>>> Building on exopi-2 under biology/bioperl DIST = [biology/bioperl:BioPerl-1.7.8.tar.gz] FULLPKGNAME = bioperl-1.7.8 RDEPENDS = [textproc/p5-XML-Twig;textproc/p5-XML-SAX;www/p5-URI;devel/p5-IO-String;textproc/p5-XML-DOM;devel/p5-List-MoreUtils;devel/p5-Module-Build;textproc/p5-XML-SAX-Base;www/p5-HTTP-Message;devel/p5-YAML;devel/p5-Error;textproc/p5-XML-LibXML;devel/p5-Test-RequiresInternet;textproc/p5-XML-Writer;devel/p5-Data-Stag;devel/p5-IPC-Run;devel/p5-Test-Most;textproc/p5-XML-SAX-Writer;textproc/p5-Libxml;devel/p5-IO-stringy;textproc/p5-XML-DOM-XPath;devel/p5-Set-Scalar;devel/p5-Graph;www/p5-libwww] distfiles size=7527658 >>> Running build in biology/bioperl at 1711573354.64 ===> biology/bioperl ===> Building from scratch bioperl-1.7.8 ===> Checking files for bioperl-1.7.8 `/exopi-cvs/ports/distfiles/BioPerl-1.7.8.tar.gz' is up to date. >> (SHA256) BioPerl-1.7.8.tar.gz: OK ===> Extracting for bioperl-1.7.8 ===> Patching for bioperl-1.7.8 ===> Compiler link: clang -> /usr/bin/clang ===> Compiler link: clang++ -> /usr/bin/clang++ ===> Compiler link: cc -> /usr/bin/cc ===> Compiler link: c++ -> /usr/bin/c++ ===> Generating configure for bioperl-1.7.8 ===> Configuring for bioperl-1.7.8 Warning: prerequisite Data::Stag 0 not found. Warning: prerequisite Error 0 not found. Warning: prerequisite Graph::Directed 0 not found. Warning: prerequisite HTTP::Request::Common 0 not found. Warning: prerequisite HTTP::Response 0 not found. Warning: prerequisite IO::Scalar 0 not found. Warning: prerequisite IO::String 0 not found. Warning: prerequisite IPC::Run 0 not found. Warning: prerequisite LWP::UserAgent 0 not found. Warning: prerequisite List::MoreUtils 0 not found. Warning: prerequisite Set::Scalar 0 not found. Warning: prerequisite Test::Memory::Cycle 0 not found. Warning: prerequisite Test::Most 0 not found. Warning: prerequisite Test::RequiresInternet 0 not found. Warning: prerequisite Test::Weaken 0 not found. Warning: prerequisite URI 0 not found. Warning: prerequisite XML::DOM 0 not found. Warning: prerequisite XML::LibXML 0 not found. Warning: prerequisite XML::LibXML::Reader 0 not found. Warning: prerequisite XML::Parser::PerlSAX 0 not found. Warning: prerequisite XML::SAX 0 not found. Warning: prerequisite XML::SAX::Base 0 not found. Warning: prerequisite XML::SAX::Writer 0 not found. Warning: prerequisite XML::Twig 0 not found. Warning: prerequisite XML::Writer 0 not found. Warning: prerequisite YAML 0 not found. Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for BioPerl Writing MYMETA.yml and MYMETA.json ===> Building for bioperl-1.7.8 cp lib/Bio/Index/EMBL.pm blib/lib/Bio/Index/EMBL.pm cp lib/Bio/Tools/RandomDistFunctions.pm blib/lib/Bio/Tools/RandomDistFunctions.pm cp lib/Bio/DB/Flat/BinarySearch.pm blib/lib/Bio/DB/Flat/BinarySearch.pm cp lib/Bio/DB/QueryI.pm blib/lib/Bio/DB/QueryI.pm cp lib/Bio/Tree/NodeNHX.pm blib/lib/Bio/Tree/NodeNHX.pm cp lib/Bio/AlignIO/emboss.pm blib/lib/Bio/AlignIO/emboss.pm cp lib/Bio/SearchIO/blast_pull.pm blib/lib/Bio/SearchIO/blast_pull.pm cp lib/Bio/Tree/TreeI.pm blib/lib/Bio/Tree/TreeI.pm cp lib/Bio/AlignIO/maf.pm blib/lib/Bio/AlignIO/maf.pm cp lib/Bio/Matrix/PSM/ProtPsm.pm blib/lib/Bio/Matrix/PSM/ProtPsm.pm cp lib/Bio/Tools/Promoterwise.pm blib/lib/Bio/Tools/Promoterwise.pm cp lib/Bio/Seq/QualI.pm blib/lib/Bio/Seq/QualI.pm cp lib/Bio/Factory/ApplicationFactoryI.pm blib/lib/Bio/Factory/ApplicationFactoryI.pm cp lib/Bio/TreeIO.pm blib/lib/Bio/TreeIO.pm cp lib/Bio/Factory/SeqAnalysisParserFactory.pm blib/lib/Bio/Factory/SeqAnalysisParserFactory.pm cp lib/Bio/Search/Result/PullResultI.pm blib/lib/Bio/Search/Result/PullResultI.pm cp lib/Bio/SeqIO/fasta.pm blib/lib/Bio/SeqIO/fasta.pm cp lib/Bio/SimpleAlign.pm blib/lib/Bio/SimpleAlign.pm cp lib/Bio/Seq.pm blib/lib/Bio/Seq.pm cp lib/Bio/Matrix/PSM/PsmHeader.pm blib/lib/Bio/Matrix/PSM/PsmHeader.pm cp lib/Bio/Search/Result/BlastResult.pm blib/lib/Bio/Search/Result/BlastResult.pm cp lib/Bio/Factory/TreeFactoryI.pm blib/lib/Bio/Factory/TreeFactoryI.pm cp lib/Bio/Annotation/Tree.pm blib/lib/Bio/Annotation/Tree.pm cp lib/Bio/Root/Root.pm blib/lib/Bio/Root/Root.pm cp lib/Bio/Tools/Run/WrapperBase/CommandExts.pm blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm cp lib/Bio/Seq/Meta/Array.pm blib/lib/Bio/Seq/Meta/Array.pm cp lib/Bio/SeqIO/tigrxml.pm blib/lib/Bio/SeqIO/tigrxml.pm cp lib/Bio/Align/StatisticsI.pm blib/lib/Bio/Align/StatisticsI.pm cp lib/Bio/SimpleAnalysisI.pm blib/lib/Bio/SimpleAnalysisI.pm cp lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm blib/lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm cp lib/Bio/SeqIO/bsml_sax.pm blib/lib/Bio/SeqIO/bsml_sax.pm cp lib/Bio/SeqIO/kegg.pm blib/lib/Bio/SeqIO/kegg.pm cp lib/Bio/Matrix/IO/phylip.pm blib/lib/Bio/Matrix/IO/phylip.pm cp lib/Bio/Tree/Tree.pm blib/lib/Bio/Tree/Tree.pm cp lib/Bio/DB/WebDBSeqI.pm blib/lib/Bio/DB/WebDBSeqI.pm cp lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm blib/lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm cp lib/Bio/Tree/Statistics.pm blib/lib/Bio/Tree/Statistics.pm cp lib/Bio/SeqFeature/Lite.pm blib/lib/Bio/SeqFeature/Lite.pm cp lib/Bio/Das/FeatureTypeI.pm blib/lib/Bio/Das/FeatureTypeI.pm cp lib/Bio/SearchIO/megablast.pm blib/lib/Bio/SearchIO/megablast.pm cp lib/Bio/SeqFeature/PositionProxy.pm blib/lib/Bio/SeqFeature/PositionProxy.pm cp lib/Bio/AlignIO/bl2seq.pm blib/lib/Bio/AlignIO/bl2seq.pm cp lib/Bio/Matrix/PSM/PsmHeaderI.pm