[Debian-med-packaging] Bug#562442: bioperl: FTBFS: tests failed
Lucas Nussbaum
lucas at lucas-nussbaum.net
Thu Dec 24 16:38:36 UTC 2009
Source: bioperl
Version: 1.6.1-1
Severity: serious
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20091223 qa-ftbfs
Justification: FTBFS on amd64
Hi,
During a rebuild of all packages in sid, your package failed to build on
amd64.
Relevant part:
> /usr/bin/fakeroot debian/rules clean
> dh_testdir
> dh_testroot
> [ ! -f Build ] || ./Build realclean
> dh_clean build-stamp install-stamp bioperl.conf biodatabases.pod \
> biodesign.pod bioperl.pod bioscripts.pod
> dpkg-source -b bioperl-1.6.1
> dpkg-source: info: using source format `1.0'
> dpkg-source: info: building bioperl using existing bioperl_1.6.1.orig.tar.gz
> dpkg-source: info: building bioperl in bioperl_1.6.1-1.diff.gz
> dpkg-source: info: building bioperl in bioperl_1.6.1-1.dsc
> debian/rules build
> dh_testdir
> perl Build.PL < /dev/null # non-interactive, uses defaults
> Checking whether your kit is complete...
> Looks good
>
> Checking prerequisites...
> * Optional prerequisite Math::Random is not installed
> (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory)
>
> ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions
> of the modules indicated above before proceeding with this installation
>
> * Could not connect to the internet (http://search.cpan.org/)
> Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] Checking features:
> Network...................disabled
> BioDBSeqFeature_mysql.....enabled
> BioDBGFF..................enabled
> BioDBSeqFeature_BDB.......enabled
> BioDBSeqFeature_SQLite....enabled
> BioDBSeqFeature_Pg........enabled
>
> Do you want to run the Bio::DB::GFF or Bio::DB::SeqFeature::Store live database tests? y/n [n] - will not run the BioDBGFF or BioDBSeqFeature live database tests
>
> Install [a]ll BioPerl scripts, [n]one, or choose groups [i]nteractively? [a] - will install all scripts
>
> Creating new 'Build' script for 'BioPerl' version '1.006001'
> ./Build
> Copying Bio/PopGen/MarkerI.pm -> blib/lib/Bio/PopGen/MarkerI.pm
> Copying Bio/MolEvol/CodonModel.pm -> blib/lib/Bio/MolEvol/CodonModel.pm
> Copying Bio/Matrix/PSM/Psm.pm -> blib/lib/Bio/Matrix/PSM/Psm.pm
> Copying Bio/Tools/Spidey/Exon.pm -> blib/lib/Bio/Tools/Spidey/Exon.pm
> Copying Bio/Matrix/PSM/ProtMatrix.pm -> blib/lib/Bio/Matrix/PSM/ProtMatrix.pm
> Copying Bio/WebAgent.pm -> blib/lib/Bio/WebAgent.pm
> Copying Bio/LiveSeq/ChainI.pm -> blib/lib/Bio/LiveSeq/ChainI.pm
> Copying Bio/Tools/EUtilities/Info/LinkInfo.pm -> blib/lib/Bio/Tools/EUtilities/Info/LinkInfo.pm
> Copying Bio/AlignIO/mega.pm -> blib/lib/Bio/AlignIO/mega.pm
> Copying Bio/LiveSeq/Mutation.pm -> blib/lib/Bio/LiveSeq/Mutation.pm
> Copying Bio/TreeIO/pag.pm -> blib/lib/Bio/TreeIO/pag.pm
> Copying Bio/Tools/HMMER/Set.pm -> blib/lib/Bio/Tools/HMMER/Set.pm
> Copying Bio/SeqIO/chaos.pm -> blib/lib/Bio/SeqIO/chaos.pm
> Copying Bio/Map/PositionWithSequence.pm -> blib/lib/Bio/Map/PositionWithSequence.pm
> Copying Bio/DB/GFF/Aggregator/so_transcript.pm -> blib/lib/Bio/DB/GFF/Aggregator/so_transcript.pm
> Copying Bio/Factory/ObjectFactory.pm -> blib/lib/Bio/Factory/ObjectFactory.pm
> Copying Bio/DB/SeqFeature/Store/berkeleydb3.pm -> blib/lib/Bio/DB/SeqFeature/Store/berkeleydb3.pm
> Copying Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm -> blib/lib/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
> Copying Bio/SearchIO/megablast.pm -> blib/lib/Bio/SearchIO/megablast.pm
> Copying Bio/Factory/SeqAnalysisParserFactoryI.pm -> blib/lib/Bio/Factory/SeqAnalysisParserFactoryI.pm
> Copying Bio/TreeIO.pm -> blib/lib/Bio/TreeIO.pm
> Copying Bio/DB/GFF/Aggregator/ucsc_unigene.pm -> blib/lib/Bio/DB/GFF/Aggregator/ucsc_unigene.pm
> Copying Bio/Search/HSP/PSLHSP.pm -> blib/lib/Bio/Search/HSP/PSLHSP.pm
> Copying Bio/Map/Physical.pm -> blib/lib/Bio/Map/Physical.pm
> Copying Bio/DB/GFF/Aggregator/ucsc_acembly.pm -> blib/lib/Bio/DB/GFF/Aggregator/ucsc_acembly.pm
> Copying Bio/Cluster/UniGeneI.pm -> blib/lib/Bio/Cluster/UniGeneI.pm
> Copying Bio/Tools/GuessSeqFormat.pm -> blib/lib/Bio/Tools/GuessSeqFormat.pm
> Copying Bio/Biblio/PubmedBookArticle.pm -> blib/lib/Bio/Biblio/PubmedBookArticle.pm
> Copying Bio/Search/Result/HmmpfamResult.pm -> blib/lib/Bio/Search/Result/HmmpfamResult.pm
> Copying Bio/Align/Utilities.pm -> blib/lib/Bio/Align/Utilities.pm
> Copying Bio/Search/HSP/WABAHSP.pm -> blib/lib/Bio/Search/HSP/WABAHSP.pm
> Copying Bio/Tools/Run/ParametersI.pm -> blib/lib/Bio/Tools/Run/ParametersI.pm
> Copying Bio/Expression/ProbeI.pm -> blib/lib/Bio/Expression/ProbeI.pm
> Copying Bio/DB/Flat.pm -> blib/lib/Bio/DB/Flat.pm
> Copying Bio/SeqFeature/Lite.pm -> blib/lib/Bio/SeqFeature/Lite.pm
> Copying Bio/SearchIO/fasta.pm -> blib/lib/Bio/SearchIO/fasta.pm
> Copying Bio/DB/SwissProt.pm -> blib/lib/Bio/DB/SwissProt.pm
> Copying Bio/TreeIO/nexus.pm -> blib/lib/Bio/TreeIO/nexus.pm
> Copying Bio/Tools/EUtilities/Query/GlobalQuery.pm -> blib/lib/Bio/Tools/EUtilities/Query/GlobalQuery.pm
> Copying Bio/Biblio/Provider.pm -> blib/lib/Bio/Biblio/Provider.pm
> Copying Bio/Tree/DistanceFactory.pm -> blib/lib/Bio/Tree/DistanceFactory.pm
> Copying Bio/Search/HSP/ModelHSP.pm -> blib/lib/Bio/Search/HSP/ModelHSP.pm
> Copying Bio/Coordinate/Graph.pm -> blib/lib/Bio/Coordinate/Graph.pm
> Copying Bio/SeqIO/tinyseq/tinyseqHandler.pm -> blib/lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm
> Copying Bio/DB/GFF/Aggregator/ucsc_sanger22.pm -> blib/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm
> Copying Bio/LocationI.pm -> blib/lib/Bio/LocationI.pm
> Copying Bio/Root/RootI.pm -> blib/lib/Bio/Root/RootI.pm
> Copying Bio/Taxonomy.pm -> blib/lib/Bio/Taxonomy.pm
> Copying Bio/TreeIO/TreeEventBuilder.pm -> blib/lib/Bio/TreeIO/TreeEventBuilder.pm
> Copying Bio/Matrix/PSM/PsmI.pm -> blib/lib/Bio/Matrix/PSM/PsmI.pm
> Copying Bio/DBLinkContainerI.pm -> blib/lib/Bio/DBLinkContainerI.pm
> Copying Bio/Location/Fuzzy.pm -> blib/lib/Bio/Location/Fuzzy.pm
> Copying Bio/SeqIO.pm -> blib/lib/Bio/SeqIO.pm
> Copying Bio/FeatureIO/bed.pm -> blib/lib/Bio/FeatureIO/bed.pm
> Copying Bio/AnalysisI.pm -> blib/lib/Bio/AnalysisI.pm
> Copying Bio/LiveSeq/AARange.pm -> blib/lib/Bio/LiveSeq/AARange.pm
> Copying Bio/DB/Biblio/biofetch.pm -> blib/lib/Bio/DB/Biblio/biofetch.pm
> Copying Bio/Index/Swissprot.pm -> blib/lib/Bio/Index/Swissprot.pm
> Copying Bio/Annotation/OntologyTerm.pm -> blib/lib/Bio/Annotation/OntologyTerm.pm
> Copying Bio/Map/SimpleMap.pm -> blib/lib/Bio/Map/SimpleMap.pm
> Copying Bio/Tools/TandemRepeatsFinder.pm -> blib/lib/Bio/Tools/TandemRepeatsFinder.pm
> Copying Bio/Coordinate/Result/Gap.pm -> blib/lib/Bio/Coordinate/Result/Gap.pm
> Copying Bio/Tools/Run/RemoteBlast.pm -> blib/lib/Bio/Tools/Run/RemoteBlast.pm
> Copying Bio/Seq/Meta/Array.pm -> blib/lib/Bio/Seq/Meta/Array.pm
> Copying Bio/FeatureIO.pm -> blib/lib/Bio/FeatureIO.pm
> Copying Bio/DB/BiblioI.pm -> blib/lib/Bio/DB/BiblioI.pm
> Copying Bio/MapIO.pm -> blib/lib/Bio/MapIO.pm
> Copying Bio/SearchIO/Writer/HSPTableWriter.pm -> blib/lib/Bio/SearchIO/Writer/HSPTableWriter.pm
> Copying Bio/Map/Clone.pm -> blib/lib/Bio/Map/Clone.pm
> Copying Bio/SearchIO/blasttable.pm -> blib/lib/Bio/SearchIO/blasttable.pm
> Copying Bio/Expression/DataSet.pm -> blib/lib/Bio/Expression/DataSet.pm
> Copying Bio/SeqFeature/Collection.pm -> blib/lib/Bio/SeqFeature/Collection.pm
> Copying Bio/Tree/TreeI.pm -> blib/lib/Bio/Tree/TreeI.pm
> Copying Bio/DB/Expression/geo.pm -> blib/lib/Bio/DB/Expression/geo.pm
> Copying Bio/Index/BlastTable.pm -> blib/lib/Bio/Index/BlastTable.pm
> Copying Bio/Map/MappableI.pm -> blib/lib/Bio/Map/MappableI.pm
> Copying Bio/Seq/BaseSeqProcessor.pm -> blib/lib/Bio/Seq/BaseSeqProcessor.pm
> Copying Bio/PullParserI.pm -> blib/lib/Bio/PullParserI.pm
> Copying Bio/SeqIO/fastq.pm -> blib/lib/Bio/SeqIO/fastq.pm
> Copying Bio/LiveSeq/SeqI.pm -> blib/lib/Bio/LiveSeq/SeqI.pm
> Copying Bio/Restriction/IO/prototype.pm -> blib/lib/Bio/Restriction/IO/prototype.pm
> Copying Bio/Tools/Analysis/Protein/ELM.pm -> blib/lib/Bio/Tools/Analysis/Protein/ELM.pm
> Copying Bio/Seq/TraceI.pm -> blib/lib/Bio/Seq/TraceI.pm
> Copying Bio/Phenotype/Phenotype.pm -> blib/lib/Bio/Phenotype/Phenotype.pm
> Copying Bio/Seq/PrimaryQual.pm -> blib/lib/Bio/Seq/PrimaryQual.pm
> Copying Bio/Variation/Allele.pm -> blib/lib/Bio/Variation/Allele.pm
> Copying Bio/Map/CytoMap.pm -> blib/lib/Bio/Map/CytoMap.pm
> Copying Bio/DB/Failover.pm -> blib/lib/Bio/DB/Failover.pm
> Copying Bio/LiveSeq/IO/Loader.pm -> blib/lib/Bio/LiveSeq/IO/Loader.pm
> Copying Bio/Search/Hit/PsiBlastHit.pm -> blib/lib/Bio/Search/Hit/PsiBlastHit.pm
> Copying Bio/Restriction/Enzyme/MultiCut.pm -> blib/lib/Bio/Restriction/Enzyme/MultiCut.pm
> Copying Bio/LiveSeq/Repeat_Unit.pm -> blib/lib/Bio/LiveSeq/Repeat_Unit.pm
> Copying Bio/DB/GFF/Adaptor/memory.pm -> blib/lib/Bio/DB/GFF/Adaptor/memory.pm
> Copying Bio/DB/UpdateableSeqI.pm -> blib/lib/Bio/DB/UpdateableSeqI.pm
> Copying Bio/DB/SeqFeature/Store/DBI/Pg.pm -> blib/lib/Bio/DB/SeqFeature/Store/DBI/Pg.pm
> Copying Bio/Restriction/IO/base.pm -> blib/lib/Bio/Restriction/IO/base.pm
> Copying Bio/Annotation/Target.pm -> blib/lib/Bio/Annotation/Target.pm
> Copying Bio/DB/RefSeq.pm -> blib/lib/Bio/DB/RefSeq.pm
> Copying Bio/Tools/RepeatMasker.pm -> blib/lib/Bio/Tools/RepeatMasker.pm
> Copying Bio/DB/GFF/Adaptor/memory/iterator.pm -> blib/lib/Bio/DB/GFF/Adaptor/memory/iterator.pm
> Copying Bio/AlignIO/xmfa.pm -> blib/lib/Bio/AlignIO/xmfa.pm
> Copying Bio/FeatureIO/vecscreen_simple.pm -> blib/lib/Bio/FeatureIO/vecscreen_simple.pm
> Copying Bio/Search/Result/HMMERResult.pm -> blib/lib/Bio/Search/Result/HMMERResult.pm
> Copying Bio/Coordinate/Result/Match.pm -> blib/lib/Bio/Coordinate/Result/Match.pm
> Copying Bio/SearchIO/wise.pm -> blib/lib/Bio/SearchIO/wise.pm
> Copying Bio/Tools/RNAMotif.pm -> blib/lib/Bio/Tools/RNAMotif.pm
> Copying Bio/Seq/PrimedSeq.pm -> blib/lib/Bio/Seq/PrimedSeq.pm
> Copying Bio/Structure/Chain.pm -> blib/lib/Bio/Structure/Chain.pm
> Copying Bio/DB/TFBS.pm -> blib/lib/Bio/DB/TFBS.pm
> Copying Bio/AlignIO/prodom.pm -> blib/lib/Bio/AlignIO/prodom.pm
> Copying Bio/Root/Test.pm -> blib/lib/Bio/Root/Test.pm
> Copying Bio/Assembly/ContigAnalysis.pm -> blib/lib/Bio/Assembly/ContigAnalysis.pm
> Copying Bio/Ontology/DocumentRegistry.pm -> blib/lib/Bio/Ontology/DocumentRegistry.pm
> Copying Bio/Coordinate/ExtrapolatingPair.pm -> blib/lib/Bio/Coordinate/ExtrapolatingPair.pm
> Copying Bio/SimpleAnalysisI.pm -> blib/lib/Bio/SimpleAnalysisI.pm
