Setting PATH to /opt/SUNWspro/bin:/usr/local/bin:/opt/csw/bin:/usr/ccs/bin:/usr/bin:/usr/sbin Start 2009-09-30T05:17:50 ActivePerl-1003 CPAN-1.9402 Going to read '/export/home/fly1003/var/cpan/Metadata' Database was generated on Wed, 30 Sep 2009 10:27:06 GMT Running make for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz Checksum for /net/nas/data/cpan/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz ok Will not use Archive::Tar, need 1.00 BioPerl-1.6.1 BioPerl-1.6.1/AUTHORS BioPerl-1.6.1/BioPerl.pm BioPerl-1.6.1/BUGS BioPerl-1.6.1/Build.PL BioPerl-1.6.1/Changes BioPerl-1.6.1/DEPENDENCIES BioPerl-1.6.1/DEPRECATED BioPerl-1.6.1/INSTALL BioPerl-1.6.1/INSTALL.SKIP BioPerl-1.6.1/INSTALL.WIN BioPerl-1.6.1/LICENSE BioPerl-1.6.1/Makefile.PL BioPerl-1.6.1/MANIFEST BioPerl-1.6.1/MANIFEST.SKIP BioPerl-1.6.1/META.yml BioPerl-1.6.1/README BioPerl-1.6.1/Bio BioPerl-1.6.1/Bio/AlignIO.pm BioPerl-1.6.1/Bio/AnalysisI.pm BioPerl-1.6.1/Bio/AnalysisParserI.pm BioPerl-1.6.1/Bio/AnalysisResultI.pm 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BioPerl-1.6.1/t/Phenotype/MiniMIMentry.t BioPerl-1.6.1/t/Phenotype/OMIMentry.t BioPerl-1.6.1/t/Phenotype/OMIMentryAllelicVariant.t BioPerl-1.6.1/t/Phenotype/OMIMparser.t BioPerl-1.6.1/t/Phenotype/Phenotype.t BioPerl-1.6.1/t/PopGen BioPerl-1.6.1/t/PopGen/Coalescent.t BioPerl-1.6.1/t/PopGen/HtSNP.t BioPerl-1.6.1/t/PopGen/MK.t BioPerl-1.6.1/t/PopGen/PopGen.t BioPerl-1.6.1/t/PopGen/PopGenSims.t BioPerl-1.6.1/t/PopGen/TagHaplotype.t BioPerl-1.6.1/t/RemoteDB BioPerl-1.6.1/t/RemoteDB/BioFetch.t BioPerl-1.6.1/t/RemoteDB/CUTG.t BioPerl-1.6.1/t/RemoteDB/EMBL.t BioPerl-1.6.1/t/RemoteDB/EntrezGene.t BioPerl-1.6.1/t/RemoteDB/EUtilities.t BioPerl-1.6.1/t/RemoteDB/GenBank.t BioPerl-1.6.1/t/RemoteDB/GenPept.t BioPerl-1.6.1/t/RemoteDB/MeSH.t BioPerl-1.6.1/t/RemoteDB/RefSeq.t BioPerl-1.6.1/t/RemoteDB/SeqHound.t BioPerl-1.6.1/t/RemoteDB/SeqRead_fail.t BioPerl-1.6.1/t/RemoteDB/SeqVersion.t BioPerl-1.6.1/t/RemoteDB/SwissProt.t BioPerl-1.6.1/t/RemoteDB/Taxonomy.t BioPerl-1.6.1/t/RemoteDB/HIV BioPerl-1.6.1/t/RemoteDB/HIV/HIV.t BioPerl-1.6.1/t/RemoteDB/HIV/HIVAnnotProcessor.t BioPerl-1.6.1/t/RemoteDB/HIV/HIVQuery.t BioPerl-1.6.1/t/RemoteDB/HIV/HIVQueryHelper.t BioPerl-1.6.1/t/RemoteDB/Query BioPerl-1.6.1/t/RemoteDB/Query/GenBank.t BioPerl-1.6.1/t/Restriction BioPerl-1.6.1/t/Restriction/Analysis-refac.t BioPerl-1.6.1/t/Restriction/Analysis.t BioPerl-1.6.1/t/Restriction/Gel.t BioPerl-1.6.1/t/Restriction/IO.t BioPerl-1.6.1/t/Root BioPerl-1.6.1/t/Root/Exception.t BioPerl-1.6.1/t/Root/RootI.t BioPerl-1.6.1/t/Root/RootIO.t BioPerl-1.6.1/t/Root/Storable.t BioPerl-1.6.1/t/Root/Tempfile.t BioPerl-1.6.1/t/Root/Utilities.t BioPerl-1.6.1/t/SearchIO BioPerl-1.6.1/t/SearchIO/blast.t BioPerl-1.6.1/t/SearchIO/blast_pull.t BioPerl-1.6.1/t/SearchIO/blasttable.t BioPerl-1.6.1/t/SearchIO/blastxml.t BioPerl-1.6.1/t/SearchIO/CigarString.t BioPerl-1.6.1/t/SearchIO/cross_match.t BioPerl-1.6.1/t/SearchIO/erpin.t BioPerl-1.6.1/t/SearchIO/exonerate.t BioPerl-1.6.1/t/SearchIO/fasta.t BioPerl-1.6.1/t/SearchIO/gmap_f9.t BioPerl-1.6.1/t/SearchIO/hmmer.t BioPerl-1.6.1/t/SearchIO/hmmer_pull.t BioPerl-1.6.1/t/SearchIO/infernal.t BioPerl-1.6.1/t/SearchIO/megablast.t BioPerl-1.6.1/t/SearchIO/psl.t BioPerl-1.6.1/t/SearchIO/rnamotif.t BioPerl-1.6.1/t/SearchIO/SearchIO.t BioPerl-1.6.1/t/SearchIO/sim4.t