blib/lib/Bio/Matrix/PSM/PsmHeaderI.pm cp lib/Bio/DescribableI.pm blib/lib/Bio/DescribableI.pm cp lib/Bio/Root/Test.pm blib/lib/Bio/Root/Test.pm cp lib/Bio/Root/RootI.pm blib/lib/Bio/Root/RootI.pm cp lib/Bio/Search/Hit/Fasta.pm blib/lib/Bio/Search/Hit/Fasta.pm cp lib/Bio/Annotation/DBLink.pm blib/lib/Bio/Annotation/DBLink.pm cp lib/Bio/AlignIO/metafasta.pm blib/lib/Bio/AlignIO/metafasta.pm cp lib/Bio/Location/AvWithinCoordPolicy.pm blib/lib/Bio/Location/AvWithinCoordPolicy.pm cp lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm blib/lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm cp lib/Bio/SearchIO/Writer/TextResultWriter.pm blib/lib/Bio/SearchIO/Writer/TextResultWriter.pm cp lib/Bio/OntologyIO/dagflat.pm blib/lib/Bio/OntologyIO/dagflat.pm cp lib/Bio/AlignIO/phylip.pm blib/lib/Bio/AlignIO/phylip.pm cp lib/BioPerl.pm blib/lib/BioPerl.pm cp lib/Bio/Seq/PrimedSeq.pm blib/lib/Bio/Seq/PrimedSeq.pm cp lib/Bio/Tools/Phylo/Molphy/Result.pm blib/lib/Bio/Tools/Phylo/Molphy/Result.pm cp lib/Bio/AlignIO/msf.pm blib/lib/Bio/AlignIO/msf.pm cp lib/Bio/TreeIO/cluster.pm blib/lib/Bio/TreeIO/cluster.pm cp lib/Bio/DB/DBFetch.pm blib/lib/Bio/DB/DBFetch.pm cp lib/Bio/SeqIO/largefasta.pm blib/lib/Bio/SeqIO/largefasta.pm cp lib/Bio/SeqFeatureI.pm blib/lib/Bio/SeqFeatureI.pm cp lib/Bio/SeqFeature/AnnotationAdaptor.pm blib/lib/Bio/SeqFeature/AnnotationAdaptor.pm cp lib/Bio/Location/Atomic.pm blib/lib/Bio/Location/Atomic.pm cp lib/Bio/Location/Simple.pm blib/lib/Bio/Location/Simple.pm cp lib/Bio/Search/StatisticsI.pm blib/lib/Bio/Search/StatisticsI.pm cp lib/Bio/Search/Iteration/GenericIteration.pm blib/lib/Bio/Search/Iteration/GenericIteration.pm cp lib/Bio/Tools/Sigcleave.pm blib/lib/Bio/Tools/Sigcleave.pm cp lib/Bio/Tools/Phylo/Phylip/ProtDist.pm blib/lib/Bio/Tools/Phylo/Phylip/ProtDist.pm cp lib/Bio/SearchIO/fasta.pm blib/lib/Bio/SearchIO/fasta.pm cp lib/Bio/DB/Failover.pm blib/lib/Bio/DB/Failover.pm cp lib/Bio/SearchIO/gmap_f9.pm blib/lib/Bio/SearchIO/gmap_f9.pm cp lib/Bio/SearchIO/FastHitEventBuilder.pm blib/lib/Bio/SearchIO/FastHitEventBuilder.pm cp lib/Bio/Matrix/PSM/SiteMatrix.pm blib/lib/Bio/Matrix/PSM/SiteMatrix.pm cp lib/Bio/SearchIO/cross_match.pm blib/lib/Bio/SearchIO/cross_match.pm cp lib/Bio/OntologyIO.pm blib/lib/Bio/OntologyIO.pm cp lib/Bio/Seq/LargeLocatableSeq.pm blib/lib/Bio/Seq/LargeLocatableSeq.pm cp lib/Bio/Tools/GuessSeqFormat.pm blib/lib/Bio/Tools/GuessSeqFormat.pm cp lib/Bio/Tools/Genemark.pm blib/lib/Bio/Tools/Genemark.pm cp lib/Bio/ParameterBaseI.pm blib/lib/Bio/ParameterBaseI.pm cp lib/Bio/DB/LocationI.pm blib/lib/Bio/DB/LocationI.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/Tools/AmpliconSearch.pm blib/lib/Bio/Tools/AmpliconSearch.pm cp lib/Bio/SeqIO/asciitree.pm blib/lib/Bio/SeqIO/asciitree.pm cp lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm blib/lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm cp lib/Bio/Search/Result/GenericResult.pm blib/lib/Bio/Search/Result/GenericResult.pm cp lib/Bio/Matrix/Scoring.pm blib/lib/Bio/Matrix/Scoring.pm cp lib/Bio/Seq/RichSeqI.pm blib/lib/Bio/Seq/RichSeqI.pm cp lib/Bio/DB/Registry.pm blib/lib/Bio/DB/Registry.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/SearchIO/exonerate.pm blib/lib/Bio/SearchIO/exonerate.pm cp lib/Bio/SearchIO/SearchWriterI.pm blib/lib/Bio/SearchIO/SearchWriterI.pm cp lib/Bio/Matrix/PSM/InstanceSite.pm blib/lib/Bio/Matrix/PSM/InstanceSite.pm cp lib/Bio/SeqFeature/Generic.pm blib/lib/Bio/SeqFeature/Generic.pm cp lib/Bio/DB/FileCache.pm blib/lib/Bio/DB/FileCache.pm cp lib/Bio/Matrix/IO.pm blib/lib/Bio/Matrix/IO.pm cp lib/Bio/Tools/Genscan.pm blib/lib/Bio/Tools/Genscan.pm cp lib/Bio/Index/Qual.pm blib/lib/Bio/Index/Qual.pm cp lib/Bio/Index/AbstractSeq.pm blib/lib/Bio/Index/AbstractSeq.pm cp lib/Bio/Tree/Compatible.pm blib/lib/Bio/Tree/Compatible.pm cp lib/Bio/Location/SplitLocationI.pm blib/lib/Bio/Location/SplitLocationI.pm cp lib/Bio/SearchIO/blasttable.pm blib/lib/Bio/SearchIO/blasttable.pm cp lib/Bio/SeqFeature/Tools/FeatureNamer.pm blib/lib/Bio/SeqFeature/Tools/FeatureNamer.pm cp lib/Bio/DB/Flat/BDB/genbank.pm blib/lib/Bio/DB/Flat/BDB/genbank.pm cp lib/Bio/Seq/BaseSeqProcessor.pm blib/lib/Bio/Seq/BaseSeqProcessor.pm cp lib/Bio/Tools/Coil.pm blib/lib/Bio/Tools/Coil.pm cp lib/Bio/Tools/FootPrinter.pm blib/lib/Bio/Tools/FootPrinter.pm cp lib/Bio/Tools/pICalculator.pm blib/lib/Bio/Tools/pICalculator.pm cp lib/Bio/SeqFeature/Gene/TranscriptI.pm blib/lib/Bio/SeqFeature/Gene/TranscriptI.pm cp lib/Bio/Ontology/OBOEngine.pm blib/lib/Bio/Ontology/OBOEngine.pm cp lib/Bio/Tools/Eponine.pm blib/lib/Bio/Tools/Eponine.pm cp lib/Bio/PrimarySeq.pm blib/lib/Bio/PrimarySeq.pm cp lib/Bio/Matrix/PSM/IO.pm blib/lib/Bio/Matrix/PSM/IO.pm cp lib/Bio/Ontology/RelationshipType.pm blib/lib/Bio/Ontology/RelationshipType.pm cp lib/Bio/Search/HSP/PullHSPI.pm blib/lib/Bio/Search/HSP/PullHSPI.pm cp lib/Bio/DB/Taxonomy/greengenes.pm blib/lib/Bio/DB/Taxonomy/greengenes.pm cp lib/Bio/Tools/Primer/Pair.pm blib/lib/Bio/Tools/Primer/Pair.pm cp lib/Bio/Seq/MetaI.pm blib/lib/Bio/Seq/MetaI.pm cp lib/Bio/Factory/ObjectBuilderI.pm blib/lib/Bio/Factory/ObjectBuilderI.pm cp lib/Bio/DB/InMemoryCache.pm blib/lib/Bio/DB/InMemoryCache.pm cp lib/Bio/SearchIO/Writer/HTMLResultWriter.pm blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm cp lib/Bio/DB/Flat.pm blib/lib/Bio/DB/Flat.pm cp lib/Bio/Search/BlastUtils.pm blib/lib/Bio/Search/BlastUtils.pm cp