> Copying Bio/IdCollectionI.pm -> blib/lib/Bio/IdCollectionI.pm
> Copying Bio/Tree/AlleleNode.pm -> blib/lib/Bio/Tree/AlleleNode.pm
> Copying Bio/Tools/Gel.pm -> blib/lib/Bio/Tools/Gel.pm
> Copying Bio/Biblio/BiblioBase.pm -> blib/lib/Bio/Biblio/BiblioBase.pm
> Copying Bio/Biblio/IO.pm -> blib/lib/Bio/Biblio/IO.pm
> Copying Bio/DB/NCBIHelper.pm -> blib/lib/Bio/DB/NCBIHelper.pm
> Copying Bio/Map/FPCMarker.pm -> blib/lib/Bio/Map/FPCMarker.pm
> Copying Bio/Root/Build.pm -> blib/lib/Bio/Root/Build.pm
> Copying Bio/DB/GFF/Feature.pm -> blib/lib/Bio/DB/GFF/Feature.pm
> Copying Bio/Phenotype/OMIM/MiniMIMentry.pm -> blib/lib/Bio/Phenotype/OMIM/MiniMIMentry.pm
> Copying Bio/UpdateableSeqI.pm -> blib/lib/Bio/UpdateableSeqI.pm
> Copying Bio/Tools/Phylo/PAML/ModelResult.pm -> blib/lib/Bio/Tools/Phylo/PAML/ModelResult.pm
> Copying Bio/Biblio/Thesis.pm -> blib/lib/Bio/Biblio/Thesis.pm
> Copying Bio/Event/EventHandlerI.pm -> blib/lib/Bio/Event/EventHandlerI.pm
> Copying Bio/DB/Fasta.pm -> blib/lib/Bio/DB/Fasta.pm
> Copying Bio/Tools/EUtilities/Summary.pm -> blib/lib/Bio/Tools/EUtilities/Summary.pm
> Copying Bio/SeqIO/table.pm -> blib/lib/Bio/SeqIO/table.pm
> Copying Bio/TreeIO/lintree.pm -> blib/lib/Bio/TreeIO/lintree.pm
> Copying Bio/Biblio.pm -> blib/lib/Bio/Biblio.pm
> Copying Bio/Phenotype/OMIM/OMIMparser.pm -> blib/lib/Bio/Phenotype/OMIM/OMIMparser.pm
> Copying Bio/DB/GFF/Adaptor/dbi/pg_fts.pm -> blib/lib/Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
> Copying Bio/Restriction/Enzyme.pm -> blib/lib/Bio/Restriction/Enzyme.pm
> Copying Bio/SeqIO/game/seqHandler.pm -> blib/lib/Bio/SeqIO/game/seqHandler.pm
> Copying Bio/Matrix/PSM/InstanceSite.pm -> blib/lib/Bio/Matrix/PSM/InstanceSite.pm
> Copying Bio/Tree/TreeFunctionsI.pm -> blib/lib/Bio/Tree/TreeFunctionsI.pm
> Copying Bio/Assembly/Tools/ContigSpectrum.pm -> blib/lib/Bio/Assembly/Tools/ContigSpectrum.pm
> Copying Bio/Matrix/MatrixI.pm -> blib/lib/Bio/Matrix/MatrixI.pm
> Copying Bio/SeqIO/largefasta.pm -> blib/lib/Bio/SeqIO/largefasta.pm
> Copying Bio/Annotation/SimpleValue.pm -> blib/lib/Bio/Annotation/SimpleValue.pm
> Copying Bio/AlignIO/emboss.pm -> blib/lib/Bio/AlignIO/emboss.pm
> Copying Bio/Tools/EUtilities/Cookie.pm -> blib/lib/Bio/Tools/EUtilities/Cookie.pm
> Copying Bio/Search/Result/BlastPullResult.pm -> blib/lib/Bio/Search/Result/BlastPullResult.pm
> Copying Bio/Align/AlignI.pm -> blib/lib/Bio/Align/AlignI.pm
> Copying Bio/DB/Query/WebQuery.pm -> blib/lib/Bio/DB/Query/WebQuery.pm
> Copying Bio/Ontology/OntologyI.pm -> blib/lib/Bio/Ontology/OntologyI.pm
> Copying Bio/SearchIO/hmmer.pm -> blib/lib/Bio/SearchIO/hmmer.pm
> Copying Bio/SeqIO/ctf.pm -> blib/lib/Bio/SeqIO/ctf.pm
> Copying Bio/Tools/SeqPattern.pm -> blib/lib/Bio/Tools/SeqPattern.pm
> Copying Bio/DB/GFF/Aggregator/gene.pm -> blib/lib/Bio/DB/GFF/Aggregator/gene.pm
> Copying Bio/DB/SeqFeature/Store/bdb.pm -> blib/lib/Bio/DB/SeqFeature/Store/bdb.pm
> Copying Bio/SearchIO/psl.pm -> blib/lib/Bio/SearchIO/psl.pm
> Copying Bio/LiveSeq/DNA.pm -> blib/lib/Bio/LiveSeq/DNA.pm
> Copying Bio/Map/EntityI.pm -> blib/lib/Bio/Map/EntityI.pm
> Copying Bio/Index/AbstractSeq.pm -> blib/lib/Bio/Index/AbstractSeq.pm
> Copying Bio/DB/SeqFeature/NormalizedFeatureI.pm -> blib/lib/Bio/DB/SeqFeature/NormalizedFeatureI.pm
> Copying Bio/AlignIO.pm -> blib/lib/Bio/AlignIO.pm
> Copying Bio/Tree/NodeI.pm -> blib/lib/Bio/Tree/NodeI.pm
> Copying Bio/Tools/Prints.pm -> blib/lib/Bio/Tools/Prints.pm
> Copying Bio/SeqFeature/Gene/Exon.pm -> blib/lib/Bio/SeqFeature/Gene/Exon.pm
> Copying Bio/TreeIO/svggraph.pm -> blib/lib/Bio/TreeIO/svggraph.pm
> Copying Bio/Matrix/PSM/IO.pm -> blib/lib/Bio/Matrix/PSM/IO.pm
> Copying Bio/Taxonomy/Tree.pm -> blib/lib/Bio/Taxonomy/Tree.pm
> Copying Bio/Ontology/RelationshipType.pm -> blib/lib/Bio/Ontology/RelationshipType.pm
> Copying Bio/SeqIO/swissdriver.pm -> blib/lib/Bio/SeqIO/swissdriver.pm
> Copying Bio/Cluster/UniGene.pm -> blib/lib/Bio/Cluster/UniGene.pm
> Copying Bio/CodonUsage/Table.pm -> blib/lib/Bio/CodonUsage/Table.pm
> Copying Bio/SeqFeature/Generic.pm -> blib/lib/Bio/SeqFeature/Generic.pm
> Copying Bio/DB/ReferenceI.pm -> blib/lib/Bio/DB/ReferenceI.pm
> Copying Bio/PopGen/PopulationI.pm -> blib/lib/Bio/PopGen/PopulationI.pm
> Copying Bio/SeqFeature/Annotated.pm -> blib/lib/Bio/SeqFeature/Annotated.pm
> Copying Bio/SearchIO/infernal.pm -> blib/lib/Bio/SearchIO/infernal.pm
> Copying Bio/SeqFeature/SimilarityPair.pm -> blib/lib/Bio/SeqFeature/SimilarityPair.pm
> Copying Bio/Search/Hit/BlastPullHit.pm -> blib/lib/Bio/Search/Hit/BlastPullHit.pm
> Copying Bio/SeqIO/raw.pm -> blib/lib/Bio/SeqIO/raw.pm
> Copying Bio/Tools/Analysis/Protein/GOR4.pm -> blib/lib/Bio/Tools/Analysis/Protein/GOR4.pm
> Copying Bio/Search/Processor.pm -> blib/lib/Bio/Search/Processor.pm
> Copying Bio/PopGen/TagHaplotype.pm -> blib/lib/Bio/PopGen/TagHaplotype.pm
> Copying Bio/Seq.pm -> blib/lib/Bio/Seq.pm
> Copying Bio/Tools/EUtilities/Info.pm -> blib/lib/Bio/Tools/EUtilities/Info.pm
> Copying Bio/Biblio/Article.pm -> blib/lib/Bio/Biblio/Article.pm
> Copying Bio/Tools/HMMER/Results.pm -> blib/lib/Bio/Tools/HMMER/Results.pm
> Copying Bio/Search/BlastUtils.pm -> blib/lib/Bio/Search/BlastUtils.pm
> Copying Bio/Biblio/Organisation.pm -> blib/lib/Bio/Biblio/Organisation.pm
> Copying Bio/Tree/RandomFactory.pm -> blib/lib/Bio/Tree/RandomFactory.pm
> Copying Bio/Tools/Phylo/PAML/Result.pm -> blib/lib/Bio/Tools/Phylo/PAML/Result.pm
> Copying Bio/Structure/IO/pdb.pm -> blib/lib/Bio/Structure/IO/pdb.pm
> Copying Bio/DescribableI.pm -> blib/lib/Bio/DescribableI.pm
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> Copying Bio/Symbol/AlphabetI.pm -> blib/lib/Bio/Symbol/AlphabetI.pm
> Copying Bio/Search/Result/ResultI.pm -> blib/lib/Bio/Search/Result/ResultI.pm
> Copying Bio/RangeI.pm -> blib/lib/Bio/RangeI.pm
> Copying Bio/Matrix/PSM/InstanceSiteI.pm -> blib/lib/Bio/Matrix/PSM/InstanceSiteI.pm
> Copying Bio/Location/SplitLocationI.pm -> blib/lib/Bio/Location/SplitLocationI.pm
> Copying Bio/DB/SeqVersion/gi.pm -> blib/lib/Bio/DB/SeqVersion/gi.pm
> Copying Bio/Tools/Phylo/Gerp.pm -> blib/lib/Bio/Tools/Phylo/Gerp.pm
> Copying Bio/SeqIO/metafasta.pm -> blib/lib/Bio/SeqIO/metafasta.pm
> Copying Bio/SeqFeature/Gene/NC_Feature.pm -> blib/lib/Bio/SeqFeature/Gene/NC_Feature.pm
> Copying Bio/SeqEvolution/EvolutionI.pm -> blib/lib/Bio/SeqEvolution/EvolutionI.pm
> Copying Bio/DB/HIV/HIVAnnotProcessor.pm -> blib/lib/Bio/DB/HIV/HIVAnnotProcessor.pm
> Copying Bio/OntologyIO.pm -> blib/lib/Bio/OntologyIO.pm
> Copying Bio/Ontology/RelationshipI.pm -> blib/lib/Bio/Ontology/RelationshipI.pm
> Copying Bio/Ontology/OBOterm.pm -> blib/lib/Bio/Ontology/OBOterm.pm
> Copying Bio/Search/HSP/PsiBlastHSP.pm -> blib/lib/Bio/Search/HSP/PsiBlastHSP.pm
> Copying Bio/Index/GenBank.pm -> blib/lib/Bio/Index/GenBank.pm
> Copying Bio/SearchIO/rnamotif.pm -> blib/lib/Bio/SearchIO/rnamotif.pm
> Copying Bio/Tools/EUtilities/EUtilDataI.pm -> blib/lib/Bio/Tools/EUtilities/EUtilDataI.pm
> Copying Bio/Biblio/MedlineJournalArticle.pm -> blib/lib/Bio/Biblio/MedlineJournalArticle.pm
> Copying Bio/PhyloNetwork/muVector.pm -> blib/lib/Bio/PhyloNetwork/muVector.pm
> Copying Bio/Restriction/IO/itype2.pm -> blib/lib/Bio/Restriction/IO/itype2.pm
> Copying Bio/CodonUsage/IO.pm -> blib/lib/Bio/CodonUsage/IO.pm
> Copying Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm -> blib/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm
> Copying Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm -> blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm
> Copying Bio/Expression/Platform.pm -> blib/lib/Bio/Expression/Platform.pm
> Copying Bio/Taxonomy/Node.pm -> blib/lib/Bio/Taxonomy/Node.pm
> Copying Bio/Variation/IO/xml.pm -> blib/lib/Bio/Variation/IO/xml.pm
> Copying Bio/DB/GFF/Aggregator/alignment.pm -> blib/lib/Bio/DB/GFF/Aggregator/alignment.pm
> Copying Bio/Matrix/Generic.pm -> blib/lib/Bio/Matrix/Generic.pm
> Copying Bio/FeatureHolderI.pm -> blib/lib/Bio/FeatureHolderI.pm
> Copying Bio/Search/Tiling/MapTileUtils.pm -> blib/lib/Bio/Search/Tiling/MapTileUtils.pm
> Copying Bio/Tools/dpAlign.pm -> blib/lib/Bio/Tools/dpAlign.pm
> Copying Bio/AlignIO/Handler/GenericAlignHandler.pm -> blib/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm
> Copying Bio/Restriction/IO.pm -> blib/lib/Bio/Restriction/IO.pm
> Copying Bio/SeqFeature/Gene/TranscriptI.pm -> blib/lib/Bio/SeqFeature/Gene/TranscriptI.pm
> Copying Bio/Cluster/FamilyI.pm -> blib/lib/Bio/Cluster/FamilyI.pm
> Copying Bio/DB/SeqFeature/Store/FeatureFileLoader.pm -> blib/lib/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm
> Copying Bio/DB/RandomAccessI.pm -> blib/lib/Bio/DB/RandomAccessI.pm
> Copying Bio/SeqIO/qual.pm -> blib/lib/Bio/SeqIO/qual.pm
> Copying Bio/SeqIO/kegg.pm -> blib/lib/Bio/SeqIO/kegg.pm
> Copying Bio/SearchIO/axt.pm -> blib/lib/Bio/SearchIO/axt.pm
> Copying Bio/Ontology/TermI.pm -> blib/lib/Bio/Ontology/TermI.pm
> Copying Bio/SeqIO/pln.pm -> blib/lib/Bio/SeqIO/pln.pm
> Copying Bio/AnalysisResultI.pm -> blib/lib/Bio/AnalysisResultI.pm
> Copying Bio/Search/Result/BlastResult.pm -> blib/lib/Bio/Search/Result/BlastResult.pm
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> Copying Bio/SeqIO/game/gameHandler.pm -> blib/lib/Bio/SeqIO/game/gameHandler.pm
> Copying Bio/DB/LocationI.pm -> blib/lib/Bio/DB/LocationI.pm
> Copying Bio/LiveSeq/Chain.pm -> blib/lib/Bio/LiveSeq/Chain.pm
> Copying Bio/ClusterIO/dbsnp.pm -> blib/lib/Bio/ClusterIO/dbsnp.pm
> Copying Bio/SearchIO/IteratedSearchResultEventBuilder.pm -> blib/lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm
> Copying Bio/Tools/Run/WrapperBase.pm -> blib/lib/Bio/Tools/Run/WrapperBase.pm
> Copying Bio/AlignIO/meme.pm -> blib/lib/Bio/AlignIO/meme.pm
> Copying Bio/AlignIO/arp.pm -> blib/lib/Bio/AlignIO/arp.pm
> Copying Bio/Map/MapI.pm -> blib/lib/Bio/Map/MapI.pm
> Copying Bio/PopGen/Marker.pm -> blib/lib/Bio/PopGen/Marker.pm
> Copying Bio/Tools/Genomewise.pm -> blib/lib/Bio/Tools/Genomewise.pm
> Copying Bio/Location/WidestCoordPolicy.pm -> blib/lib/Bio/Location/WidestCoordPolicy.pm
> Copying Bio/DB/SeqFeature/Store/GFF2Loader.pm -> blib/lib/Bio/DB/SeqFeature/Store/GFF2Loader.pm
> Copying Bio/DB/Flat/BDB/embl.pm -> blib/lib/Bio/DB/Flat/BDB/embl.pm
> Copying Bio/Search/HSP/BlastHSP.pm -> blib/lib/Bio/Search/HSP/BlastHSP.pm
> Copying Bio/LiveSeq/Mutator.pm -> blib/lib/Bio/LiveSeq/Mutator.pm
> Copying Bio/Phenotype/Measure.pm -> blib/lib/Bio/Phenotype/Measure.pm