BioPerl-1.6.1/t/SearchIO/SimilarityPair.t BioPerl-1.6.1/t/SearchIO/Tiling.t BioPerl-1.6.1/t/SearchIO/waba.t BioPerl-1.6.1/t/SearchIO/wise.t BioPerl-1.6.1/t/SearchIO/Writer BioPerl-1.6.1/t/SearchIO/Writer/GbrowseGFF.t BioPerl-1.6.1/t/SearchIO/Writer/HitTableWriter.t BioPerl-1.6.1/t/SearchIO/Writer/HSPTableWriter.t BioPerl-1.6.1/t/SearchIO/Writer/HTMLWriter.t BioPerl-1.6.1/t/Seq BioPerl-1.6.1/t/Seq/DBLink.t BioPerl-1.6.1/t/Seq/EncodedSeq.t BioPerl-1.6.1/t/Seq/LargeLocatableSeq.t BioPerl-1.6.1/t/Seq/LargePSeq.t BioPerl-1.6.1/t/Seq/LocatableSeq.t BioPerl-1.6.1/t/Seq/MetaSeq.t BioPerl-1.6.1/t/Seq/PrimaryQual.t BioPerl-1.6.1/t/Seq/PrimarySeq.t BioPerl-1.6.1/t/Seq/PrimedSeq.t BioPerl-1.6.1/t/Seq/Quality.t BioPerl-1.6.1/t/Seq/Seq.t BioPerl-1.6.1/t/Seq/WithQuality.t BioPerl-1.6.1/t/SeqFeature BioPerl-1.6.1/t/SeqFeature/FeatureIO.t BioPerl-1.6.1/t/SeqFeature/Location.t BioPerl-1.6.1/t/SeqFeature/LocationFactory.t BioPerl-1.6.1/t/SeqFeature/Primer.t BioPerl-1.6.1/t/SeqFeature/Range.t BioPerl-1.6.1/t/SeqFeature/RangeI.t BioPerl-1.6.1/t/SeqFeature/SeqAnalysisParser.t BioPerl-1.6.1/t/SeqFeature/SeqFeatAnnotated.t BioPerl-1.6.1/t/SeqFeature/SeqFeatCollection.t BioPerl-1.6.1/t/SeqFeature/SeqFeature.t BioPerl-1.6.1/t/SeqFeature/SeqFeaturePrimer.t BioPerl-1.6.1/t/SeqFeature/Unflattener.t BioPerl-1.6.1/t/SeqFeature/Unflattener2.t BioPerl-1.6.1/t/SeqIO BioPerl-1.6.1/t/SeqIO/abi.t BioPerl-1.6.1/t/SeqIO/ace.t BioPerl-1.6.1/t/SeqIO/agave.t BioPerl-1.6.1/t/SeqIO/alf.t BioPerl-1.6.1/t/SeqIO/asciitree.t BioPerl-1.6.1/t/SeqIO/bsml.t BioPerl-1.6.1/t/SeqIO/bsml_sax.t BioPerl-1.6.1/t/SeqIO/chadoxml.t BioPerl-1.6.1/t/SeqIO/chaos.t BioPerl-1.6.1/t/SeqIO/chaosxml.t BioPerl-1.6.1/t/SeqIO/ctf.t BioPerl-1.6.1/t/SeqIO/embl.t BioPerl-1.6.1/t/SeqIO/entrezgene.t BioPerl-1.6.1/t/SeqIO/excel.t BioPerl-1.6.1/t/SeqIO/exp.t BioPerl-1.6.1/t/SeqIO/fasta.t BioPerl-1.6.1/t/SeqIO/fastq.t BioPerl-1.6.1/t/SeqIO/flybase_chadoxml.t BioPerl-1.6.1/t/SeqIO/game.t BioPerl-1.6.1/t/SeqIO/gcg.t BioPerl-1.6.1/t/SeqIO/genbank.t BioPerl-1.6.1/t/SeqIO/Handler.t BioPerl-1.6.1/t/SeqIO/interpro.t BioPerl-1.6.1/t/SeqIO/kegg.t BioPerl-1.6.1/t/SeqIO/largefasta.t BioPerl-1.6.1/t/SeqIO/lasergene.t BioPerl-1.6.1/t/SeqIO/locuslink.t BioPerl-1.6.1/t/SeqIO/metafasta.t BioPerl-1.6.1/t/SeqIO/MultiFile.t BioPerl-1.6.1/t/SeqIO/Multiple_fasta.t BioPerl-1.6.1/t/SeqIO/phd.t BioPerl-1.6.1/t/SeqIO/pir.t BioPerl-1.6.1/t/SeqIO/pln.t BioPerl-1.6.1/t/SeqIO/qual.t BioPerl-1.6.1/t/SeqIO/raw.t BioPerl-1.6.1/t/SeqIO/scf.t BioPerl-1.6.1/t/SeqIO/SeqBuilder.t BioPerl-1.6.1/t/SeqIO/Splicedseq.t BioPerl-1.6.1/t/SeqIO/strider.t BioPerl-1.6.1/t/SeqIO/swiss.t BioPerl-1.6.1/t/SeqIO/tab.t BioPerl-1.6.1/t/SeqIO/table.t BioPerl-1.6.1/t/SeqIO/tigr.t BioPerl-1.6.1/t/SeqIO/tigrxml.t BioPerl-1.6.1/t/SeqIO/tinyseq.t BioPerl-1.6.1/t/SeqIO/ztr.t BioPerl-1.6.1/t/SeqTools BioPerl-1.6.1/t/SeqTools/Backtranslate.t BioPerl-1.6.1/t/SeqTools/CodonTable.t BioPerl-1.6.1/t/SeqTools/ECnumber.t BioPerl-1.6.1/t/SeqTools/GuessSeqFormat.t BioPerl-1.6.1/t/SeqTools/OddCodes.t BioPerl-1.6.1/t/SeqTools/SeqPattern.t BioPerl-1.6.1/t/SeqTools/SeqStats.t BioPerl-1.6.1/t/SeqTools/SeqUtils.t BioPerl-1.6.1/t/SeqTools/SeqWords.t BioPerl-1.6.1/t/Structure BioPerl-1.6.1/t/Structure/IO.t BioPerl-1.6.1/t/Structure/Structure.t BioPerl-1.6.1/t/Tools BioPerl-1.6.1/t/Tools/ePCR.t BioPerl-1.6.1/t/Tools/Est2Genome.t BioPerl-1.6.1/t/Tools/FootPrinter.t