lib/Bio/DB/Taxonomy.pm blib/lib/Bio/DB/Taxonomy.pm cp lib/Bio/Ontology/Relationship.pm blib/lib/Bio/Ontology/Relationship.pm cp lib/Bio/Search/HSP/GenericHSP.pm blib/lib/Bio/Search/HSP/GenericHSP.pm cp lib/Bio/TreeIO/TreeEventBuilder.pm blib/lib/Bio/TreeIO/TreeEventBuilder.pm cp lib/Bio/SeqIO/bsml.pm blib/lib/Bio/SeqIO/bsml.pm cp lib/Bio/SeqIO.pm blib/lib/Bio/SeqIO.pm cp lib/Bio/SeqFeature/Similarity.pm blib/lib/Bio/SeqFeature/Similarity.pm cp lib/Bio/AlignIO/mase.pm blib/lib/Bio/AlignIO/mase.pm cp lib/Bio/AlignIO/nexus.pm blib/lib/Bio/AlignIO/nexus.pm cp lib/Bio/DB/Flat/BDB/swiss.pm blib/lib/Bio/DB/Flat/BDB/swiss.pm cp lib/Bio/Tools/tRNAscanSE.pm blib/lib/Bio/Tools/tRNAscanSE.pm cp lib/Bio/SeqFeature/Computation.pm blib/lib/Bio/SeqFeature/Computation.pm cp lib/Bio/SeqFeature/Gene/Exon.pm blib/lib/Bio/SeqFeature/Gene/Exon.pm cp lib/Bio/Annotation/AnnotationFactory.pm blib/lib/Bio/Annotation/AnnotationFactory.pm cp lib/Bio/Ontology/SimpleOntologyEngine.pm blib/lib/Bio/Ontology/SimpleOntologyEngine.pm cp lib/Bio/AlignIO/prodom.pm blib/lib/Bio/AlignIO/prodom.pm cp lib/Bio/Tools/SeqStats.pm blib/lib/Bio/Tools/SeqStats.pm cp lib/Bio/Taxon.pm blib/lib/Bio/Taxon.pm cp lib/Bio/Seq/Meta.pm blib/lib/Bio/Seq/Meta.pm cp lib/Bio/Matrix/PSM/IO/mast.pm blib/lib/Bio/Matrix/PSM/IO/mast.pm cp lib/Bio/DB/Query/WebQuery.pm blib/lib/Bio/DB/Query/WebQuery.pm cp lib/Bio/AlignIO/clustalw.pm blib/lib/Bio/AlignIO/clustalw.pm cp lib/Bio/Annotation/OntologyTerm.pm blib/lib/Bio/Annotation/OntologyTerm.pm cp lib/Bio/Root/IO.pm blib/lib/Bio/Root/IO.pm cp lib/Bio/DBLinkContainerI.pm blib/lib/Bio/DBLinkContainerI.pm cp lib/Bio/DB/ReferenceI.pm blib/lib/Bio/DB/ReferenceI.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/SeqFeature/Gene/Poly_A_site.pm blib/lib/Bio/SeqFeature/Gene/Poly_A_site.pm cp lib/Bio/Factory/SequenceProcessorI.pm blib/lib/Bio/Factory/SequenceProcessorI.pm cp lib/Bio/SeqIO/msout.pm blib/lib/Bio/SeqIO/msout.pm cp lib/Bio/Seq/PrimaryQual.pm blib/lib/Bio/Seq/PrimaryQual.pm cp lib/Bio/Search/HSP/BlastHSP.pm blib/lib/Bio/Search/HSP/BlastHSP.pm cp lib/Bio/SearchIO/SearchResultEventBuilder.pm blib/lib/Bio/SearchIO/SearchResultEventBuilder.pm cp lib/Bio/AnalysisI.pm blib/lib/Bio/AnalysisI.pm cp lib/Bio/TreeIO/lintree.pm blib/lib/Bio/TreeIO/lintree.pm cp lib/Bio/SearchIO/Writer/GbrowseGFF.pm blib/lib/Bio/SearchIO/Writer/GbrowseGFF.pm cp lib/Bio/Search/Result/INFERNALResult.pm blib/lib/Bio/Search/Result/INFERNALResult.pm cp lib/Bio/OntologyIO/obo.pm blib/lib/Bio/OntologyIO/obo.pm cp lib/Bio/Tree/RandomFactory.pm blib/lib/Bio/Tree/RandomFactory.pm cp lib/Bio/Tools/Genewise.pm blib/lib/Bio/Tools/Genewise.pm cp lib/Bio/Root/Utilities.pm blib/lib/Bio/Root/Utilities.pm cp lib/Bio/Search/Tiling/MapTiling.pm blib/lib/Bio/Search/Tiling/MapTiling.pm cp lib/Bio/Tools/Est2Genome.pm blib/lib/Bio/Tools/Est2Genome.pm cp lib/Bio/SearchIO/sim4.pm blib/lib/Bio/SearchIO/sim4.pm cp lib/Bio/AlignIO/meme.pm blib/lib/Bio/AlignIO/meme.pm cp lib/Bio/DB/Fasta.pm blib/lib/Bio/DB/Fasta.pm cp lib/Bio/Matrix/PSM/IO/psiblast.pm blib/lib/Bio/Matrix/PSM/IO/psiblast.pm cp lib/Bio/Search/BlastStatistics.pm blib/lib/Bio/Search/BlastStatistics.pm cp lib/Bio/SeqIO/metafasta.pm blib/lib/Bio/SeqIO/metafasta.pm cp lib/Bio/Tools/Phylo/Molphy.pm blib/lib/Bio/Tools/Phylo/Molphy.pm cp lib/Bio/SearchIO/blast.pm blib/lib/Bio/SearchIO/blast.pm cp lib/Bio/Search/SearchUtils.pm blib/lib/Bio/Search/SearchUtils.pm cp lib/Bio/Search/Hit/PullHitI.pm blib/lib/Bio/Search/Hit/PullHitI.pm cp lib/Bio/SeqFeature/Gene/NC_Feature.pm blib/lib/Bio/SeqFeature/Gene/NC_Feature.pm cp lib/Bio/Annotation/Comment.pm blib/lib/Bio/Annotation/Comment.pm cp lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm cp lib/Bio/Matrix/PSM/IO/masta.pm blib/lib/Bio/Matrix/PSM/IO/masta.pm cp lib/Bio/Ontology/InterProTerm.pm blib/lib/Bio/Ontology/InterProTerm.pm cp lib/Bio/AnalysisResultI.pm blib/lib/Bio/AnalysisResultI.pm cp lib/Bio/DB/UpdateableSeqI.pm blib/lib/Bio/DB/UpdateableSeqI.pm cp lib/Bio/Tools/ESTScan.pm blib/lib/Bio/Tools/ESTScan.pm cp lib/Bio/Tools/Lucy.pm blib/lib/Bio/Tools/Lucy.pm cp lib/Bio/SeqIO/fastq.pm blib/lib/Bio/SeqIO/fastq.pm cp lib/Bio/OntologyIO/goflat.pm blib/lib/Bio/OntologyIO/goflat.pm cp lib/Bio/SeqFeature/FeaturePair.pm blib/lib/Bio/SeqFeature/FeaturePair.pm cp lib/Bio/SeqIO/seqxml.pm blib/lib/Bio/SeqIO/seqxml.pm cp lib/Bio/SeqIO/game/seqHandler.pm blib/lib/Bio/SeqIO/game/seqHandler.pm cp lib/Bio/Search/DatabaseI.pm blib/lib/Bio/Search/DatabaseI.pm cp lib/Bio/UpdateableSeqI.pm blib/lib/Bio/UpdateableSeqI.pm cp lib/Bio/AnalysisParserI.pm blib/lib/Bio/AnalysisParserI.pm cp lib/Bio/Tools/Spidey/Exon.pm blib/lib/Bio/Tools/Spidey/Exon.pm cp lib/Bio/Align/ProteinStatistics.pm blib/lib/Bio/Align/ProteinStatistics.pm cp lib/Bio/Location/NarrowestCoordPolicy.pm blib/lib/Bio/Location/NarrowestCoordPolicy.pm cp lib/Bio/Tools/Prediction/Gene.pm blib/lib/Bio/Tools/Prediction/Gene.pm cp lib/Bio/SeqFeature/Tools/IDHandler.pm blib/lib/Bio/SeqFeature/Tools/IDHandler.pm cp lib/Bio/Location/Split.pm blib/lib/Bio/Location/Split.pm cp lib/Bio/Tools/SeqPattern.pm blib/lib/Bio/Tools/SeqPattern.pm cp lib/Bio/AlignIO/Handler/GenericAlignHandler.pm blib/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm cp lib/Bio/SeqFeature/Gene/Promoter.pm blib/lib/Bio/SeqFeature/Gene/Promoter.pm cp lib/Bio/DB/Taxonomy/flatfile.pm blib/lib/Bio/DB/Taxonomy/flatfile.pm cp lib/Bio/SeqIO/embldriver.pm blib/lib/Bio/SeqIO/embldriver.pm cp