> Copying Bio/SeqFeature/Gene/Intron.pm -> blib/lib/Bio/SeqFeature/Gene/Intron.pm
> Copying Bio/Tools/Eponine.pm -> blib/lib/Bio/Tools/Eponine.pm
> Copying Bio/DB/GFF/RelSegment.pm -> blib/lib/Bio/DB/GFF/RelSegment.pm
> Copying Bio/Seq/LargeSeqI.pm -> blib/lib/Bio/Seq/LargeSeqI.pm
> Copying Bio/DB/SeqFeature/Store/GFF3Loader.pm -> blib/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm
> Copying Bio/SeqIO/lasergene.pm -> blib/lib/Bio/SeqIO/lasergene.pm
> Copying Bio/Map/OrderedPosition.pm -> blib/lib/Bio/Map/OrderedPosition.pm
> Copying Bio/DB/GFF/Aggregator/ucsc_ensgene.pm -> blib/lib/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
> Copying Bio/Annotation/TypeManager.pm -> blib/lib/Bio/Annotation/TypeManager.pm
> Copying Bio/SeqIO/MultiFile.pm -> blib/lib/Bio/SeqIO/MultiFile.pm
> Copying Bio/Tools/Tmhmm.pm -> blib/lib/Bio/Tools/Tmhmm.pm
> Copying Bio/PopGen/IO/hapmap.pm -> blib/lib/Bio/PopGen/IO/hapmap.pm
> Copying Bio/FeatureIO/gtf.pm -> blib/lib/Bio/FeatureIO/gtf.pm
> Copying Bio/Factory/SeqAnalysisParserFactory.pm -> blib/lib/Bio/Factory/SeqAnalysisParserFactory.pm
> Copying Bio/SeqFeature/Gene/UTR.pm -> blib/lib/Bio/SeqFeature/Gene/UTR.pm
> Copying Bio/Map/CytoMarker.pm -> blib/lib/Bio/Map/CytoMarker.pm
> Copying Bio/AlignIO/selex.pm -> blib/lib/Bio/AlignIO/selex.pm
> Copying Bio/Search/Result/PullResultI.pm -> blib/lib/Bio/Search/Result/PullResultI.pm
> Copying Bio/Seq/SeqBuilder.pm -> blib/lib/Bio/Seq/SeqBuilder.pm
> Copying Bio/Biblio/Service.pm -> blib/lib/Bio/Biblio/Service.pm
> Copying Bio/Search/HSP/BlastPullHSP.pm -> blib/lib/Bio/Search/HSP/BlastPullHSP.pm
> Copying Bio/Biblio/MedlineJournal.pm -> blib/lib/Bio/Biblio/MedlineJournal.pm
> Copying Bio/DB/GenPept.pm -> blib/lib/Bio/DB/GenPept.pm
> Copying Bio/Map/TranscriptionFactor.pm -> blib/lib/Bio/Map/TranscriptionFactor.pm
> Copying Bio/Search/DatabaseI.pm -> blib/lib/Bio/Search/DatabaseI.pm
> Copying Bio/SeqIO/game/featHandler.pm -> blib/lib/Bio/SeqIO/game/featHandler.pm
> Copying Bio/Index/Blast.pm -> blib/lib/Bio/Index/Blast.pm
> Copying Bio/Tools/Blat.pm -> blib/lib/Bio/Tools/Blat.pm
> Copying Bio/FeatureIO/ptt.pm -> blib/lib/Bio/FeatureIO/ptt.pm
> Copying Bio/DB/SeqFeature/Store/memory.pm -> blib/lib/Bio/DB/SeqFeature/Store/memory.pm
> Copying Bio/Tools/EUtilities/Query.pm -> blib/lib/Bio/Tools/EUtilities/Query.pm
> Copying Bio/Symbol/SymbolI.pm -> blib/lib/Bio/Symbol/SymbolI.pm
> Copying Bio/Tools/EPCR.pm -> blib/lib/Bio/Tools/EPCR.pm
> Copying Bio/Tools/pSW.pm -> blib/lib/Bio/Tools/pSW.pm
> Copying Bio/Location/NarrowestCoordPolicy.pm -> blib/lib/Bio/Location/NarrowestCoordPolicy.pm
> Copying Bio/SeqIO/bsml_sax.pm -> blib/lib/Bio/SeqIO/bsml_sax.pm
> Copying Bio/SeqIO/gbdriver.pm -> blib/lib/Bio/SeqIO/gbdriver.pm
> Copying Bio/AnnotatableI.pm -> blib/lib/Bio/AnnotatableI.pm
> Copying Bio/Tools/EUtilities/Link/LinkSet.pm -> blib/lib/Bio/Tools/EUtilities/Link/LinkSet.pm
> Copying Bio/Tools/Run/GenericParameters.pm -> blib/lib/Bio/Tools/Run/GenericParameters.pm
> Copying Bio/Biblio/Proceeding.pm -> blib/lib/Bio/Biblio/Proceeding.pm
> Copying Bio/TreeIO/newick.pm -> blib/lib/Bio/TreeIO/newick.pm
> Copying Bio/SeqFeature/Gene/GeneStructure.pm -> blib/lib/Bio/SeqFeature/Gene/GeneStructure.pm
> Copying Bio/Biblio/Book.pm -> blib/lib/Bio/Biblio/Book.pm
> Copying Bio/SearchIO/Writer/HTMLResultWriter.pm -> blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm
> Copying Bio/Tree/Statistics.pm -> blib/lib/Bio/Tree/Statistics.pm
> Copying Bio/Align/PairwiseStatistics.pm -> blib/lib/Bio/Align/PairwiseStatistics.pm
> Copying Bio/Assembly/IO.pm -> blib/lib/Bio/Assembly/IO.pm
> Copying Bio/SeqIO/tinyseq.pm -> blib/lib/Bio/SeqIO/tinyseq.pm
> Copying Bio/Ontology/TermFactory.pm -> blib/lib/Bio/Ontology/TermFactory.pm
> Copying Bio/Tools/SeqWords.pm -> blib/lib/Bio/Tools/SeqWords.pm
> Copying Bio/DB/GFF/Adaptor/dbi/oracleace.pm -> blib/lib/Bio/DB/GFF/Adaptor/dbi/oracleace.pm
> Copying Bio/Expression/FeatureI.pm -> blib/lib/Bio/Expression/FeatureI.pm
> Copying Bio/Map/OrderedPositionWithDistance.pm -> blib/lib/Bio/Map/OrderedPositionWithDistance.pm
> Copying Bio/DB/SeqFeature/Store/berkeleydb.pm -> blib/lib/Bio/DB/SeqFeature/Store/berkeleydb.pm
> Copying Bio/Matrix/PSM/ProtPsm.pm -> blib/lib/Bio/Matrix/PSM/ProtPsm.pm
> Copying Bio/SeqIO/game.pm -> blib/lib/Bio/SeqIO/game.pm
> Copying Bio/Biblio/IO/pubmed2ref.pm -> blib/lib/Bio/Biblio/IO/pubmed2ref.pm
> Copying Bio/Index/Abstract.pm -> blib/lib/Bio/Index/Abstract.pm
> Copying Bio/Search/Iteration/IterationI.pm -> blib/lib/Bio/Search/Iteration/IterationI.pm
> Copying Bio/SearchIO/blastxml.pm -> blib/lib/Bio/SearchIO/blastxml.pm
> Copying Bio/Tools/HMMER/Domain.pm -> blib/lib/Bio/Tools/HMMER/Domain.pm
> Copying Bio/DB/GFF/Adaptor/dbi/oracle.pm -> blib/lib/Bio/DB/GFF/Adaptor/dbi/oracle.pm
> Copying Bio/PhyloNetwork/TreeFactoryX.pm -> blib/lib/Bio/PhyloNetwork/TreeFactoryX.pm
> Copying Bio/SeqFeature/Tools/FeatureNamer.pm -> blib/lib/Bio/SeqFeature/Tools/FeatureNamer.pm
> Copying Bio/SeqIO/flybase_chadoxml.pm -> blib/lib/Bio/SeqIO/flybase_chadoxml.pm
> Copying Bio/Coordinate/GeneMapper.pm -> blib/lib/Bio/Coordinate/GeneMapper.pm
> Copying Bio/Biblio/IO/medlinexml.pm -> blib/lib/Bio/Biblio/IO/medlinexml.pm
> Copying Bio/SeqIO/ace.pm -> blib/lib/Bio/SeqIO/ace.pm
> Copying Bio/Location/FuzzyLocationI.pm -> blib/lib/Bio/Location/FuzzyLocationI.pm
> Copying Bio/DB/TFBS/transfac_pro.pm -> blib/lib/Bio/DB/TFBS/transfac_pro.pm
> Copying Bio/Search/Hit/Fasta.pm -> blib/lib/Bio/Search/Hit/Fasta.pm
> Copying Bio/Root/Exception.pm -> blib/lib/Bio/Root/Exception.pm
> Copying Bio/Factory/TreeFactoryI.pm -> blib/lib/Bio/Factory/TreeFactoryI.pm
> Copying Bio/Expression/Contact.pm -> blib/lib/Bio/Expression/Contact.pm
> Copying Bio/SearchIO/cross_match.pm -> blib/lib/Bio/SearchIO/cross_match.pm
> Copying Bio/Assembly/IO/ace.pm -> blib/lib/Bio/Assembly/IO/ace.pm
> Copying Bio/Expression/Sample.pm -> blib/lib/Bio/Expression/Sample.pm
> Copying Bio/Map/RelativeI.pm -> blib/lib/Bio/Map/RelativeI.pm
> Copying Bio/DB/Biblio/soap.pm -> blib/lib/Bio/DB/Biblio/soap.pm
> Copying Bio/SeqIO/tab.pm -> blib/lib/Bio/SeqIO/tab.pm
> Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS
> Deleting blib/script/bp_sreformat.PLS.bak
> blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl
> Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS
> Deleting blib/script/seqconvert.PLS.bak
> blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl
> Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS
> Deleting blib/script/parse_hmmsearch.PLS.bak
> blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl
> Copying scripts/DB-HIV/hivq.PLS -> blib/script/hivq.PLS
> Deleting blib/script/hivq.PLS.bak
> blib/script/hivq.PLS -> blib/script/bp_hivq.pl
> Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS
> Deleting blib/script/bp_seqret.PLS.bak
> blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl
> Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS
> Deleting blib/script/meta_gff.PLS.bak
> blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl
> Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS
> Deleting blib/script/tree2pag.PLS.bak
> blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl
> Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS
> Deleting blib/script/nexus2nh.PLS.bak
> blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl
> Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS
> Deleting blib/script/filter_search.PLS.bak
> blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl
> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS
> blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl
> Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS
> Deleting blib/script/generate_histogram.PLS.bak
> blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl
> Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS
> Deleting blib/script/heterogeneity_test.PLS.bak
> blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl
> Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS
> Deleting blib/script/flanks.PLS.bak
> blib/script/flanks.PLS -> blib/script/bp_flanks.pl
> Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS
> Deleting blib/script/load_gff.PLS.bak
> blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl
> Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS
> Deleting blib/script/split_seq.PLS.bak
> blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl
> Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS
> Deleting blib/script/biogetseq.PLS.bak
> blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl
> Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS
> Deleting blib/script/bp_fetch.PLS.bak
> blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl
> Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS
> Deleting blib/script/mutate.PLS.bak
> blib/script/mutate.PLS -> blib/script/bp_mutate.pl
> Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS
> Deleting blib/script/process_sgd.PLS.bak
> blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl
> Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS
> Deleting blib/script/bp_index.PLS.bak
> blib/script/bp_index.PLS -> blib/script/bp_index.pl
> Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS
> Deleting blib/script/dbsplit.PLS.bak
> blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl
> Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS
> Deleting blib/script/oligo_count.PLS.bak
> blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl
> Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS
> Deleting blib/script/hmmer_to_table.PLS.bak
> blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl
> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS
> Deleting blib/script/bp_seqfeature_load.PLS.bak
> blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl
> Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS
> Deleting blib/script/process_gadfly.PLS.bak
> blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl
> Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS
> Deleting blib/script/fastam9_to_table.PLS.bak
> blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl
> Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS
> Deleting blib/script/seq_length.PLS.bak
> blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl
> Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS
> Deleting blib/script/biofetch_genbank_proxy.PLS.bak
> blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl
> Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS
> Deleting blib/script/extract_feature_seq.PLS.bak
> blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl
> Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS
> Deleting blib/script/genbank2gff.PLS.bak
> blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl
> Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS
> Deleting blib/script/bulk_load_gff.PLS.bak
> blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl
> Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS
> Deleting blib/script/taxid4species.PLS.bak
> blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl
> Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS
> Deleting blib/script/blast2tree.PLS.bak
> blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl
> Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS
> Deleting blib/script/search2gff.PLS.bak
> blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl
> Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS
> Deleting blib/script/unflatten_seq.PLS.bak
> blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl
> Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS
> Deleting blib/script/make_mrna_protein.PLS.bak
> blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl
> Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS
> Deleting blib/script/search2tribe.PLS.bak
> blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl
> Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS
> Deleting blib/script/bioflat_index.PLS.bak
> blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl
> Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS
> Deleting blib/script/query_entrez_taxa.PLS.bak
> blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl
> Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS
> Deleting blib/script/pairwise_kaks.PLS.bak
> blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl
> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS
> Deleting blib/script/bp_seqfeature_delete.PLS.bak
> blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl
> Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS
> Deleting blib/script/fast_load_gff.PLS.bak
> blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl
> Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS
> Deleting blib/script/chaos_plot.PLS.bak
> blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl
> Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS
> Deleting blib/script/taxonomy2tree.PLS.bak
> blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl
> Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS
> Deleting blib/script/bp_mrtrans.PLS.bak
> blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl
> Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS
> Deleting blib/script/search2alnblocks.PLS.bak
> blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl
> Copying scripts/Bio-DB-EUtilities/einfo.PLS -> blib/script/einfo.PLS
> Deleting blib/script/einfo.PLS.bak
> blib/script/einfo.PLS -> blib/script/bp_einfo.pl
> Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS
> Deleting blib/script/download_query_genbank.PLS.bak
> blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl
> Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS
> Deleting blib/script/bp_nrdb.PLS.bak
> blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl
> Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS
> Deleting blib/script/mask_by_search.PLS.bak
> blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl
> Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS
> Deleting blib/script/gccalc.PLS.bak
> blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl
> Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS
> Deleting blib/script/classify_hits_kingdom.PLS.bak
> blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl
> Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS
> Deleting blib/script/composite_LD.PLS.bak
> blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl
> Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS
> Deleting blib/script/aacomp.PLS.bak
> blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl
> Copying scripts/utilities/revtrans-motif.PLS -> blib/script/revtrans-motif.PLS
> Deleting blib/script/revtrans-motif.PLS.bak
> blib/script/revtrans-motif.PLS -> blib/script/bp_revtrans-motif.pl
> Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS
> Deleting blib/script/process_wormbase.PLS.bak
> blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl
> Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS
> Deleting blib/script/local_taxonomydb_query.PLS.bak
> blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl
> Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS
> Deleting blib/script/biblio.PLS.bak
> blib/script/biblio.PLS -> blib/script/bp_biblio.pl
> Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS
> Deleting blib/script/seqretsplit.PLS.bak
> blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl
> Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS
> Deleting blib/script/remote_blast.PLS.bak
> blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl
> Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS
> Deleting blib/script/genbank2gff3.PLS.bak
> blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl
> Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS
> Deleting blib/script/search2table.PLS.bak
> blib/script/search2table.PLS -> blib/script/bp_search2table.pl
> Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS
> Deleting blib/script/search2BSML.PLS.bak
> blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl
> Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS
> Deleting blib/script/translate_seq.PLS.bak
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> Copying Bio/DB/HIV/lanl-schema.xml -> blib/lib/Bio/DB/HIV/lanl-schema.xml
> Writing config notes to blib/lib/Bio/ConfigData.pm
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> Manifying blib/script/bp_translate_seq.pl -> blib/bindoc/bp_translate_seq.pl.1p
> Manifying blib/script/bp_flanks.pl -> blib/bindoc/bp_flanks.pl.1p
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> Manifying blib/script/bp_hmmer_to_table.pl -> blib/bindoc/bp_hmmer_to_table.pl.1p
> Manifying blib/script/bp_mask_by_search.pl -> blib/bindoc/bp_mask_by_search.pl.1p
> Manifying blib/script/bp_seqretsplit.pl -> blib/bindoc/bp_seqretsplit.pl.1p
> Manifying blib/script/bp_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1p
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> Manifying blib/script/bp_search2BSML.pl -> blib/bindoc/bp_search2BSML.pl.1p
> Manifying blib/script/bp_biofetch_genbank_proxy.pl -> blib/bindoc/bp_biofetch_genbank_proxy.pl.1p
> Manifying blib/script/bp_search2tribe.pl -> blib/bindoc/bp_search2tribe.pl.1p
> Manifying blib/script/bp_search2gff.pl -> blib/bindoc/bp_search2gff.pl.1p
> Manifying blib/script/bp_seqconvert.pl -> blib/bindoc/bp_seqconvert.pl.1p
> Manifying blib/script/bp_meta_gff.pl -> blib/bindoc/bp_meta_gff.pl.1p
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> Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1p
> Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1p
> Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.pl.1p
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> Manifying blib/script/bp_fastam9_to_table.pl -> blib/bindoc/bp_fastam9_to_table.pl.1p
> Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1p
> Manifying blib/script/bp_process_wormbase.pl -> blib/bindoc/bp_process_wormbase.pl.1p
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> Manifying blib/lib/Bio/Root/Exception.pm -> blib/libdoc/Bio::Root::Exception.3pm
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> Manifying blib/lib/Bio/Search/HSP/WABAHSP.pm -> blib/libdoc/Bio::Search::HSP::WABAHSP.3pm
> Manifying blib/lib/Bio/Biblio/Ref.pm -> blib/libdoc/Bio::Biblio::Ref.3pm
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> Manifying blib/lib/Bio/Biblio/MedlineArticle.pm -> blib/libdoc/Bio::Biblio::MedlineArticle.3pm
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> Manifying blib/lib/Bio/SeqIO/flybase_chadoxml.pm -> blib/libdoc/Bio::SeqIO::flybase_chadoxml.3pm
> Manifying blib/lib/Bio/Map/RelativeI.pm -> blib/libdoc/Bio::Map::RelativeI.3pm
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> Manifying blib/lib/Bio/ClusterIO/unigene.pm -> blib/libdoc/Bio::ClusterIO::unigene.3pm
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> Manifying blib/lib/Bio/Coordinate/Utils.pm -> blib/libdoc/Bio::Coordinate::Utils.3pm
> Manifying blib/lib/Bio/Tools/EUtilities/History.pm -> blib/libdoc/Bio::Tools::EUtilities::History.3pm
> Manifying blib/lib/Bio/PopGen/Statistics.pm -> blib/libdoc/Bio::PopGen::Statistics.3pm
> Manifying blib/lib/Bio/DB/EntrezGene.pm -> blib/libdoc/Bio::DB::EntrezGene.3pm
> Manifying blib/lib/Bio/AnnotationI.pm -> blib/libdoc/Bio::AnnotationI.3pm
> Manifying blib/lib/Bio/Ontology/Relationship.pm -> blib/libdoc/Bio::Ontology::Relationship.3pm
> Manifying blib/lib/Bio/Tools/Analysis/Protein/HNN.pm -> blib/libdoc/Bio::Tools::Analysis::Protein::HNN.3pm
> Manifying blib/lib/Bio/Tools/SeqWords.pm -> blib/libdoc/Bio::Tools::SeqWords.3pm
> Manifying blib/lib/Bio/SeqIO/raw.pm -> blib/libdoc/Bio::SeqIO::raw.3pm
> Manifying blib/lib/Bio/Seq/SeqBuilder.pm -> blib/libdoc/Bio::Seq::SeqBuilder.3pm
> Manifying blib/lib/Bio/SeqFeature/TypedSeqFeatureI.pm -> blib/libdoc/Bio::SeqFeature::TypedSeqFeatureI.3pm
> Manifying blib/lib/Bio/Search/Iteration/IterationI.pm -> blib/libdoc/Bio::Search::Iteration::IterationI.3pm
> Manifying blib/lib/Bio/PopGen/HtSNP.pm -> blib/libdoc/Bio::PopGen::HtSNP.3pm
> Manifying blib/lib/Bio/LiveSeq/Chain.pm -> blib/libdoc/Bio::LiveSeq::Chain.3pm
> Manifying blib/lib/Bio/Search/Result/ResultFactory.pm -> blib/libdoc/Bio::Search::Result::ResultFactory.3pm
> Manifying blib/lib/Bio/LiveSeq/Mutation.pm -> blib/libdoc/Bio::LiveSeq::Mutation.3pm
> Manifying blib/lib/Bio/Map/SimpleMap.pm -> blib/libdoc/Bio::Map::SimpleMap.3pm
> Manifying blib/lib/Bio/DB/SeqFeature/Store/GFF2Loader.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::GFF2Loader.3pm
> Manifying blib/lib/Bio/DB/SeqFeature/Store/DBI/Pg.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::DBI::Pg.3pm
> Manifying blib/lib/Bio/Matrix/PSM/InstanceSiteI.pm -> blib/libdoc/Bio::Matrix::PSM::InstanceSiteI.3pm
> Manifying blib/lib/Bio/Tools/HMMER/Domain.pm -> blib/libdoc/Bio::Tools::HMMER::Domain.3pm