BioPerl-1.6.1/t/Tools/Geneid.t BioPerl-1.6.1/t/Tools/Genewise.t BioPerl-1.6.1/t/Tools/Genomewise.t BioPerl-1.6.1/t/Tools/Genpred.t BioPerl-1.6.1/t/Tools/GFF.t BioPerl-1.6.1/t/Tools/Hmmer.t BioPerl-1.6.1/t/Tools/IUPAC.t BioPerl-1.6.1/t/Tools/Lucy.t BioPerl-1.6.1/t/Tools/Match.t BioPerl-1.6.1/t/Tools/pICalculator.t BioPerl-1.6.1/t/Tools/Primer3.t BioPerl-1.6.1/t/Tools/Promoterwise.t BioPerl-1.6.1/t/Tools/Pseudowise.t BioPerl-1.6.1/t/Tools/QRNA.t BioPerl-1.6.1/t/Tools/RandDistFunctions.t BioPerl-1.6.1/t/Tools/RepeatMasker.t BioPerl-1.6.1/t/Tools/rnamotif.t BioPerl-1.6.1/t/Tools/Seg.t BioPerl-1.6.1/t/Tools/Sigcleave.t BioPerl-1.6.1/t/Tools/Signalp.t BioPerl-1.6.1/t/Tools/Sim4.t BioPerl-1.6.1/t/Tools/SiRNA.t BioPerl-1.6.1/t/Tools/TandemRepeatsFinder.t BioPerl-1.6.1/t/Tools/TargetP.t BioPerl-1.6.1/t/Tools/Tmhmm.t BioPerl-1.6.1/t/Tools/tRNAscanSE.t BioPerl-1.6.1/t/Tools/Alignment BioPerl-1.6.1/t/Tools/Alignment/Consed.t BioPerl-1.6.1/t/Tools/Analysis BioPerl-1.6.1/t/Tools/Analysis/DNA BioPerl-1.6.1/t/Tools/Analysis/DNA/ESEfinder.t BioPerl-1.6.1/t/Tools/Analysis/Protein BioPerl-1.6.1/t/Tools/Analysis/Protein/Domcut.t BioPerl-1.6.1/t/Tools/Analysis/Protein/ELM.t BioPerl-1.6.1/t/Tools/Analysis/Protein/GOR4.t BioPerl-1.6.1/t/Tools/Analysis/Protein/HNN.t BioPerl-1.6.1/t/Tools/Analysis/Protein/Mitoprot.t BioPerl-1.6.1/t/Tools/Analysis/Protein/NetPhos.t BioPerl-1.6.1/t/Tools/Analysis/Protein/Scansite.t BioPerl-1.6.1/t/Tools/Analysis/Protein/Sopma.t BioPerl-1.6.1/t/Tools/EMBOSS BioPerl-1.6.1/t/Tools/EMBOSS/Palindrome.t BioPerl-1.6.1/t/Tools/EUtilities BioPerl-1.6.1/t/Tools/EUtilities/egquery.t BioPerl-1.6.1/t/Tools/EUtilities/einfo.t BioPerl-1.6.1/t/Tools/EUtilities/elink_acheck.t BioPerl-1.6.1/t/Tools/EUtilities/elink_lcheck.t BioPerl-1.6.1/t/Tools/EUtilities/elink_llinks.t BioPerl-1.6.1/t/Tools/EUtilities/elink_ncheck.t BioPerl-1.6.1/t/Tools/EUtilities/elink_neighbor.t BioPerl-1.6.1/t/Tools/EUtilities/elink_neighbor_history.t BioPerl-1.6.1/t/Tools/EUtilities/elink_scores.t BioPerl-1.6.1/t/Tools/EUtilities/epost.t BioPerl-1.6.1/t/Tools/EUtilities/esearch.t BioPerl-1.6.1/t/Tools/EUtilities/espell.t BioPerl-1.6.1/t/Tools/EUtilities/esummary.t BioPerl-1.6.1/t/Tools/EUtilities/EUtilParameters.t BioPerl-1.6.1/t/Tools/Phylo BioPerl-1.6.1/t/Tools/Phylo/Gerp.t BioPerl-1.6.1/t/Tools/Phylo/Molphy.t BioPerl-1.6.1/t/Tools/Phylo/PAML.t BioPerl-1.6.1/t/Tools/Phylo/Phylip BioPerl-1.6.1/t/Tools/Phylo/Phylip/ProtDist.t BioPerl-1.6.1/t/Tools/Run BioPerl-1.6.1/t/Tools/Run/RemoteBlast.t BioPerl-1.6.1/t/Tools/Run/RemoteBlast_rpsblast.t BioPerl-1.6.1/t/Tools/Run/StandAloneBlast.t BioPerl-1.6.1/t/Tools/Run/WrapperBase.t BioPerl-1.6.1/t/Tools/Signalp BioPerl-1.6.1/t/Tools/Signalp/ExtendedSignalp.t BioPerl-1.6.1/t/Tools/Spidey BioPerl-1.6.1/t/Tools/Spidey/Spidey.t BioPerl-1.6.1/t/Tree BioPerl-1.6.1/t/Tree/Compatible.t BioPerl-1.6.1/t/Tree/Node.t BioPerl-1.6.1/t/Tree/RandomTreeFactory.t BioPerl-1.6.1/t/Tree/Tree.t BioPerl-1.6.1/t/Tree/TreeIO.t BioPerl-1.6.1/t/Tree/TreeStatistics.t BioPerl-1.6.1/t/Tree/PhyloNetwork BioPerl-1.6.1/t/Tree/PhyloNetwork/Factory.t BioPerl-1.6.1/t/Tree/PhyloNetwork/GraphViz.t BioPerl-1.6.1/t/Tree/PhyloNetwork/MuVector.t BioPerl-1.6.1/t/Tree/PhyloNetwork/PhyloNetwork.t BioPerl-1.6.1/t/Tree/PhyloNetwork/RandomFactory.t BioPerl-1.6.1/t/Tree/PhyloNetwork/TreeFactory.t BioPerl-1.6.1/t/Tree/TreeIO