lib/Bio/DB/SeqI.pm blib/lib/Bio/DB/SeqI.pm cp lib/Bio/AlignIO/po.pm blib/lib/Bio/AlignIO/po.pm cp lib/Bio/Tools/Primer3.pm blib/lib/Bio/Tools/Primer3.pm cp lib/Bio/SeqFeature/Tools/Unflattener.pm blib/lib/Bio/SeqFeature/Tools/Unflattener.pm cp lib/Bio/CodonUsage/Table.pm blib/lib/Bio/CodonUsage/Table.pm cp lib/Bio/DB/Flat/BDB/fasta.pm blib/lib/Bio/DB/Flat/BDB/fasta.pm cp lib/Bio/Tools/Primer/AssessorI.pm blib/lib/Bio/Tools/Primer/AssessorI.pm cp lib/Bio/Factory/DriverFactory.pm blib/lib/Bio/Factory/DriverFactory.pm cp lib/Bio/SeqIO/swiss.pm blib/lib/Bio/SeqIO/swiss.pm cp lib/Bio/Das/SegmentI.pm blib/lib/Bio/Das/SegmentI.pm cp lib/Bio/PrimarySeqI.pm blib/lib/Bio/PrimarySeqI.pm cp lib/Bio/SearchIO/axt.pm blib/lib/Bio/SearchIO/axt.pm cp lib/Bio/DB/GFF/Util/Binning.pm blib/lib/Bio/DB/GFF/Util/Binning.pm cp lib/Bio/Annotation/StructuredValue.pm blib/lib/Bio/Annotation/StructuredValue.pm cp lib/Bio/Tools/Run/Phylo/PhyloBase.pm blib/lib/Bio/Tools/Run/Phylo/PhyloBase.pm cp lib/Bio/Factory/AnalysisI.pm blib/lib/Bio/Factory/AnalysisI.pm cp lib/Bio/Index/Blast.pm blib/lib/Bio/Index/Blast.pm cp lib/Bio/DB/GFF/Util/Rearrange.pm blib/lib/Bio/DB/GFF/Util/Rearrange.pm cp lib/Bio/SeqIO/ace.pm blib/lib/Bio/SeqIO/ace.pm cp lib/Bio/Search/Result/BlastPullResult.pm blib/lib/Bio/Search/Result/BlastPullResult.pm cp lib/Bio/SeqIO/game/featHandler.pm blib/lib/Bio/SeqIO/game/featHandler.pm cp lib/Bio/Factory/SequenceStreamI.pm blib/lib/Bio/Factory/SequenceStreamI.pm cp lib/Bio/SeqIO/tigr.pm blib/lib/Bio/SeqIO/tigr.pm cp lib/Bio/Matrix/Mlagan.pm blib/lib/Bio/Matrix/Mlagan.pm cp lib/Bio/SeqIO/tab.pm blib/lib/Bio/SeqIO/tab.pm cp lib/Bio/Search/Result/CrossMatchResult.pm blib/lib/Bio/Search/Result/CrossMatchResult.pm cp lib/Bio/SeqFeature/Gene/GeneStructure.pm blib/lib/Bio/SeqFeature/Gene/GeneStructure.pm cp lib/Bio/SearchIO/infernal.pm blib/lib/Bio/SearchIO/infernal.pm cp lib/Bio/DB/GenericWebAgent.pm blib/lib/Bio/DB/GenericWebAgent.pm cp lib/Bio/AlignIO/fasta.pm blib/lib/Bio/AlignIO/fasta.pm cp lib/Bio/Seq/Quality.pm blib/lib/Bio/Seq/Quality.pm cp lib/Bio/SeqIO/FTHelper.pm blib/lib/Bio/SeqIO/FTHelper.pm cp lib/Bio/Seq/SequenceTrace.pm blib/lib/Bio/Seq/SequenceTrace.pm cp lib/Bio/Ontology/TermFactory.pm blib/lib/Bio/Ontology/TermFactory.pm cp lib/Bio/Search/HSP/HSPFactory.pm blib/lib/Bio/Search/HSP/HSPFactory.pm cp lib/Bio/Location/Fuzzy.pm blib/lib/Bio/Location/Fuzzy.pm cp lib/Bio/SeqFeature/CollectionI.pm blib/lib/Bio/SeqFeature/CollectionI.pm cp lib/Bio/Location/CoordinatePolicyI.pm blib/lib/Bio/Location/CoordinatePolicyI.pm cp lib/Bio/SeqFeature/Gene/Transcript.pm blib/lib/Bio/SeqFeature/Gene/Transcript.pm cp lib/Bio/SearchIO/rnamotif.pm blib/lib/Bio/SearchIO/rnamotif.pm cp lib/Bio/SeqAnalysisParserI.pm blib/lib/Bio/SeqAnalysisParserI.pm cp lib/Bio/SearchIO/EventHandlerI.pm blib/lib/Bio/SearchIO/EventHandlerI.pm cp lib/Bio/Matrix/PSM/InstanceSiteI.pm blib/lib/Bio/Matrix/PSM/InstanceSiteI.pm cp lib/Bio/DB/RandomAccessI.pm blib/lib/Bio/DB/RandomAccessI.pm cp lib/Bio/Tools/Sim4/Exon.pm blib/lib/Bio/Tools/Sim4/Exon.pm cp lib/Bio/Tools/Blat.pm blib/lib/Bio/Tools/Blat.pm cp lib/Bio/LocationI.pm blib/lib/Bio/LocationI.pm cp lib/Bio/TreeIO/pag.pm blib/lib/Bio/TreeIO/pag.pm cp lib/Bio/Search/Tiling/TilingI.pm blib/lib/Bio/Search/Tiling/TilingI.pm cp lib/Bio/Align/DNAStatistics.pm blib/lib/Bio/Align/DNAStatistics.pm cp lib/Bio/Tools/ipcress.pm blib/lib/Bio/Tools/ipcress.pm cp lib/Bio/Tools/IUPAC.pm blib/lib/Bio/Tools/IUPAC.pm cp lib/Bio/Factory/SeqAnalysisParserFactoryI.pm blib/lib/Bio/Factory/SeqAnalysisParserFactoryI.pm cp lib/Bio/Tools/Primer/Feature.pm blib/lib/Bio/Tools/Primer/Feature.pm cp lib/Bio/Search/HSP/HSPI.pm blib/lib/Bio/Search/HSP/HSPI.pm cp lib/Bio/Search/HSP/PSLHSP.pm blib/lib/Bio/Search/HSP/PSLHSP.pm cp lib/Bio/OntologyIO/InterProParser.pm blib/lib/Bio/OntologyIO/InterProParser.pm cp lib/Bio/SeqFeature/Gene/UTR.pm blib/lib/Bio/SeqFeature/Gene/UTR.pm cp lib/Bio/AnnotatableI.pm blib/lib/Bio/AnnotatableI.pm cp lib/Bio/OntologyIO/simplehierarchy.pm blib/lib/Bio/OntologyIO/simplehierarchy.pm cp lib/Bio/SearchIO.pm blib/lib/Bio/SearchIO.pm cp lib/Bio/Event/EventGeneratorI.pm blib/lib/Bio/Event/EventGeneratorI.pm cp lib/Bio/Search/HSP/BlastPullHSP.pm blib/lib/Bio/Search/HSP/BlastPullHSP.pm cp lib/Bio/Tools/MZEF.pm blib/lib/Bio/Tools/MZEF.pm cp lib/Bio/Tools/Pseudowise.pm blib/lib/Bio/Tools/Pseudowise.pm cp lib/Bio/Index/Fastq.pm blib/lib/Bio/Index/Fastq.pm cp lib/Bio/Range.pm blib/lib/Bio/Range.pm cp lib/Bio/Tools/Fgenesh.pm blib/lib/Bio/Tools/Fgenesh.pm cp lib/Bio/SearchIO/Writer/HitTableWriter.pm blib/lib/Bio/SearchIO/Writer/HitTableWriter.pm cp lib/Bio/Seq/SeqFactory.pm blib/lib/Bio/Seq/SeqFactory.pm cp lib/Bio/SearchIO/psl.pm blib/lib/Bio/SearchIO/psl.pm cp lib/Bio/Search/Tiling/MapTileUtils.pm blib/lib/Bio/Search/Tiling/MapTileUtils.pm cp lib/Bio/IdCollectionI.pm blib/lib/Bio/IdCollectionI.pm cp lib/Bio/SeqIO/locuslink.pm blib/lib/Bio/SeqIO/locuslink.pm cp lib/Bio/DB/IndexedBase.pm blib/lib/Bio/DB/IndexedBase.pm cp lib/Bio/Search/HSP/FastaHSP.pm blib/lib/Bio/Search/HSP/FastaHSP.pm cp lib/Bio/TreeIO/newick.pm blib/lib/Bio/TreeIO/newick.pm cp lib/Bio/Tools/GFF.pm blib/lib/Bio/Tools/GFF.pm cp lib/Bio/Tools/SeqPattern/Backtranslate.pm blib/lib/Bio/Tools/SeqPattern/Backtranslate.pm cp lib/Bio/Tools/Sim4/Results.pm blib/lib/Bio/Tools/Sim4/Results.pm cp lib/Bio/Index/SwissPfam.pm blib/lib/Bio/Index/SwissPfam.pm cp lib/Bio/SeqIO/gbdriver.pm