> Manifying blib/lib/Bio/Search/Hit/ModelHit.pm -> blib/libdoc/Bio::Search::Hit::ModelHit.3pm
> Manifying blib/lib/Bio/Map/Physical.pm -> blib/libdoc/Bio::Map::Physical.3pm
> Manifying blib/lib/Bio/Structure/SecStr/STRIDE/Res.pm -> blib/libdoc/Bio::Structure::SecStr::STRIDE::Res.3pm
> Manifying blib/lib/Bio/DB/InMemoryCache.pm -> blib/libdoc/Bio::DB::InMemoryCache.3pm
> Manifying blib/lib/Bio/Perl.pm -> blib/libdoc/Bio::Perl.3pm
> Manifying blib/lib/Bio/SeqIO/game/gameWriter.pm -> blib/libdoc/Bio::SeqIO::game::gameWriter.3pm
> Manifying blib/lib/Bio/SeqIO/abi.pm -> blib/libdoc/Bio::SeqIO::abi.3pm
> Manifying blib/lib/Bio/LiveSeq/AARange.pm -> blib/libdoc/Bio::LiveSeq::AARange.3pm
> Manifying blib/lib/Bio/PrimarySeq.pm -> blib/libdoc/Bio::PrimarySeq.3pm
> Manifying blib/lib/Bio/DB/Flat/BDB/fasta.pm -> blib/libdoc/Bio::DB::Flat::BDB::fasta.3pm
> Manifying blib/lib/Bio/Tools/Run/GenericParameters.pm -> blib/libdoc/Bio::Tools::Run::GenericParameters.3pm
> Manifying blib/lib/Bio/SeqIO/lasergene.pm -> blib/libdoc/Bio::SeqIO::lasergene.3pm
> Manifying blib/lib/Bio/PopGen/IO/prettybase.pm -> blib/libdoc/Bio::PopGen::IO::prettybase.3pm
> Manifying blib/lib/Bio/Assembly/IO/ace.pm -> blib/libdoc/Bio::Assembly::IO::ace.3pm
> Manifying blib/lib/Bio/Matrix/PSM/IO/transfac.pm -> blib/libdoc/Bio::Matrix::PSM::IO::transfac.3pm
> Manifying blib/lib/Bio/SimpleAnalysisI.pm -> blib/libdoc/Bio::SimpleAnalysisI.3pm
> Manifying blib/lib/Bio/Symbol/SymbolI.pm -> blib/libdoc/Bio::Symbol::SymbolI.3pm
> Manifying blib/lib/Bio/LiveSeq/IO/BioPerl.pm -> blib/libdoc/Bio::LiveSeq::IO::BioPerl.3pm
> Manifying blib/lib/Bio/Annotation/OntologyTerm.pm -> blib/libdoc/Bio::Annotation::OntologyTerm.3pm
> Manifying blib/lib/Bio/Tools/Run/RemoteBlast.pm -> blib/libdoc/Bio::Tools::Run::RemoteBlast.3pm
> Manifying blib/lib/Bio/Phenotype/MeSH/Term.pm -> blib/libdoc/Bio::Phenotype::MeSH::Term.3pm
> Manifying blib/lib/Bio/Tools/Pseudowise.pm -> blib/libdoc/Bio::Tools::Pseudowise.3pm
> Manifying blib/lib/Bio/DB/HIV.pm -> blib/libdoc/Bio::DB::HIV.3pm
> Manifying blib/lib/Bio/Matrix/IO.pm -> blib/libdoc/Bio::Matrix::IO.3pm
> Manifying blib/lib/Bio/Map/Gene.pm -> blib/libdoc/Bio::Map::Gene.3pm
> Manifying blib/lib/Bio/Map/Prediction.pm -> blib/libdoc/Bio::Map::Prediction.3pm
> Manifying blib/lib/Bio/SeqFeature/AnnotationAdaptor.pm -> blib/libdoc/Bio::SeqFeature::AnnotationAdaptor.3pm
> Manifying blib/lib/Bio/Biblio/Person.pm -> blib/libdoc/Bio::Biblio::Person.3pm
> Manifying blib/lib/Bio/Search/BlastStatistics.pm -> blib/libdoc/Bio::Search::BlastStatistics.3pm
> Manifying blib/lib/Bio/PopGen/MarkerI.pm -> blib/libdoc/Bio::PopGen::MarkerI.3pm
> Manifying blib/lib/Bio/Tools/Grail.pm -> blib/libdoc/Bio::Tools::Grail.3pm
> Manifying blib/lib/Bio/Search/HSP/ModelHSP.pm -> blib/libdoc/Bio::Search::HSP::ModelHSP.3pm
> Manifying blib/lib/Bio/DB/WebDBSeqI.pm -> blib/libdoc/Bio::DB::WebDBSeqI.3pm
> Manifying blib/lib/Bio/AlignIO/clustalw.pm -> blib/libdoc/Bio::AlignIO::clustalw.3pm
> Manifying blib/lib/Bio/TreeIO/newick.pm -> blib/libdoc/Bio::TreeIO::newick.3pm
> Manifying blib/lib/Bio/Tools/EUtilities/Link/LinkSet.pm -> blib/libdoc/Bio::Tools::EUtilities::Link::LinkSet.3pm
> Manifying blib/lib/Bio/PopGen/Utilities.pm -> blib/libdoc/Bio::PopGen::Utilities.3pm
> Manifying blib/lib/Bio/Tools/Analysis/DNA/ESEfinder.pm -> blib/libdoc/Bio::Tools::Analysis::DNA::ESEfinder.3pm
> Manifying blib/lib/Bio/Search/HSP/FastaHSP.pm -> blib/libdoc/Bio::Search::HSP::FastaHSP.3pm
> Manifying blib/lib/Bio/Phenotype/OMIM/MiniMIMentry.pm -> blib/libdoc/Bio::Phenotype::OMIM::MiniMIMentry.3pm
> Manifying blib/lib/Bio/Tools/Analysis/Protein/ELM.pm -> blib/libdoc/Bio::Tools::Analysis::Protein::ELM.3pm
> Manifying blib/lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm -> blib/libdoc/Bio::Tools::Analysis::SimpleAnalysisBase.3pm
> Manifying blib/lib/Bio/FeatureIO/gtf.pm -> blib/libdoc/Bio::FeatureIO::gtf.3pm
> Manifying blib/lib/Bio/AnnotatableI.pm -> blib/libdoc/Bio::AnnotatableI.3pm
> Manifying blib/lib/Bio/DB/RefSeq.pm -> blib/libdoc/Bio::DB::RefSeq.3pm
> Manifying blib/lib/Bio/Seq/Meta/Array.pm -> blib/libdoc/Bio::Seq::Meta::Array.3pm
> Manifying blib/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::GFF3Loader.3pm
> Manifying blib/lib/Bio/PopGen/TagHaplotype.pm -> blib/libdoc/Bio::PopGen::TagHaplotype.3pm
> Manifying blib/lib/Bio/Seq/SeqWithQuality.pm -> blib/libdoc/Bio::Seq::SeqWithQuality.3pm
> Manifying blib/lib/Bio/Variation/SeqDiff.pm -> blib/libdoc/Bio::Variation::SeqDiff.3pm
> Manifying blib/lib/Bio/Structure/IO.pm -> blib/libdoc/Bio::Structure::IO.3pm
> Manifying blib/lib/Bio/Matrix/IO/mlagan.pm -> blib/libdoc/Bio::Matrix::IO::mlagan.3pm
> Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/oracle.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::oracle.3pm
> Manifying blib/lib/Bio/DB/Qual.pm -> blib/libdoc/Bio::DB::Qual.3pm
> ./Build test
> Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS
> Deleting blib/script/bp_sreformat.PLS.bak
> blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl
> Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS
> Deleting blib/script/seqconvert.PLS.bak
> blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl
> Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS
> Deleting blib/script/parse_hmmsearch.PLS.bak
> blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl
> Copying scripts/DB-HIV/hivq.PLS -> blib/script/hivq.PLS
> Deleting blib/script/hivq.PLS.bak
> blib/script/hivq.PLS -> blib/script/bp_hivq.pl
> Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS
> Deleting blib/script/bp_seqret.PLS.bak
> blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl
> Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS
> Deleting blib/script/meta_gff.PLS.bak
> blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl
> Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS
> Deleting blib/script/tree2pag.PLS.bak
> blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl
> Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS
> Deleting blib/script/nexus2nh.PLS.bak
> blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl
> Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS
> Deleting blib/script/filter_search.PLS.bak
> blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl
> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS
> blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl
> Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS
> Deleting blib/script/generate_histogram.PLS.bak
> blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl
> Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS
> Deleting blib/script/heterogeneity_test.PLS.bak
> blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl
> Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS
> Deleting blib/script/flanks.PLS.bak
> blib/script/flanks.PLS -> blib/script/bp_flanks.pl
> Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS
> Deleting blib/script/load_gff.PLS.bak
> blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl
> Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS
> Deleting blib/script/split_seq.PLS.bak
> blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl
> Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS
> Deleting blib/script/biogetseq.PLS.bak
> blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl
> Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS
> Deleting blib/script/bp_fetch.PLS.bak
> blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl
> Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS
> Deleting blib/script/mutate.PLS.bak
> blib/script/mutate.PLS -> blib/script/bp_mutate.pl
> Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS
> Deleting blib/script/process_sgd.PLS.bak
> blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl
> Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS
> Deleting blib/script/bp_index.PLS.bak
> blib/script/bp_index.PLS -> blib/script/bp_index.pl
> Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS
> Deleting blib/script/dbsplit.PLS.bak
> blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl
> Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS
> Deleting blib/script/oligo_count.PLS.bak
> blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl
> Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS
> Deleting blib/script/hmmer_to_table.PLS.bak
> blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl
> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS
> Deleting blib/script/bp_seqfeature_load.PLS.bak
> blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl
> Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS
> Deleting blib/script/process_gadfly.PLS.bak
> blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl
> Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS
> Deleting blib/script/fastam9_to_table.PLS.bak
> blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl
> Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS
> Deleting blib/script/seq_length.PLS.bak
> blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl
> Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS
> Deleting blib/script/biofetch_genbank_proxy.PLS.bak
> blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl
> Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS
> Deleting blib/script/extract_feature_seq.PLS.bak
> blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl
> Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS
> Deleting blib/script/genbank2gff.PLS.bak
> blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl
> Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS
> Deleting blib/script/bulk_load_gff.PLS.bak
> blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl
> Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS
> Deleting blib/script/taxid4species.PLS.bak
> blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl
> Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS
> Deleting blib/script/blast2tree.PLS.bak
> blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl
> Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS
> Deleting blib/script/search2gff.PLS.bak
> blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl
> Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS
> Deleting blib/script/unflatten_seq.PLS.bak
> blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl
> Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS
> Deleting blib/script/make_mrna_protein.PLS.bak
> blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl
> Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS
> Deleting blib/script/search2tribe.PLS.bak
> blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl
> Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS
> Deleting blib/script/bioflat_index.PLS.bak
> blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl
> Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS
> Deleting blib/script/query_entrez_taxa.PLS.bak
> blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl
> Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS
> Deleting blib/script/pairwise_kaks.PLS.bak
> blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl
> Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS
> Deleting blib/script/bp_seqfeature_delete.PLS.bak
> blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl
> Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS
> Deleting blib/script/fast_load_gff.PLS.bak
> blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl
> Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS
> Deleting blib/script/chaos_plot.PLS.bak
> blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl
> Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS
> Deleting blib/script/taxonomy2tree.PLS.bak
> blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl
> Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS
> Deleting blib/script/bp_mrtrans.PLS.bak
> blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl
> Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS
> Deleting blib/script/search2alnblocks.PLS.bak
> blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl
> Copying scripts/Bio-DB-EUtilities/einfo.PLS -> blib/script/einfo.PLS
> Deleting blib/script/einfo.PLS.bak
> blib/script/einfo.PLS -> blib/script/bp_einfo.pl
> Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS
> Deleting blib/script/download_query_genbank.PLS.bak
> blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl
> Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS
> Deleting blib/script/bp_nrdb.PLS.bak
> blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl
> Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS
> Deleting blib/script/mask_by_search.PLS.bak
> blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl
> Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS
> Deleting blib/script/gccalc.PLS.bak
> blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl
> Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS
> Deleting blib/script/classify_hits_kingdom.PLS.bak
> blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl
> Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS
> Deleting blib/script/composite_LD.PLS.bak
> blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl
> Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS
> Deleting blib/script/aacomp.PLS.bak
> blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl
> Copying scripts/utilities/revtrans-motif.PLS -> blib/script/revtrans-motif.PLS
> Deleting blib/script/revtrans-motif.PLS.bak
> blib/script/revtrans-motif.PLS -> blib/script/bp_revtrans-motif.pl
> Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS
> Deleting blib/script/process_wormbase.PLS.bak
> blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl
> Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS
> Deleting blib/script/local_taxonomydb_query.PLS.bak
> blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl
> Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS
> Deleting blib/script/biblio.PLS.bak
> blib/script/biblio.PLS -> blib/script/bp_biblio.pl
> Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS
> Deleting blib/script/seqretsplit.PLS.bak
> blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl
> Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS
> Deleting blib/script/remote_blast.PLS.bak
> blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl
> Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS
> Deleting blib/script/genbank2gff3.PLS.bak
> blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl
> Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS
> Deleting blib/script/search2table.PLS.bak
> blib/script/search2table.PLS -> blib/script/bp_search2table.pl
> Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS
> Deleting blib/script/search2BSML.PLS.bak
> blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl
> Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS
> Deleting blib/script/translate_seq.PLS.bak
> blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl
> t/Align/AlignStats.t ......................... ok
> t/Align/AlignUtil.t .......................... ok
> t/Align/SimpleAlign.t ........................ ok
> t/Align/TreeBuild.t .......................... ok
> t/Align/Utilities.t .......................... ok
> t/AlignIO/AlignIO.t .......................... ok
> t/AlignIO/arp.t .............................. ok
> t/AlignIO/bl2seq.t ........................... ok
> t/AlignIO/clustalw.t ......................... ok
> t/AlignIO/emboss.t ........................... ok
> t/AlignIO/fasta.t ............................ ok
> t/AlignIO/largemultifasta.t .................. ok
> t/AlignIO/maf.t .............................. ok
> t/AlignIO/mase.t ............................. ok
> t/AlignIO/mega.t ............................. ok
> t/AlignIO/meme.t ............................. ok
> t/AlignIO/metafasta.t ........................ ok
> t/AlignIO/msf.t .............................. ok
> t/AlignIO/nexus.t ............................ ok
> t/AlignIO/pfam.t ............................. ok
> t/AlignIO/phylip.t ........................... ok
> t/AlignIO/po.t ............................... ok
> t/AlignIO/prodom.t ........................... ok
> t/AlignIO/psi.t .............................. ok
> t/AlignIO/selex.t ............................ ok
> t/AlignIO/stockholm.t ........................ ok
> t/AlignIO/xmfa.t ............................. ok
> t/Alphabet.t ................................. ok
> t/Annotation/Annotation.t .................... ok
> t/Annotation/AnnotationAdaptor.t ............. ok
> t/Assembly/Assembly.t ........................ ok
> t/Assembly/ContigSpectrum.t .................. ok
> t/Biblio/Biblio.t ............................ ok
> t/Biblio/References.t ........................ ok
> t/Biblio/biofetch.t .......................... skipped: Network tests have not been requested
> t/Biblio/eutils.t ............................ skipped: Network tests have not been requested
> t/ClusterIO/ClusterIO.t ...................... ok
> t/ClusterIO/SequenceFamily.t ................. ok
> t/ClusterIO/unigene.t ........................ ok
> t/Coordinate/CoordinateGraph.t ............... ok
> t/Coordinate/CoordinateMapper.t .............. ok
> t/Coordinate/GeneCoordinateMapper.t .......... ok
> t/LiveSeq/Chain.t ............................ ok
> t/LiveSeq/LiveSeq.t .......................... ok
> t/LiveSeq/Mutation.t ......................... ok
> t/LiveSeq/Mutator.t .......................... ok
> t/LocalDB/BioDBGFF.t ......................... ok
> t/LocalDB/BlastIndex.t ....................... ok
> t/LocalDB/DBFasta.t .......................... ok
> t/LocalDB/DBQual.t ........................... ok
> t/LocalDB/Flat.t ............................. ok
> t/LocalDB/Index.t ............................ ok
> t/LocalDB/Registry.t ......................... ok
> t/LocalDB/SeqFeature.t ....................... ok
> t/LocalDB/transfac_pro.t ..................... ok
> t/Map/Cyto.t ................................. ok
> t/Map/Linkage.t .............................. ok
> t/Map/Map.t .................................. ok
> t/Map/MapIO.t ................................ ok
> t/Map/MicrosatelliteMarker.t ................. ok
> t/Map/Physical.t ............................. ok
> t/Matrix/IO/masta.t .......................... ok
> t/Matrix/IO/psm.t ............................ ok
> t/Matrix/InstanceSite.t ...................... ok
> t/Matrix/Matrix.t ............................ ok
> t/Matrix/ProtMatrix.t ........................ ok
> t/Matrix/ProtPsm.t ........................... ok
> t/Matrix/SiteMatrix.t ........................ ok
> t/Ontology/GOterm.t .......................... ok
> t/Ontology/GraphAdaptor.t .................... ok
> t/Ontology/IO/go.t ........................... ok
> t/Ontology/IO/interpro.t ..................... ok
> t/Ontology/IO/obo.t .......................... ok
> t/Ontology/Ontology.t ........................ ok
> t/Ontology/OntologyEngine.t .................. ok
> t/Ontology/OntologyStore.t ................... skipped: Network tests have not been requested
> t/Ontology/Relationship.t .................... ok
> t/Ontology/RelationshipType.t ................ ok
> t/Ontology/Term.t ............................ ok
> t/Perl.t ..................................... ok
> t/Phenotype/Correlate.t ...................... ok
> t/Phenotype/MeSH.t ........................... ok
> t/Phenotype/Measure.t ........................ ok
> t/Phenotype/MiniMIMentry.t ................... ok
> t/Phenotype/OMIMentry.t ...................... ok
> t/Phenotype/OMIMentryAllelicVariant.t ........ ok
> t/Phenotype/OMIMparser.t ..................... ok
> t/Phenotype/Phenotype.t ...................... ok
> t/PodSyntax.t ................................ ok
> t/PopGen/Coalescent.t ........................ ok
> t/PopGen/HtSNP.t ............................. ok
> t/PopGen/MK.t ................................ ok
> t/PopGen/PopGen.t ............................ ok
> t/PopGen/PopGenSims.t ........................ ok
> t/PopGen/TagHaplotype.t ...................... ok
> t/RemoteDB/BioFetch.t ........................ skipped: Network tests have not been requested
> t/RemoteDB/CUTG.t ............................ ok
> t/RemoteDB/EMBL.t ............................ skipped: Network tests have not been requested
> t/RemoteDB/EUtilities.t ...................... skipped: Network tests have not been requested
> t/RemoteDB/EntrezGene.t ...................... skipped: Network tests have not been requested
> t/RemoteDB/GenBank.t ......................... skipped: Network tests have not been requested
> t/RemoteDB/GenPept.t ......................... skipped: Network tests have not been requested
> t/RemoteDB/HIV/HIV.t ......................... ok
> t/RemoteDB/HIV/HIVAnnotProcessor.t ........... ok
> Use of uninitialized value $rest[0] in join or string at (eval 67) line 15.