BioPerl-1.6.1/t/Tree/TreeIO/lintree.t BioPerl-1.6.1/t/Tree/TreeIO/newick.t BioPerl-1.6.1/t/Tree/TreeIO/nexus.t BioPerl-1.6.1/t/Tree/TreeIO/nhx.t BioPerl-1.6.1/t/Tree/TreeIO/phyloxml.t BioPerl-1.6.1/t/Tree/TreeIO/svggraph.t BioPerl-1.6.1/t/Tree/TreeIO/tabtree.t BioPerl-1.6.1/t/Variation BioPerl-1.6.1/t/Variation/AAChange.t BioPerl-1.6.1/t/Variation/AAReverseMutate.t BioPerl-1.6.1/t/Variation/Allele.t BioPerl-1.6.1/t/Variation/DNAMutation.t BioPerl-1.6.1/t/Variation/RNAChange.t BioPerl-1.6.1/t/Variation/SeqDiff.t BioPerl-1.6.1/t/Variation/SNP.t BioPerl-1.6.1/t/Variation/Variation_IO.t CPAN.pm: Going to build C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz >>> /export/home/fly1003/bin/perl Makefile.PL # running Build.PL /export/home/fly1003/bin/perl Build.PL Checking whether your kit is complete... Looks good Checking prerequisites... - ERROR: DB_File is not installed (I think I'm being run by CPAN/CPANPLUS, so will rely on it to handle prerequisite installation) I'll get CPAN to prepend the installation of this Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] * Optional prerequisite Bio::ASN1::EntrezGene is not installed (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!]) * Optional prerequisite XML::SAX::Writer is not installed (wanted for writing xml, used by Bio::SeqIO::tigrxml) * Optional prerequisite GraphViz is not installed (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) * Optional prerequisite List::MoreUtils is not installed (wanted for Back- or reverse-translation of sequences, used by Bio::Tools::SeqPattern and Bio::Tools::SeqPattern::BackTranslate) ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation - DB_File is not installed - DBD::Pg is not installed Checking features: Network...................enabled BioDBSeqFeature_mysql.....enabled BioDBGFF..................enabled BioDBSeqFeature_BDB.......disabled BioDBSeqFeature_SQLite....enabled BioDBSeqFeature_Pg........disabled 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 Do you want to run tests that require connection to servers across the internet (likely to cause some failures)? y/n [n] - will not run internet-requiring tests Creating new 'Build' script for 'BioPerl' version '1.006001' ---- Unsatisfied dependencies detected during ---- ---- CJFIELDS/BioPerl-1.6.1.tar.gz ---- DB_File [requires] Running make test Delayed until after prerequisites Running test for module 'DB_File' ______________________ D i s t r o P r e f s ______________________ DB_File.yml[0] Running make for P/PM/PMQS/DB_File-1.820.tar.gz Disabled via prefs file '/export/home/fly1003/etc/distroprefs/DB_File.yml' doc 0 PMQS/DB_File-1.820.tar.gz [disabled] -- NA Disabled via prefs file '/export/home/fly1003/etc/distroprefs/DB_File.yml' doc 0 Running make for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz Has already been unwrapped into directory /export/home/fly1003/var/cpan/build/BioPerl-1.6.1-RKMIUZ CPAN.pm: Going to build C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz Warning: Prerequisite 'DB_File => 0' for 'CJFIELDS/BioPerl-1.6.1.tar.gz' failed when processing 'PMQS/DB_File-1.820.tar.gz' with 'unwrapped => NO Disabled via prefs file '/export/home/fly1003/etc/distroprefs/DB_File.yml' doc 0'. Continuing, but chances to succeed are limited. >>> make /export/home/fly1003/bin/perl Build --makefile_env_macros 1 Copying Bio/PopGen/MarkerI.pm -> blib/lib/Bio/PopGen/MarkerI.pm Copying Bio/Matrix/PSM/Psm.pm -> blib/lib/Bio/Matrix/PSM/Psm.pm Copying Bio/MolEvol/CodonModel.pm -> blib/lib/Bio/MolEvol/CodonModel.