blib/lib/Bio/SeqIO/gbdriver.pm cp lib/Bio/HandlerBaseI.pm blib/lib/Bio/HandlerBaseI.pm cp lib/Bio/SeqIO/raw.pm blib/lib/Bio/SeqIO/raw.pm cp lib/Bio/Matrix/PSM/ProtMatrix.pm blib/lib/Bio/Matrix/PSM/ProtMatrix.pm cp lib/Bio/Index/Swissprot.pm blib/lib/Bio/Index/Swissprot.pm cp lib/Bio/SeqI.pm blib/lib/Bio/SeqI.pm cp lib/Bio/Align/AlignI.pm blib/lib/Bio/Align/AlignI.pm cp lib/Bio/Matrix/IO/mlagan.pm blib/lib/Bio/Matrix/IO/mlagan.pm cp lib/Bio/Search/Hit/HitFactory.pm blib/lib/Bio/Search/Hit/HitFactory.pm cp lib/Bio/Seq/SeqFastaSpeedFactory.pm blib/lib/Bio/Seq/SeqFastaSpeedFactory.pm cp lib/Bio/SeqFeature/SimilarityPair.pm blib/lib/Bio/SeqFeature/SimilarityPair.pm cp lib/Bio/Annotation/TypeManager.pm blib/lib/Bio/Annotation/TypeManager.pm cp lib/Bio/Root/TestObject.pm blib/lib/Bio/Root/TestObject.pm cp lib/Bio/Tools/Seg.pm blib/lib/Bio/Tools/Seg.pm cp lib/Bio/Tools/Primer/Assessor/Base.pm blib/lib/Bio/Tools/Primer/Assessor/Base.pm cp lib/Bio/Ontology/DocumentRegistry.pm blib/lib/Bio/Ontology/DocumentRegistry.pm cp lib/Bio/SeqFeature/SubSeq.pm blib/lib/Bio/SeqFeature/SubSeq.pm cp lib/Bio/Tools/Alignment/Consed.pm blib/lib/Bio/Tools/Alignment/Consed.pm cp lib/Bio/Tools/Run/ParametersI.pm blib/lib/Bio/Tools/Run/ParametersI.pm cp lib/Bio/Tools/TandemRepeatsFinder.pm blib/lib/Bio/Tools/TandemRepeatsFinder.pm cp lib/Bio/Tools/SeqWords.pm blib/lib/Bio/Tools/SeqWords.pm cp lib/Bio/Seq/SeqBuilder.pm blib/lib/Bio/Seq/SeqBuilder.pm cp lib/Bio/TreeIO/nhx.pm blib/lib/Bio/TreeIO/nhx.pm cp lib/Bio/SeqIO/pir.pm blib/lib/Bio/SeqIO/pir.pm cp lib/Bio/SeqIO/game/gameWriter.pm blib/lib/Bio/SeqIO/game/gameWriter.pm cp lib/Bio/SeqIO/table.pm blib/lib/Bio/SeqIO/table.pm cp lib/Bio/SeqFeature/TypedSeqFeatureI.pm blib/lib/Bio/SeqFeature/TypedSeqFeatureI.pm cp lib/Bio/FeatureHolderI.pm blib/lib/Bio/FeatureHolderI.pm cp lib/Bio/Factory/LocationFactoryI.pm blib/lib/Bio/Factory/LocationFactoryI.pm cp lib/Bio/Tools/Run/GenericParameters.pm blib/lib/Bio/Tools/Run/GenericParameters.pm cp lib/Bio/Matrix/Generic.pm blib/lib/Bio/Matrix/Generic.pm cp lib/Bio/Index/GenBank.pm blib/lib/Bio/Index/GenBank.pm cp lib/Bio/SearchIO/Writer/ResultTableWriter.pm blib/lib/Bio/SearchIO/Writer/ResultTableWriter.pm cp lib/Bio/IdentifiableI.pm blib/lib/Bio/IdentifiableI.pm cp lib/Bio/SeqFeature/Gene/Intron.pm blib/lib/Bio/SeqFeature/Gene/Intron.pm cp lib/Bio/AlignIO/xmfa.pm blib/lib/Bio/AlignIO/xmfa.pm cp lib/Bio/DB/Flat/BDB/embl.pm blib/lib/Bio/DB/Flat/BDB/embl.pm cp lib/Bio/SeqIO/phd.pm blib/lib/Bio/SeqIO/phd.pm cp lib/Bio/SeqIO/genbank.pm blib/lib/Bio/SeqIO/genbank.pm cp lib/Bio/Factory/FTLocationFactory.pm blib/lib/Bio/Factory/FTLocationFactory.pm cp lib/Bio/Tools/OddCodes.pm blib/lib/Bio/Tools/OddCodes.pm cp lib/Bio/Align/Utilities.pm blib/lib/Bio/Align/Utilities.pm cp lib/Bio/Location/FuzzyLocationI.pm blib/lib/Bio/Location/FuzzyLocationI.pm cp lib/Bio/Root/HTTPget.pm blib/lib/Bio/Root/HTTPget.pm cp lib/Bio/Search/Processor.pm blib/lib/Bio/Search/Processor.pm cp lib/Bio/Tools/TargetP.pm blib/lib/Bio/Tools/TargetP.pm cp lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm blib/lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm cp lib/Bio/Search/Hit/HitI.pm blib/lib/Bio/Search/Hit/HitI.pm cp lib/Bio/Search/Result/ResultFactory.pm blib/lib/Bio/Search/Result/ResultFactory.pm cp lib/Bio/Tools/Profile.pm blib/lib/Bio/Tools/Profile.pm cp lib/Bio/Factory/ObjectFactoryI.pm blib/lib/Bio/Factory/ObjectFactoryI.pm cp lib/Bio/Search/Result/ResultI.pm blib/lib/Bio/Search/Result/ResultI.pm cp lib/Bio/Tools/PrositeScan.pm blib/lib/Bio/Tools/PrositeScan.pm cp lib/Bio/Tools/ECnumber.pm blib/lib/Bio/Tools/ECnumber.pm cp lib/Bio/Ontology/OntologyEngineI.pm blib/lib/Bio/Ontology/OntologyEngineI.pm cp lib/Bio/Annotation/Collection.pm blib/lib/Bio/Annotation/Collection.pm cp lib/Bio/Ontology/TermI.pm blib/lib/Bio/Ontology/TermI.pm cp lib/Bio/Ontology/OntologyStore.pm blib/lib/Bio/Ontology/OntologyStore.pm cp lib/Bio/SearchIO/Writer/HSPTableWriter.pm blib/lib/Bio/SearchIO/Writer/HSPTableWriter.pm cp lib/Bio/Matrix/PSM/IO/transfac.pm blib/lib/Bio/Matrix/PSM/IO/transfac.pm cp lib/Bio/Tools/QRNA.pm blib/lib/Bio/Tools/QRNA.pm cp lib/Bio/Tree/DistanceFactory.pm blib/lib/Bio/Tree/DistanceFactory.pm cp lib/Bio/TreeIO/tabtree.pm blib/lib/Bio/TreeIO/tabtree.pm cp lib/Bio/Tools/EPCR.pm blib/lib/Bio/Tools/EPCR.pm cp lib/Bio/Annotation/SimpleValue.pm blib/lib/Bio/Annotation/SimpleValue.pm cp lib/Bio/Root/Version.pm blib/lib/Bio/Root/Version.pm cp lib/Bio/Annotation/Relation.pm blib/lib/Bio/Annotation/Relation.pm cp lib/Bio/Tree/Node.pm blib/lib/Bio/Tree/Node.pm cp lib/Bio/Matrix/PSM/SiteMatrixI.pm blib/lib/Bio/Matrix/PSM/SiteMatrixI.pm cp lib/Bio/AlignIO.pm blib/lib/Bio/AlignIO.pm cp lib/Bio/Factory/SequenceFactoryI.pm blib/lib/Bio/Factory/SequenceFactoryI.pm cp lib/Bio/Tools/Genomewise.pm blib/lib/Bio/Tools/Genomewise.pm cp lib/Bio/Location/WidestCoordPolicy.pm blib/lib/Bio/Location/WidestCoordPolicy.pm cp lib/Bio/AlignIO/pfam.pm blib/lib/Bio/AlignIO/pfam.pm cp lib/Bio/SeqFeature/Primer.pm blib/lib/Bio/SeqFeature/Primer.pm cp lib/Bio/Seq/TraceI.pm blib/lib/Bio/Seq/TraceI.pm cp lib/Bio/SeqFeature/Gene/GeneStructureI.pm blib/lib/Bio/SeqFeature/Gene/GeneStructureI.pm cp lib/Bio/Tools/Run/AnalysisFactory.pm blib/lib/Bio/Tools/Run/AnalysisFactory.pm cp lib/Bio/Ontology/OntologyI.pm blib/lib/Bio/Ontology/OntologyI.pm cp lib/Bio/SeqIO/scf.pm blib/lib/Bio/SeqIO/scf.pm cp lib/Bio/Tools/AnalysisResult.pm