> t/RemoteDB/HIV/HIVQuery.t .................... ok
> t/RemoteDB/HIV/HIVQueryHelper.t .............. ok
> t/RemoteDB/MeSH.t ............................ skipped: Network tests have not been requested
> t/RemoteDB/Query/GenBank.t ................... skipped: Network tests have not been requested
> t/RemoteDB/RefSeq.t .......................... ok
> t/RemoteDB/SeqHound.t ........................ skipped: Network tests have not been requested
> t/RemoteDB/SeqRead_fail.t .................... skipped: Network tests have not been requested
> t/RemoteDB/SeqVersion.t ...................... ok
> t/RemoteDB/SwissProt.t ....................... skipped: Network tests have not been requested
> t/RemoteDB/Taxonomy.t ........................ ok
> t/Restriction/Analysis-refac.t ............... ok
> t/Restriction/Analysis.t ..................... ok
> t/Restriction/Gel.t .......................... ok
> t/Restriction/IO.t ........................... ok
> t/Root/Exception.t ........................... ok
> t/Root/RootI.t ............................... ok
> t/Root/RootIO.t .............................. ok
> t/Root/Storable.t ............................ ok
> t/Root/Tempfile.t ............................ ok
> t/Root/Utilities.t ........................... ok
> t/SearchDist.t ............................... skipped: The optional module Bio::Ext::Align (or dependencies thereof) was not installed
> t/SearchIO/CigarString.t ..................... ok
> t/SearchIO/SearchIO.t ........................ ok
> t/SearchIO/SimilarityPair.t .................. ok
> t/SearchIO/Tiling.t .......................... ok
> t/SearchIO/Writer/GbrowseGFF.t ............... ok
> t/SearchIO/Writer/HSPTableWriter.t ........... ok
> t/SearchIO/Writer/HTMLWriter.t ............... ok
> t/SearchIO/Writer/HitTableWriter.t ........... ok
> t/SearchIO/blast.t ........................... ok
> t/SearchIO/blast_pull.t ...................... ok
> t/SearchIO/blasttable.t ...................... ok
>
> --------------------- WARNING ---------------------
> MSG: error in parsing a report:
> http error : Operation in progress
>
> ---------------------------------------------------
>
> # Failed test at t/SearchIO/blastxml.t line 350.
> # got: '0'
> # expected: '1'
> Can't call method "database_name" on an undefined value at t/SearchIO/blastxml.t line 351.
> # Looks like you planned 391 tests but ran 228.
> # Looks like you failed 1 test of 228 run.
> # Looks like your test exited with 9 just after 228.
> t/SearchIO/blastxml.t ........................
> Dubious, test returned 9 (wstat 2304, 0x900)
> Failed 164/391 subtests
> t/SearchIO/cross_match.t ..................... ok
> t/SearchIO/erpin.t ........................... ok
> t/SearchIO/exonerate.t ....................... ok
> t/SearchIO/fasta.t ........................... ok
> t/SearchIO/gmap_f9.t ......................... ok
> t/SearchIO/hmmer.t ........................... ok
> t/SearchIO/hmmer_pull.t ...................... ok
> t/SearchIO/infernal.t ........................ ok
> t/SearchIO/megablast.t ....................... ok
> t/SearchIO/psl.t ............................. ok
> t/SearchIO/rnamotif.t ........................ ok
> t/SearchIO/sim4.t ............................ ok
> t/SearchIO/waba.t ............................ ok
> t/SearchIO/wise.t ............................ ok
> t/Seq/DBLink.t ............................... ok
> t/Seq/EncodedSeq.t ........................... ok
> t/Seq/LargeLocatableSeq.t .................... ok
> t/Seq/LargePSeq.t ............................ ok
> t/Seq/LocatableSeq.t ......................... ok
> t/Seq/MetaSeq.t .............................. ok
> t/Seq/PrimaryQual.t .......................... ok
> t/Seq/PrimarySeq.t ........................... ok
> t/Seq/PrimedSeq.t ............................ ok
> t/Seq/Quality.t .............................. ok
> t/Seq/Seq.t .................................. ok
> t/Seq/WithQuality.t .......................... ok
> t/SeqEvolution.t ............................. ok
> t/SeqFeature/FeatureIO.t ..................... ok
> t/SeqFeature/Location.t ...................... ok
> t/SeqFeature/LocationFactory.t ............... ok
> t/SeqFeature/Primer.t ........................ ok
> t/SeqFeature/Range.t ......................... ok
> t/SeqFeature/RangeI.t ........................ ok
> t/SeqFeature/SeqAnalysisParser.t ............. ok
> t/SeqFeature/SeqFeatAnnotated.t .............. skipped: Network tests have not been requested
> t/SeqFeature/SeqFeatCollection.t ............. ok
> t/SeqFeature/SeqFeature.t .................... ok
> t/SeqFeature/SeqFeaturePrimer.t .............. ok
> t/SeqFeature/Unflattener.t ................... ok
> t/SeqFeature/Unflattener2.t .................. ok
> t/SeqIO.t .................................... ok
> t/SeqIO/Handler.t ............................ ok
> t/SeqIO/MultiFile.t .......................... ok
> t/SeqIO/Multiple_fasta.t ..................... ok
> t/SeqIO/SeqBuilder.t ......................... ok
> t/SeqIO/Splicedseq.t ......................... ok
> t/SeqIO/abi.t ................................ skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
> t/SeqIO/ace.t ................................ ok
> t/SeqIO/agave.t .............................. ok
> t/SeqIO/alf.t ................................ skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
> t/SeqIO/asciitree.t .......................... ok
> t/SeqIO/bsml.t ............................... ok
> http error : Operation in progress
> # Looks like you planned 15 tests but ran 1.
> # Looks like your test exited with 9 just after 1.
> t/SeqIO/bsml_sax.t ...........................
> Dubious, test returned 9 (wstat 2304, 0x900)
> Failed 14/15 subtests
> t/SeqIO/chadoxml.t ........................... ok
> t/SeqIO/chaos.t .............................. ok
> t/SeqIO/chaosxml.t ........................... ok
> t/SeqIO/ctf.t ................................ skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
> t/SeqIO/embl.t ............................... ok
> t/SeqIO/entrezgene.t ......................... ok
> t/SeqIO/excel.t .............................. ok
> t/SeqIO/exp.t ................................ skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
> t/SeqIO/fasta.t .............................. ok
> t/SeqIO/fastq.t .............................. ok
> t/SeqIO/flybase_chadoxml.t ................... ok
> t/SeqIO/game.t ............................... ok
> t/SeqIO/gcg.t ................................ ok
> t/SeqIO/genbank.t ............................ ok
> t/SeqIO/interpro.t ........................... ok
> t/SeqIO/kegg.t ............................... ok
> t/SeqIO/largefasta.t ......................... ok
> t/SeqIO/lasergene.t .......................... ok
> t/SeqIO/locuslink.t .......................... ok
> t/SeqIO/metafasta.t .......................... ok
> t/SeqIO/phd.t ................................ ok
> t/SeqIO/pir.t ................................ ok
> t/SeqIO/pln.t ................................ skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
> t/SeqIO/qual.t ............................... ok
> t/SeqIO/raw.t ................................ ok
> t/SeqIO/scf.t ................................ ok
> t/SeqIO/strider.t ............................ ok
> t/SeqIO/swiss.t .............................. ok
> t/SeqIO/tab.t ................................ ok
> t/SeqIO/table.t .............................. ok
> t/SeqIO/tigr.t ............................... ok
> t/SeqIO/tigrxml.t ............................ ok
> t/SeqIO/tinyseq.t ............................ ok
> t/SeqIO/ztr.t ................................ skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
> t/SeqTools/Backtranslate.t ................... ok
> t/SeqTools/CodonTable.t ...................... ok
> t/SeqTools/ECnumber.t ........................ ok
> t/SeqTools/GuessSeqFormat.t .................. ok
> t/SeqTools/OddCodes.t ........................ ok
> t/SeqTools/SeqPattern.t ...................... ok
> t/SeqTools/SeqStats.t ........................ ok
> t/SeqTools/SeqUtils.t ........................ ok
> t/SeqTools/SeqWords.t ........................ ok
> t/Species.t .................................. ok
> t/Structure/IO.t ............................. ok
> t/Structure/Structure.t ...................... ok
> t/Symbol.t ................................... ok
> t/TaxonTree.t ................................ skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated
> t/Tools/Alignment/Consed.t ................... ok
> t/Tools/Analysis/DNA/ESEfinder.t ............. skipped: Network tests have not been requested
> t/Tools/Analysis/Protein/Domcut.t ............ skipped: Network tests have not been requested
> t/Tools/Analysis/Protein/ELM.t ............... skipped: Network tests have not been requested
> t/Tools/Analysis/Protein/GOR4.t .............. skipped: Network tests have not been requested
> t/Tools/Analysis/Protein/HNN.t ............... skipped: Network tests have not been requested
> t/Tools/Analysis/Protein/Mitoprot.t .......... skipped: Network tests have not been requested
> t/Tools/Analysis/Protein/NetPhos.t ........... skipped: Network tests have not been requested
> t/Tools/Analysis/Protein/Scansite.t .......... ok
> t/Tools/Analysis/Protein/Sopma.t ............. ok
> t/Tools/EMBOSS/Palindrome.t .................. ok
> t/Tools/EUtilities/EUtilParameters.t ......... ok
> http error : Operation in progress
> # Looks like you planned 19 tests but ran 1.