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/AlignIO/mega.pm -> blib/lib/Bio/AlignIO/mega.pm Copying Bio/Tools/EUtilities/Info/LinkInfo.pm -> blib/lib/Bio/Tools/EUtilities/Info/LinkInfo.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/Map/PositionWithSequence.pm -> blib/lib/Bio/Map/PositionWithSequence.pm Copying Bio/SeqIO/chaos.pm -> blib/lib/Bio/SeqIO/chaos.pm Copying Bio/Factory/ObjectFactory.pm -> blib/lib/Bio/Factory/ObjectFactory.pm Copying Bio/DB/GFF/Aggregator/so_transcript.pm -> blib/lib/Bio/DB/GFF/Aggregator/so_transcript.pm Copying Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm -> blib/lib/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm Copying Bio/DB/SeqFeature/Store/berkeleydb3.pm -> blib/lib/Bio/DB/SeqFeature/Store/berkeleydb3.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/Cluster/UniGeneI.pm -> blib/lib/Bio/Cluster/UniGeneI.pm Copying Bio/DB/GFF/Aggregator/ucsc_acembly.pm -> blib/lib/Bio/DB/GFF/Aggregator/ucsc_acembly.pm Copying Bio/Map/Physical.pm -> blib/lib/Bio/Map/Physical.pm Copying Bio/Tools/GuessSeqFormat.pm -> blib/lib/Bio/Tools/GuessSeqFormat.pm Copying Bio/Search/Result/HmmpfamResult.pm -> blib/lib/Bio/Search/Result/HmmpfamResult.pm Copying Bio/Biblio/PubmedBookArticle.pm -> blib/lib/Bio/Biblio/PubmedBookArticle.pm Copying Bio/Search/HSP/WABAHSP.pm -> blib/lib/Bio/Search/HSP/WABAHSP.pm Copying Bio/Align/Utilities.pm -> blib/lib/Bio/Align/Utilities.pm Copying Bio/Expression/ProbeI.pm -> blib/lib/Bio/Expression/ProbeI.pm Copying Bio/Tools/Run/ParametersI.pm -> blib/lib/Bio/Tools/Run/ParametersI.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/DB/SwissProt.pm -> blib/lib/Bio/DB/SwissProt.pm Copying Bio/SearchIO/fasta.pm -> blib/lib/Bio/SearchIO/fasta.pm Copying Bio/Tools/EUtilities/Query/GlobalQuery.pm -> blib/lib/Bio/Tools/EUtilities/Query/GlobalQuery.pm Copying Bio/TreeIO/nexus.pm -> blib/lib/Bio/TreeIO/nexus.pm Copying Bio/Biblio/Provider.pm -> blib/lib/Bio/Biblio/Provider.pm Copying Bio/Coordinate/Graph.pm -> blib/lib/Bio/Coordinate/Graph.pm Copying Bio/Search/HSP/ModelHSP.pm -> blib/lib/Bio/Search/HSP/ModelHSP.pm Copying Bio/Tree/DistanceFactory.pm -> blib/lib/Bio/Tree/DistanceFactory.pm Copying Bio/DB/GFF/Aggregator/ucsc_sanger22.pm -> blib/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm Copying Bio/SeqIO/tinyseq/tinyseqHandler.pm -> blib/lib/Bio/SeqIO/tinyseq/tinyseqHandler.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/Matrix/PSM/PsmI.pm -> blib/lib/Bio/Matrix/PSM/PsmI.pm Copying Bio/TreeIO/TreeEventBuilder.pm -> blib/lib/Bio/TreeIO/TreeEventBuilder.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/Coordinate/Result/Gap.pm -> blib/lib/Bio/Coordinate/Result/Gap.pm Copying Bio/Tools/TandemRepeatsFinder.pm -> blib/lib/Bio/Tools/TandemRepeatsFinder.pm Copying Bio/Seq/Meta/Array.pm -> blib/lib/Bio/Seq/Meta/Array.pm Copying Bio/Tools/Run/RemoteBlast.pm -> blib/lib/Bio/Tools/Run/RemoteBlast.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/Map/Clone.pm -> blib/lib/Bio/Map/Clone.pm Copying Bio/SearchIO/Writer/HSPTableWriter.pm -> blib/lib/Bio/SearchIO/Writer/HSPTableWriter.