blib/lib/Bio/Tools/AnalysisResult.pm cp lib/Bio/OntologyIO/soflat.pm blib/lib/Bio/OntologyIO/soflat.pm cp lib/Bio/Search/GenericDatabase.pm blib/lib/Bio/Search/GenericDatabase.pm cp lib/Bio/SeqIO/tinyseq.pm blib/lib/Bio/SeqIO/tinyseq.pm cp lib/Bio/SeqIO/mbsout.pm blib/lib/Bio/SeqIO/mbsout.pm cp lib/Bio/Tools/Glimmer.pm blib/lib/Bio/Tools/Glimmer.pm cp lib/Bio/SeqIO/game/gameHandler.pm blib/lib/Bio/SeqIO/game/gameHandler.pm cp lib/Bio/Annotation/Reference.pm blib/lib/Bio/Annotation/Reference.pm cp lib/Bio/Ontology/OBOterm.pm blib/lib/Bio/Ontology/OBOterm.pm cp lib/Bio/Tools/Prints.pm blib/lib/Bio/Tools/Prints.pm cp lib/Bio/Seq/RichSeq.pm blib/lib/Bio/Seq/RichSeq.pm cp lib/Bio/Tools/Phylo/Gerp.pm blib/lib/Bio/Tools/Phylo/Gerp.pm cp lib/Bio/Search/Hit/BlastHit.pm blib/lib/Bio/Search/Hit/BlastHit.pm cp lib/Bio/Matrix/IO/scoring.pm blib/lib/Bio/Matrix/IO/scoring.pm cp lib/Bio/Tools/isPcr.pm blib/lib/Bio/Tools/isPcr.pm cp lib/Bio/SeqIO/MultiFile.pm blib/lib/Bio/SeqIO/MultiFile.pm cp lib/Bio/Search/Result/WABAResult.pm blib/lib/Bio/Search/Result/WABAResult.pm cp lib/Bio/SeqIO/game/gameSubs.pm blib/lib/Bio/SeqIO/game/gameSubs.pm cp lib/Bio/Align/PairwiseStatistics.pm blib/lib/Bio/Align/PairwiseStatistics.pm cp lib/Bio/SeqIO/qual.pm blib/lib/Bio/SeqIO/qual.pm cp lib/Bio/Root/Exception.pm blib/lib/Bio/Root/Exception.pm cp lib/Bio/Tools/Geneid.pm blib/lib/Bio/Tools/Geneid.pm cp lib/Bio/Seq/LargePrimarySeq.pm blib/lib/Bio/Seq/LargePrimarySeq.pm cp lib/Bio/SeqUtils.pm blib/lib/Bio/SeqUtils.pm cp lib/Bio/RangeI.pm blib/lib/Bio/RangeI.pm cp lib/Bio/Matrix/PSM/Psm.pm blib/lib/Bio/Matrix/PSM/Psm.pm cp lib/Bio/Species.pm blib/lib/Bio/Species.pm cp lib/Bio/DasI.pm blib/lib/Bio/DasI.pm cp lib/Bio/WebAgent.pm blib/lib/Bio/WebAgent.pm cp lib/Bio/Ontology/PathI.pm blib/lib/Bio/Ontology/PathI.pm cp lib/Bio/Index/Abstract.pm blib/lib/Bio/Index/Abstract.pm cp lib/Bio/Seq/LargeSeq.pm blib/lib/Bio/Seq/LargeSeq.pm cp lib/Bio/Annotation/Target.pm blib/lib/Bio/Annotation/Target.pm cp lib/Bio/SeqIO/swissdriver.pm blib/lib/Bio/SeqIO/swissdriver.pm cp lib/Bio/Tools/Prediction/Exon.pm blib/lib/Bio/Tools/Prediction/Exon.pm cp lib/Bio/Tree/NodeI.pm blib/lib/Bio/Tree/NodeI.pm cp lib/Bio/SeqFeature/Collection.pm blib/lib/Bio/SeqFeature/Collection.pm cp lib/Bio/Tools/RepeatMasker.pm blib/lib/Bio/Tools/RepeatMasker.pm cp lib/Bio/Tools/Signalp.pm blib/lib/Bio/Tools/Signalp.pm cp lib/Bio/LocatableSeq.pm blib/lib/Bio/LocatableSeq.pm cp lib/Bio/Tree/TreeFunctionsI.pm blib/lib/Bio/Tree/TreeFunctionsI.pm cp lib/Bio/PullParserI.pm blib/lib/Bio/PullParserI.pm cp lib/Bio/Search/Iteration/IterationI.pm blib/lib/Bio/Search/Iteration/IterationI.pm cp lib/Bio/Index/Fasta.pm blib/lib/Bio/Index/Fasta.pm cp lib/Bio/AlignIO/psi.pm blib/lib/Bio/AlignIO/psi.pm cp lib/Bio/Matrix/PhylipDist.pm blib/lib/Bio/Matrix/PhylipDist.pm cp lib/Bio/Tree/AnnotatableNode.pm blib/lib/Bio/Tree/AnnotatableNode.pm cp lib/Bio/SeqIO/gbxml.pm blib/lib/Bio/SeqIO/gbxml.pm cp lib/Bio/Seq/LargeSeqI.pm blib/lib/Bio/Seq/LargeSeqI.pm cp lib/Bio/SearchIO/erpin.pm blib/lib/Bio/SearchIO/erpin.pm cp lib/Bio/Ontology/RelationshipFactory.pm blib/lib/Bio/Ontology/RelationshipFactory.pm cp lib/Bio/SeqIO/embl.pm blib/lib/Bio/SeqIO/embl.pm cp lib/Bio/DB/Taxonomy/list.pm blib/lib/Bio/DB/Taxonomy/list.pm cp lib/Bio/AlignIO/largemultifasta.pm blib/lib/Bio/AlignIO/largemultifasta.pm cp lib/Bio/SearchIO/wise.pm blib/lib/Bio/SearchIO/wise.pm cp lib/Bio/Search/HSP/WABAHSP.pm blib/lib/Bio/Search/HSP/WABAHSP.pm cp lib/Bio/Matrix/PSM/IO/meme.pm blib/lib/Bio/Matrix/PSM/IO/meme.pm cp lib/Bio/Tools/Signalp/ExtendedSignalp.pm blib/lib/Bio/Tools/Signalp/ExtendedSignalp.pm cp lib/Bio/Tools/Match.pm blib/lib/Bio/Tools/Match.pm cp lib/Bio/Tools/Grail.pm blib/lib/Bio/Tools/Grail.pm cp lib/Bio/Search/Hit/BlastPullHit.pm blib/lib/Bio/Search/Hit/BlastPullHit.pm cp lib/Bio/Index/BlastTable.pm blib/lib/Bio/Index/BlastTable.pm cp lib/Bio/DB/Qual.pm blib/lib/Bio/DB/Qual.pm cp lib/Bio/TreeIO/nexus.pm blib/lib/Bio/TreeIO/nexus.pm cp lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm blib/lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm cp lib/Bio/Search/HSP/PsiBlastHSP.pm blib/lib/Bio/Search/HSP/PsiBlastHSP.pm cp lib/Bio/Matrix/MatrixI.pm blib/lib/Bio/Matrix/MatrixI.pm cp lib/Bio/AnnotationCollectionI.pm blib/lib/Bio/AnnotationCollectionI.pm cp lib/Bio/Search/Hit/GenericHit.pm blib/lib/Bio/Search/Hit/GenericHit.pm cp lib/Bio/AlignIO/proda.pm blib/lib/Bio/AlignIO/proda.pm cp lib/Bio/Tools/EMBOSS/Palindrome.pm blib/lib/Bio/Tools/EMBOSS/Palindrome.pm cp lib/Bio/Ontology/GOterm.pm blib/lib/Bio/Ontology/GOterm.pm cp lib/Bio/Tools/Tmhmm.pm blib/lib/Bio/Tools/Tmhmm.pm cp lib/Bio/AlignIO/selex.pm blib/lib/Bio/AlignIO/selex.pm cp lib/Bio/Matrix/PSM/PsmI.pm blib/lib/Bio/Matrix/PSM/PsmI.pm cp lib/Bio/Search/HSP/ModelHSP.pm blib/lib/Bio/Search/HSP/ModelHSP.pm cp lib/Bio/Seq/EncodedSeq.pm blib/lib/Bio/Seq/EncodedSeq.pm cp lib/Bio/TreeIO/NewickParser.pm blib/lib/Bio/TreeIO/NewickParser.pm cp lib/Bio/AlignIO/mega.pm blib/lib/Bio/AlignIO/mega.pm cp lib/Bio/SeqFeature/Amplicon.pm blib/lib/Bio/SeqFeature/Amplicon.pm cp lib/Bio/Ontology/RelationshipI.pm blib/lib/Bio/Ontology/RelationshipI.pm cp lib/Bio/AnnotationI.pm blib/lib/Bio/AnnotationI.pm cp lib/Bio/Root/Storable.pm blib/lib/Bio/Root/Storable.pm cp lib/Bio/Search/GenericStatistics.pm blib/lib/Bio/Search/GenericStatistics.pm cp lib/Bio/Ontology/Term.pm blib/lib/Bio/Ontology/Term.pm cp lib/Bio/Seq/SimulatedRead.pm