> # Looks like your test exited with 9 just after 1.
> t/Tools/EUtilities/egquery.t .................
> Dubious, test returned 9 (wstat 2304, 0x900)
> Failed 18/19 subtests
> http error : Operation in progress
> # Looks like you planned 51 tests but ran 2.
> # Looks like your test exited with 9 just after 2.
> t/Tools/EUtilities/einfo.t ...................
> Dubious, test returned 9 (wstat 2304, 0x900)
> Failed 49/51 subtests
> http error : Operation in progress
> # Looks like you planned 130 tests but ran 3.
> # Looks like your test exited with 9 just after 3.
> t/Tools/EUtilities/elink_acheck.t ............
> Dubious, test returned 9 (wstat 2304, 0x900)
> Failed 127/130 subtests
> http error : Operation in progress
> # Looks like you planned 64 tests but ran 3.
> # Looks like your test exited with 9 just after 3.
> t/Tools/EUtilities/elink_lcheck.t ............
> Dubious, test returned 9 (wstat 2304, 0x900)
> Failed 61/64 subtests
> http error : Operation in progress
> # Looks like you planned 86 tests but ran 3.
> # Looks like your test exited with 9 just after 3.
> t/Tools/EUtilities/elink_llinks.t ............
> Dubious, test returned 9 (wstat 2304, 0x900)
> Failed 83/86 subtests
> http error : Operation in progress
> # Looks like you planned 60 tests but ran 3.
> # Looks like your test exited with 9 just after 3.
> t/Tools/EUtilities/elink_ncheck.t ............
> Dubious, test returned 9 (wstat 2304, 0x900)
> Failed 57/60 subtests
> http error : Operation in progress
> # Looks like you planned 63 tests but ran 3.
> # Looks like your test exited with 9 just after 3.
> t/Tools/EUtilities/elink_neighbor.t ..........
> Dubious, test returned 9 (wstat 2304, 0x900)
> Failed 60/63 subtests
> http error : Operation in progress
> # Looks like you planned 65 tests but ran 3.
> # Looks like your test exited with 9 just after 3.
> t/Tools/EUtilities/elink_neighbor_history.t ..
> Dubious, test returned 9 (wstat 2304, 0x900)
> Failed 62/65 subtests
> http error : Operation in progress
> # Looks like you planned 58 tests but ran 3.
> # Looks like your test exited with 9 just after 3.
> t/Tools/EUtilities/elink_scores.t ............
> Dubious, test returned 9 (wstat 2304, 0x900)
> Failed 55/58 subtests
> http error : Operation in progress
> # Looks like you planned 17 tests but ran 6.
> # Looks like your test exited with 9 just after 6.
> t/Tools/EUtilities/epost.t ...................
> Dubious, test returned 9 (wstat 2304, 0x900)
> Failed 11/17 subtests
> http error : Operation in progress
> # Looks like you planned 33 tests but ran 2.
> # Looks like your test exited with 9 just after 2.
> t/Tools/EUtilities/esearch.t .................
> Dubious, test returned 9 (wstat 2304, 0x900)
> Failed 31/33 subtests
> http error : Operation in progress
> # Looks like you planned 22 tests but ran 2.
> # Looks like your test exited with 2 just after 2.
> t/Tools/EUtilities/espell.t ..................
> Dubious, test returned 2 (wstat 512, 0x200)
> Failed 20/22 subtests
> http error : Operation in progress
> # Looks like you planned 83 tests but ran 3.
> # Looks like your test exited with 9 just after 3.
> t/Tools/EUtilities/esummary.t ................
> Dubious, test returned 9 (wstat 2304, 0x900)
> Failed 80/83 subtests
> t/Tools/Est2Genome.t ......................... ok
> t/Tools/FootPrinter.t ........................ ok
> t/Tools/GFF.t ................................ ok
> t/Tools/Geneid.t ............................. ok
> t/Tools/Genewise.t ........................... ok
> t/Tools/Genomewise.t ......................... ok
> t/Tools/Genpred.t ............................ ok
> t/Tools/Hmmer.t .............................. ok
> t/Tools/IUPAC.t .............................. ok
> t/Tools/Lucy.t ............................... ok
> t/Tools/Match.t .............................. ok
> t/Tools/Phylo/Gerp.t ......................... ok
> t/Tools/Phylo/Molphy.t ....................... ok
> t/Tools/Phylo/PAML.t ......................... ok
> t/Tools/Phylo/Phylip/ProtDist.t .............. ok
> t/Tools/Primer3.t ............................ ok
> t/Tools/Promoterwise.t ....................... ok
> t/Tools/Pseudowise.t ......................... ok
> t/Tools/QRNA.t ............................... ok
> t/Tools/RandDistFunctions.t .................. ok
> t/Tools/RepeatMasker.t ....................... ok
> t/Tools/Run/RemoteBlast.t .................... skipped: Network tests have not been requested
> t/Tools/Run/RemoteBlast_rpsblast.t ........... skipped: Network tests have not been requested
> t/Tools/Run/StandAloneBlast.t ................ ok
> t/Tools/Run/WrapperBase.t .................... ok
> t/Tools/Seg.t ................................ ok
> t/Tools/SiRNA.t .............................. ok
> t/Tools/Sigcleave.t .......................... ok
> t/Tools/Signalp.t ............................ ok
> t/Tools/Signalp/ExtendedSignalp.t ............ ok
> t/Tools/Sim4.t ............................... ok
> t/Tools/Spidey/Spidey.t ...................... ok
> t/Tools/TandemRepeatsFinder.t ................ ok
> t/Tools/TargetP.t ............................ ok
> t/Tools/Tmhmm.t .............................. ok
> t/Tools/ePCR.t ............................... ok
> t/Tools/pICalculator.t ....................... ok
> t/Tools/rnamotif.t ........................... skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated
> t/Tools/tRNAscanSE.t ......................... ok
> t/Tree/Compatible.t .......................... ok
> t/Tree/Node.t ................................ ok
> t/Tree/PhyloNetwork/Factory.t ................ ok
> t/Tree/PhyloNetwork/GraphViz.t ............... ok
> t/Tree/PhyloNetwork/MuVector.t ............... ok
> t/Tree/PhyloNetwork/PhyloNetwork.t ........... ok
> t/Tree/PhyloNetwork/RandomFactory.t .......... skipped: The optional module Math::Random (or dependencies thereof) was not installed
> t/Tree/PhyloNetwork/TreeFactory.t ............ ok
> t/Tree/RandomTreeFactory.t ................... ok
> t/Tree/Tree.t ................................ ok
> t/Tree/TreeIO.t .............................. ok
> t/Tree/TreeIO/lintree.t ...................... ok
> t/Tree/TreeIO/newick.t ....................... ok
> t/Tree/TreeIO/nexus.t ........................ ok
> t/Tree/TreeIO/nhx.t .......................... ok
> t/Tree/TreeIO/phyloxml.t ..................... ok
> Use of uninitialized value $txt[0] in join or string at /usr/share/perl5/SVG/Element.pm line 1195, <GEN0> line 1.
> t/Tree/TreeIO/svggraph.t ..................... ok
> t/Tree/TreeIO/tabtree.t ...................... ok
> t/Tree/TreeStatistics.t ...................... ok
> t/Variation/AAChange.t ....................... ok
> t/Variation/AAReverseMutate.t ................ ok
> t/Variation/Allele.t ......................... ok
> t/Variation/DNAMutation.t .................... ok
> t/Variation/RNAChange.t ...................... ok
> t/Variation/SNP.t ............................ ok
> t/Variation/SeqDiff.t ........................ ok
> t/Variation/Variation_IO.t ................... ok
>
> Test Summary Report
> -------------------
> t/SearchIO/blastxml.t (Wstat: 2304 Tests: 228 Failed: 1)
> Failed test: 228
> Non-zero exit status: 9
> Parse errors: Bad plan. You planned 391 tests but ran 228.
> t/SeqIO/bsml_sax.t (Wstat: 2304 Tests: 1 Failed: 0)
> Non-zero exit status: 9
> Parse errors: Bad plan. You planned 15 tests but ran 1.
> t/Tools/EUtilities/egquery.t (Wstat: 2304 Tests: 1 Failed: 0)
> Non-zero exit status: 9
> Parse errors: Bad plan. You planned 19 tests but ran 1.
> t/Tools/EUtilities/einfo.t (Wstat: 2304 Tests: 2 Failed: 0)
> Non-zero exit status: 9
> Parse errors: Bad plan. You planned 51 tests but ran 2.
> t/Tools/EUtilities/elink_acheck.t (Wstat: 2304 Tests: 3 Failed: 0)
> Non-zero exit status: 9
> Parse errors: Bad plan. You planned 130 tests but ran 3.
> t/Tools/EUtilities/elink_lcheck.t (Wstat: 2304 Tests: 3 Failed: 0)
> Non-zero exit status: 9
> Parse errors: Bad plan. You planned 64 tests but ran 3.
> t/Tools/EUtilities/elink_llinks.t (Wstat: 2304 Tests: 3 Failed: 0)
> Non-zero exit status: 9
> Parse errors: Bad plan. You planned 86 tests but ran 3.
> t/Tools/EUtilities/elink_ncheck.t (Wstat: 2304 Tests: 3 Failed: 0)
> Non-zero exit status: 9
> Parse errors: Bad plan. You planned 60 tests but ran 3.
> t/Tools/EUtilities/elink_neighbor.t (Wstat: 2304 Tests: 3 Failed: 0)
> Non-zero exit status: 9
> Parse errors: Bad plan. You planned 63 tests but ran 3.
> t/Tools/EUtilities/elink_neighbor_history.t (Wstat: 2304 Tests: 3 Failed: 0)
> Non-zero exit status: 9
> Parse errors: Bad plan. You planned 65 tests but ran 3.
> t/Tools/EUtilities/elink_scores.t (Wstat: 2304 Tests: 3 Failed: 0)
> Non-zero exit status: 9
> Parse errors: Bad plan. You planned 58 tests but ran 3.
> t/Tools/EUtilities/epost.t (Wstat: 2304 Tests: 6 Failed: 0)
> Non-zero exit status: 9
> Parse errors: Bad plan. You planned 17 tests but ran 6.
> t/Tools/EUtilities/esearch.t (Wstat: 2304 Tests: 2 Failed: 0)
> Non-zero exit status: 9
> Parse errors: Bad plan. You planned 33 tests but ran 2.
> t/Tools/EUtilities/espell.t (Wstat: 512 Tests: 2 Failed: 0)
> Non-zero exit status: 2
> Parse errors: Bad plan. You planned 22 tests but ran 2.
> t/Tools/EUtilities/esummary.t (Wstat: 2304 Tests: 3 Failed: 0)
> Non-zero exit status: 9
> Parse errors: Bad plan. You planned 83 tests but ran 3.
> Files=329, Tests=19188, 184 wallclock secs ( 2.61 usr 1.06 sys + 103.65 cusr 9.02 csys = 116.34 CPU)
> Result: FAIL
> Failed 15/329 test programs. 1/19188 subtests failed.
> make: *** [build-stamp] Error 255
The full build log is available from:
http://people.debian.org/~lucas/logs/2009/12/23/bioperl_1.6.1-1_lsid64.buildlog
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on about 50 AMD64 nodes
of the Grid'5000 platform, using a clean chroot. Internet was not
accessible from the build systems.
--
| Lucas Nussbaum
| lucas at lucas-nussbaum.net http://www.lucas-nussbaum.net/ |
| jabber: lucas at nussbaum.fr GPG: 1024D/023B3F4F |
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