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/DB/Expression/geo.pm -> blib/lib/Bio/DB/Expression/geo.pm Copying Bio/Tree/TreeI.pm -> blib/lib/Bio/Tree/TreeI.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/Phenotype/Phenotype.pm -> blib/lib/Bio/Phenotype/Phenotype.pm Copying Bio/Seq/TraceI.pm -> blib/lib/Bio/Seq/TraceI.pm Copying Bio/Seq/PrimaryQual.pm -> blib/lib/Bio/Seq/PrimaryQual.pm Copying Bio/DB/Failover.pm -> blib/lib/Bio/DB/Failover.pm Copying Bio/Map/CytoMap.pm -> blib/lib/Bio/Map/CytoMap.pm Copying Bio/Variation/Allele.pm -> blib/lib/Bio/Variation/Allele.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/LiveSeq/Repeat_Unit.pm -> blib/lib/Bio/LiveSeq/Repeat_Unit.pm Copying Bio/Restriction/Enzyme/MultiCut.pm -> blib/lib/Bio/Restriction/Enzyme/MultiCut.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/Annotation/Target.pm -> blib/lib/Bio/Annotation/Target.pm Copying Bio/Restriction/IO/base.pm -> blib/lib/Bio/Restriction/IO/base.pm Copying Bio/DB/RefSeq.pm -> blib/lib/Bio/DB/RefSeq.pm Copying Bio/DB/GFF/Adaptor/memory/iterator.pm -> blib/lib/Bio/DB/GFF/Adaptor/memory/iterator.pm Copying Bio/Tools/RepeatMasker.pm -> blib/lib/Bio/Tools/RepeatMasker.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/Coordinate/Result/Match.pm -> blib/lib/Bio/Coordinate/Result/Match.pm Copying Bio/Search/Result/HMMERResult.pm -> blib/lib/Bio/Search/Result/HMMERResult.pm Copying Bio/SearchIO/wise.pm -> blib/lib/Bio/SearchIO/wise.pm Copying Bio/Seq/PrimedSeq.pm -> blib/lib/Bio/Seq/PrimedSeq.pm Copying Bio/Tools/RNAMotif.pm -> blib/lib/Bio/Tools/RNAMotif.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/Assembly/ContigAnalysis.pm -> blib/lib/Bio/Assembly/ContigAnalysis.pm Copying Bio/Root/Test.pm -> blib/lib/Bio/Root/Test.pm Copying Bio/Coordinate/ExtrapolatingPair.pm -> blib/lib/Bio/Coordinate/ExtrapolatingPair.pm Copying Bio/Ontology/DocumentRegistry.pm -> blib/lib/Bio/Ontology/DocumentRegistry.pm Copying Bio/SimpleAnalysisI.pm -> blib/lib/Bio/SimpleAnalysisI.pm Copying Bio/IdCollectionI.pm -> blib/lib/Bio/IdCollectionI.pm Copying Bio/Tools/Gel.pm -> blib/lib/Bio/Tools/Gel.pm Copying Bio/Tree/AlleleNode.pm -> blib/lib/Bio/Tree/AlleleNode.pm Copying Bio/DB/NCBIHelper.pm -> blib/lib/Bio/DB/NCBIHelper.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/Root/Build.pm -> blib/lib/Bio/Root/Build.pm Copying Bio/Map/FPCMarker.pm -> blib/lib/Bio/Map/FPCMarker.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/Event/EventHandlerI.pm -> blib/lib/Bio/Event/EventHandlerI.pm Copying Bio/Biblio/Thesis.pm -> blib/lib/Bio/Biblio/Thesis.pm Copying Bio/DB/Fasta.pm -> blib/lib/Bio/DB/Fasta.pm Copying Bio/SeqIO/table.pm -> blib/lib/Bio/SeqIO/table.pm Copying Bio/Tools/EUtilities/Summary.pm -> blib/lib/Bio/Tools/EUtilities/Summary.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/Matrix/PSM/InstanceSite.pm -> blib/lib/Bio/Matrix/PSM/InstanceSite.pm Copying Bio/SeqIO/game/seqHandler.pm -> blib/lib/Bio/SeqIO/game/seqHandler.pm Copying Bio/Assembly/Tools/ContigSpectrum.pm -> blib/lib/Bio/Assembly/Tools/ContigSpectrum.pm Copying Bio/Tree/TreeFunctionsI.pm -> blib/lib/Bio/Tree/TreeFunctionsI.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/Align/AlignI.pm -> blib/lib/Bio/Align/AlignI.pm Copying Bio/Search/Result/BlastPullResult.pm -> blib/lib/Bio/Search/Result/BlastPullResult.pm Copying Bio/Tools/EUtilities/Cookie.pm -> blib/lib/Bio/Tools/EUtilities/Cookie.