixI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/PsmHeader.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/InstanceSite.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/PsmHeaderI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/ProtPsm.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/SiteMatrixI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/InstanceSiteI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/ProtMatrix.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/Psm.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/transfac.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/mast.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/meme.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/transfac.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/psiblast.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/masta.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/FuzzyLocationI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/NarrowestCoordPolicy.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Simple.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Split.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/AvWithinCoordPolicy.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/SplitLocationI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Fuzzy.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/WidestCoordPolicy.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/CoordinatePolicyI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Atomic.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/TermI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OntologyI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OBOEngine.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/RelationshipFactory.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/Path.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OntologyStore.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/SimpleOntologyEngine.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/RelationshipI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/TermFactory.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/Term.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OntologyEngineI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OBOterm.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/PathI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/Ontology.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/RelationshipType.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/InterProTerm.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/Relationship.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/GOterm.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/DocumentRegistry.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Das/FeatureTypeI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Split.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Simple.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/NarrowestCoordPolicy.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/FuzzyLocationI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/CoordinatePolicyI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/AvWithinCoordPolicy.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/WidestCoordPolicy.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Das/SegmentI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/EMBL.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/BlastTable.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/SwissPfam.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Fastq.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Abstract.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Qual.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/AbstractSeq.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Fasta.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/GenBank.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Swissprot.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Blast.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Das/FeatureTypeI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Event/EventGeneratorI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Event/EventHandlerI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SequenceFactoryI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/TreeFactoryI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/FTLocationFactory.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/DriverFactory.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SeqAnalysisParserFactory.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/ObjectFactoryI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SequenceProcessorI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/FTLocationFactory.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/LocationFactoryI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/TreeFactoryI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SeqAnalysisParserFactoryI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SeqAnalysisParserFactory.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/ApplicationFactoryI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/ObjectBuilderI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SequenceStreamI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/LocationFactoryI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SequenceProcessorI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/ObjectBuilderI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/AnalysisI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/ObjectFactory.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/DriverFactory.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SequenceFactoryI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Fasta.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/SwissPfam.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Blast.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/AbstractSeq.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/BlastTable.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Fastq.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/GenBank.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Abstract.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Qual.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/EMBL.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Swissprot.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/CodonUsage/IO.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/CodonUsage/Table.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/WebDBSeqI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/InMemoryCache.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/SeqI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Failover.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Registry.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/LocationI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/FileCache.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Fasta.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/DBFetch.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/RandomAccessI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/SeqI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/UpdateableSeqI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/ReferenceI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/QueryI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/FileCache.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Fasta.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/IndexedBase.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/QueryI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/GenericWebAgent.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/LocationI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/ReferenceI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Qual.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/GFF/Util/Binning.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/GFF/Util/Rearrange.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Query/WebQuery.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/list.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/silva.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/greengenes.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/flatfile.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BinarySearch.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Failover.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/RandomAccessI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BinarySearch.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB/swiss.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB/fasta.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB/embl.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB/fasta.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB/genbank.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/TypeManager.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Query/WebQuery.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/greengenes.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/silva.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/flatfile.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/list.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/GFF/Util/Binning.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/GFF/Util/Rearrange.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Tree.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/StructuredValue.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/TagTree.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Target.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/SimpleValue.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/OntologyTerm.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Target.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/TypeManager.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/TagTree.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Comment.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Relation.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Collection.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Reference.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/DBLink.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/AnnotationFactory.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Reference.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Relation.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/PairwiseStatistics.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/DNAStatistics.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/AlignI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/Utilities.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/StatisticsI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/ProteinStatistics.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/selex.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/po.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/maf.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/fasta.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/largemultifasta.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/psi.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/mase.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/OntologyTerm.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/msf.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/bl2seq.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/proda.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/meme.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/prodom.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/mega.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/nexus.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/emboss.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/po.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/pfam.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/mega.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/meme.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/psi.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/clustalw.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/metafasta.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/emboss.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/phylip.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/xmfa.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/mase.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/selex.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/arp.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/metafasta.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/prodom.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/nexus.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/fasta.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/maf.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/xmfa.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/proda.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/largemultifasta.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/Handler/GenericAlignHandler.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/AlignI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/PairwiseStatistics.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/Utilities.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/DNAStatistics.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/StatisticsI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/ProteinStatistics.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_unflatten_seq.1p Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_tree2pag.1p Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_translate_seq.1p @@ -18703,45 +18739,45 @@ Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Align::PairwiseStatistics.3pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Align::DNAStatistics.3pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Align::AlignI.3pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_translate_seq Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_unflatten_seq +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_split_seq Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_tree2pag +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqretsplit Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_taxonomy2tree Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_taxid4species -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_translate_seq +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqpart Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_sreformat -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_split_seq -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqretsplit Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqret -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2table +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_seq_length Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqconvert -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqpart Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqcut -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_process_gadfly -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_seq_length -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_oligo_count -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2tribe -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_process_sgd -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_revtrans-motif Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2alnblocks Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2gff -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_make_mrna_protein -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_mrtrans +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_revtrans-motif +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_process_sgd +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2table +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2tribe +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_process_gadfly +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_oligo_count Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_nrdb Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_mutate -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_mask_by_search Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_nexus2nh +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_mask_by_search +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_mrtrans Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_local_taxonomydb_query -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_filter_search -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_genbank2gff3 Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_gccalc -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_bioflat_index -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_index +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_find-blast-matches +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_make_mrna_protein +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_filter_search Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_fetch -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_dbsplit +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_index Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_extract_feature_seq +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_genbank2gff3 Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_fastam9_to_table -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_find-blast-matches +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_dbsplit Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_biogetseq +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_bioflat_index Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_aacomp make[1]: Leaving directory '/build/reproducible-path/bioperl-1.7.8' dh_install @@ -18777,12 +18813,14 @@ 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/103686/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/103686/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/3437517 and its subdirectories -I: Current time: Wed Sep 3 13:13:15 -12 2025 -I: pbuilder-time-stamp: 1756948395 +I: removing directory /srv/workspace/pbuilder/103686 and its subdirectories +I: Current time: Wed Oct 7 21:40:38 +14 2026 +I: pbuilder-time-stamp: 1791358838