blib/lib/Bio/Seq/SimulatedRead.pm cp lib/Bio/CodonUsage/IO.pm blib/lib/Bio/CodonUsage/IO.pm cp lib/Bio/AlignIO/arp.pm blib/lib/Bio/AlignIO/arp.pm cp lib/Bio/Search/Hit/ModelHit.pm blib/lib/Bio/Search/Hit/ModelHit.pm cp lib/Bio/SeqFeature/Gene/ExonI.pm blib/lib/Bio/SeqFeature/Gene/ExonI.pm cp lib/Bio/Factory/ObjectFactory.pm blib/lib/Bio/Factory/ObjectFactory.pm cp lib/Bio/Event/EventHandlerI.pm blib/lib/Bio/Event/EventHandlerI.pm cp lib/Bio/OntologyIO/Handlers/InterProHandler.pm blib/lib/Bio/OntologyIO/Handlers/InterProHandler.pm cp lib/Bio/SearchIO/waba.pm blib/lib/Bio/SearchIO/waba.pm cp lib/Bio/Tools/Run/Analysis.pm blib/lib/Bio/Tools/Run/Analysis.pm cp lib/Bio/TreeIO/phyloxml.pm blib/lib/Bio/TreeIO/phyloxml.pm cp lib/Bio/Search/Hit/PsiBlastHit.pm blib/lib/Bio/Search/Hit/PsiBlastHit.pm cp lib/Bio/SeqFeature/Tools/TypeMapper.pm blib/lib/Bio/SeqFeature/Tools/TypeMapper.pm cp lib/Bio/Ontology/Ontology.pm blib/lib/Bio/Ontology/Ontology.pm cp lib/Bio/Ontology/Path.pm blib/lib/Bio/Ontology/Path.pm cp lib/Bio/DB/Flat/BDB.pm blib/lib/Bio/DB/Flat/BDB.pm cp lib/Bio/Tools/CodonTable.pm blib/lib/Bio/Tools/CodonTable.pm cp lib/Bio/SeqIO/game.pm blib/lib/Bio/SeqIO/game.pm cp bin/bp_aacomp blib/script/bp_aacomp "/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 "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- 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_extract_feature_seq cp bin/bp_fastam9_to_table blib/script/bp_fastam9_to_table "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- 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_fetch cp bin/bp_filter_search blib/script/bp_filter_search "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- 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_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_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_make_mrna_protein cp bin/bp_mask_by_search blib/script/bp_mask_by_search "/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 "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- 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_process_gadfly cp bin/bp_process_sgd blib/script/bp_process_sgd "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_process_sgd 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_search2gff cp bin/bp_search2table blib/script/bp_search2table "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2table cp bin/bp_search2tribe blib/script/bp_search2tribe "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2tribe cp bin/bp_seq_length blib/script/bp_seq_length "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seq_length cp bin/bp_seqconvert blib/script/bp_seqconvert "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqconvert 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_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_taxid4species cp bin/bp_taxonomy2tree blib/script/bp_taxonomy2tree "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- 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_translate_seq cp bin/bp_tree2pag blib/script/bp_tree2pag "/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 Manifying 40 pod documents Manifying 471 pod documents >>> Running package in biology/bioperl at 1711573384.43 ===> biology/bioperl ===> Faking installation for bioperl-1.7.8 Manifying 40 pod documents Manifying 471 pod documents Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/BioPerl.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/TreeIO.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/SimpleAlign.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Seq.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/SimpleAnalysisI.pm Installing 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/exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tools/Tmhmm.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tools/CodonTable.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tools/Run/WrapperBase.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tools/Run/ParametersI.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tools/Run/GenericParameters.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tools/Run/AnalysisFactory.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tools/Run/Analysis.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tools/Run/WrapperBase/CommandExts.pm Installing 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/exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tools/Primer/AssessorI.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tools/Primer/Feature.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tools/Primer/Assessor/Base.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tools/Spidey/Results.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tools/Spidey/Exon.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tools/Prediction/Gene.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tools/Prediction/Exon.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tools/Sim4/Exon.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tools/Sim4/Results.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tools/SeqPattern/Backtranslate.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tools/Analysis/SimpleAnalysisBase.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tools/Signalp/ExtendedSignalp.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tools/EMBOSS/Palindrome.