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/SeqFeature/Gene/Exon.pm -> blib/lib/Bio/SeqFeature/Gene/Exon.pm Copying Bio/Tools/Prints.pm -> blib/lib/Bio/Tools/Prints.pm Copying Bio/Matrix/PSM/IO.pm -> blib/lib/Bio/Matrix/PSM/IO.pm Copying Bio/TreeIO/svggraph.pm -> blib/lib/Bio/TreeIO/svggraph.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/Cluster/UniGene.pm -> blib/lib/Bio/Cluster/UniGene.pm Copying Bio/SeqIO/swissdriver.pm -> blib/lib/Bio/SeqIO/swissdriver.pm Copying Bio/CodonUsage/Table.pm -> blib/lib/Bio/CodonUsage/Table.pm Copying Bio/DB/ReferenceI.pm -> blib/lib/Bio/DB/ReferenceI.pm Copying Bio/SeqFeature/Generic.pm -> blib/lib/Bio/SeqFeature/Generic.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/PopGen/TagHaplotype.pm -> blib/lib/Bio/PopGen/TagHaplotype.pm Copying Bio/Search/Processor.pm -> blib/lib/Bio/Search/Processor.pm Copying Bio/Tools/Analysis/Protein/GOR4.pm -> blib/lib/Bio/Tools/Analysis/Protein/GOR4.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/Biblio/Organisation.pm -> blib/lib/Bio/Biblio/Organisation.pm Copying Bio/Search/BlastUtils.pm -> blib/lib/Bio/Search/BlastUtils.pm Copying Bio/Tree/RandomFactory.pm -> blib/lib/Bio/Tree/RandomFactory.pm Copying Bio/Structure/IO/pdb.pm -> blib/lib/Bio/Structure/IO/pdb.pm Copying Bio/Tools/Phylo/PAML/Result.pm -> blib/lib/Bio/Tools/Phylo/PAML/Result.pm Copying Bio/DescribableI.pm -> blib/lib/Bio/DescribableI.pm Copying Bio/Structure/StructureI.pm -> blib/lib/Bio/Structure/StructureI.pm Copying Bio/Search/Result/ResultI.pm -> blib/lib/Bio/Search/Result/ResultI.pm Copying Bio/Symbol/AlphabetI.pm -> blib/lib/Bio/Symbol/AlphabetI.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/DB/SeqVersion/gi.pm -> blib/lib/Bio/DB/SeqVersion/gi.pm Copying Bio/Location/SplitLocationI.pm -> blib/lib/Bio/Location/SplitLocationI.pm Copying Bio/SeqFeature/Gene/NC_Feature.pm -> blib/lib/Bio/SeqFeature/Gene/NC_Feature.pm Copying Bio/SeqIO/metafasta.pm -> blib/lib/Bio/SeqIO/metafasta.pm Copying Bio/Tools/Phylo/Gerp.pm -> blib/lib/Bio/Tools/Phylo/Gerp.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/SearchIO/rnamotif.pm -> blib/lib/Bio/SearchIO/rnamotif.pm Copying Bio/Index/GenBank.pm -> blib/lib/Bio/Index/GenBank.pm Copying Bio/Tools/EUtilities/EUtilDataI.pm -> blib/lib/Bio/Tools/EUtilities/EUtilDataI.pm Copying Bio/Restriction/IO/itype2.pm -> blib/lib/Bio/Restriction/IO/itype2.pm Copying Bio/PhyloNetwork/muVector.pm -> blib/lib/Bio/PhyloNetwork/muVector.pm Copying Bio/Biblio/MedlineJournalArticle.pm -> blib/lib/Bio/Biblio/MedlineJournalArticle.pm Copying Bio/CodonUsage/IO.pm -> blib/lib/Bio/CodonUsage/IO.pm Copying Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm -> blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm Copying Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm -> blib/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.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/Tools/dpAlign.pm -> blib/lib/Bio/Tools/dpAlign.pm Copying Bio/Search/Tiling/MapTileUtils.pm -> blib/lib/Bio/Search/Tiling/MapTileUtils.pm Copying Bio/AlignIO/Handler/GenericAlignHandler.pm -> blib/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm Copying Bio/SeqFeature/Gene/TranscriptI.pm -> blib/lib/Bio/SeqFeature/Gene/TranscriptI.pm Copying Bio/Restriction/IO.pm -> blib/lib/Bio/Restriction/IO.pm Copying Bio/DB/SeqFeature/Store/FeatureFileLoader.pm -> blib/lib/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm Copying Bio/Cluster/FamilyI.pm -> blib/lib/Bio/Cluster/FamilyI.