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/DB/QueryI.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/DB/WebDBSeqI.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/DB/DBFetch.pm Installing 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Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/DB/GFF/Util/Rearrange.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tree/NodeNHX.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tree/TreeI.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tree/Tree.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tree/Statistics.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tree/Compatible.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tree/RandomFactory.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tree/DistanceFactory.pm Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/libdata/perl5/site_perl/Bio/Tree/Node.pm Installing 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/exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_mrtrans Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_mutate Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_nexus2nh Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_nrdb Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_oligo_count Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_process_gadfly Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_process_sgd Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_revtrans-motif Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_search2alnblocks Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_search2gff Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_search2table Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_search2tribe Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_seq_length Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_seqconvert Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_seqcut Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_seqpart Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_seqret Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_seqretsplit Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_split_seq Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_sreformat Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_taxid4species Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_taxonomy2tree Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_translate_seq Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_tree2pag Installing /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/bin/bp_unflatten_seq Appending installation info to /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/./libdata/perl5/amd64-openbsd/perllocal.pod /exopi-obj/pobj/bioperl-1.7.8/bin/install -d -m 755 /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/share/examples/bioperl/; cd /exopi-obj/pobj/bioperl-1.7.8/BioPerl-1.7.8/examples/ && pax -rw . /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/share/examples/bioperl/; chown -R root:bin /exopi-obj/pobj/bioperl-1.7.8/fake-amd64/usr/local/share/examples/bioperl/ ===> Building package for bioperl-1.7.8 Create /exopi-cvs/ports/packages/amd64/no-arch/bioperl-1.7.8.tgz Creating package bioperl-1.7.8 reading plist| checking dependencies| checking dependencies|devel/p5-Data-Stag checking dependencies|devel/p5-Error checking dependencies|devel/p5-Graph checking dependencies|devel/p5-IO-String checking dependencies|devel/p5-IO-stringy checking dependencies|devel/p5-IPC-Run checking dependencies|devel/p5-List-MoreUtils checking dependencies|devel/p5-Module-Build checking dependencies|devel/p5-Set-Scalar checking dependencies|devel/p5-Test-Most checking dependencies|devel/p5-Test-RequiresInternet checking dependencies|devel/p5-YAML checking dependencies|textproc/p5-Libxml checking dependencies|textproc/p5-XML-DOM-XPath checking dependencies|textproc/p5-XML-DOM checking dependencies|textproc/p5-XML-LibXML checking dependencies|textproc/p5-XML-SAX-Base checking dependencies|textproc/p5-XML-SAX-Writer checking dependencies|textproc/p5-XML-SAX checking dependencies|textproc/p5-XML-Twig checking dependencies|textproc/p5-XML-Writer checking dependencies|www/p5-HTTP-Message checking dependencies|www/p5-URI checking dependencies|www/p5-libwww checksumming| checksumming| | 0% checksumming| | 1% checksumming|* | 1% checksumming|* | 2% checksumming|** | 2% checksumming|** | 3% checksumming|** | 4% checksumming|*** | 4% checksumming|*** | 5% checksumming|*** | 6% 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archiving|************************************************************* | 95% archiving|************************************************************* | 96% archiving|************************************************************** | 96% archiving|************************************************************** | 97% archiving|*************************************************************** | 98% archiving|*************************************************************** | 99% archiving|****************************************************************|100% Link to /exopi-cvs/ports/packages/amd64/all/bioperl-1.7.8.tgz Link to /exopi-cvs/ports/packages/amd64/ftp/bioperl-1.7.8.tgz >>> Running clean in biology/bioperl at 1711573411.88 ===> biology/bioperl ===> Cleaning for bioperl-1.7.8 >>> Ended at 1711573412.74 max_stuck=8.08/build=29.78/package=27.45/clean=0.89