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/SeqIO/pln.pm -> blib/lib/Bio/SeqIO/pln.pm Copying Bio/Ontology/TermI.pm -> blib/lib/Bio/Ontology/TermI.pm Copying Bio/AnalysisResultI.pm -> blib/lib/Bio/AnalysisResultI.pm Copying Bio/Search/Result/BlastResult.pm -> blib/lib/Bio/Search/Result/BlastResult.pm Copying Bio/Map/PositionHandlerI.pm -> blib/lib/Bio/Map/PositionHandlerI.pm Copying Bio/PopGen/Simulation/Coalescent.pm -> blib/lib/Bio/PopGen/Simulation/Coalescent.pm Copying Bio/Assembly/ScaffoldI.pm -> blib/lib/Bio/Assembly/ScaffoldI.pm Copying Bio/Annotation/AnnotationFactory.pm -> blib/lib/Bio/Annotation/AnnotationFactory.pm Copying Bio/Taxon.pm -> blib/lib/Bio/Taxon.pm Copying Bio/SeqIO/locuslink.pm -> blib/lib/Bio/SeqIO/locuslink.pm Copying Bio/Phenotype/MeSH/Twig.pm -> blib/lib/Bio/Phenotype/MeSH/Twig.pm Copying Bio/Tools/Sim4/Exon.pm -> blib/lib/Bio/Tools/Sim4/Exon.pm Copying Bio/Structure/Atom.pm -> blib/lib/Bio/Structure/Atom.pm Copying Bio/PopGen/Genotype.pm -> blib/lib/Bio/PopGen/Genotype.pm Copying Bio/Tools/pICalculator.pm -> blib/lib/Bio/Tools/pICalculator.pm Copying Bio/Tools/Phylo/Molphy/Result.pm -> blib/lib/Bio/Tools/Phylo/Molphy/Result.pm Copying Bio/DB/GFF/Aggregator/match.pm -> blib/lib/Bio/DB/GFF/Aggregator/match.pm Copying Bio/DB/GFF/Aggregator/ucsc_softberry.pm -> blib/lib/Bio/DB/GFF/Aggregator/ucsc_softberry.pm Copying Bio/Map/PositionI.pm -> blib/lib/Bio/Map/PositionI.pm Copying Bio/Biblio/BookArticle.pm -> blib/lib/Bio/Biblio/BookArticle.pm Copying Bio/Search/Tiling/TilingI.pm -> blib/lib/Bio/Search/Tiling/TilingI.pm Copying Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm -> blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm Copying Bio/Restriction/IO/withrefm.pm -> blib/lib/Bio/Restriction/IO/withrefm.pm Copying Bio/DB/Flat/BDB/swiss.pm -> blib/lib/Bio/DB/Flat/BDB/swiss.pm Copying Bio/Tools/SeqStats.pm -> blib/lib/Bio/Tools/SeqStats.pm Copying Bio/LiveSeq/Transcript.pm -> blib/lib/Bio/LiveSeq/Transcript.pm Copying Bio/Ontology/OntologyEngineI.pm -> blib/lib/Bio/Ontology/OntologyEngineI.pm Copying Bio/Ontology/Term.pm -> blib/lib/Bio/Ontology/Term.pm Copying Bio/Search/HSP/FastaHSP.pm -> blib/lib/Bio/Search/HSP/FastaHSP.pm Copying Bio/Tools/Primer/Assessor/Base.pm -> blib/lib/Bio/Tools/Primer/Assessor/Base.pm Copying Bio/Tools/Match.pm -> blib/lib/Bio/Tools/Match.pm Copying Bio/DB/Taxonomy/list.pm -> blib/lib/Bio/DB/Taxonomy/list.pm Copying Bio/DB/Flat/BDB.pm -> blib/lib/Bio/DB/Flat/BDB.pm Copying Bio/AlignIO/mase.pm -> blib/lib/Bio/AlignIO/mase.pm Copying Bio/SeqFeature/Gene/Transcript.pm -> blib/lib/Bio/SeqFeature/Gene/Transcript.pm Copying Bio/SeqFeature/Tools/TypeMapper.pm -> blib/lib/Bio/SeqFeature/Tools/TypeMapper.pm Copying Bio/SeqIO/scf.pm -> blib/lib/Bio/SeqIO/scf.pm Copying Bio/MapIO/mapmaker.pm -> blib/lib/Bio/MapIO/mapmaker.pm Copying Bio/Ontology/OntologyStore.pm -> blib/lib/Bio/Ontology/OntologyStore.pm Copying 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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/Symbol/SymbolI.pm -> blib/lib/Bio/Symbol/SymbolI.pm Copying Bio/Tools/EUtilities/Query.pm -> blib/lib/Bio/Tools/EUtilities/Query.pm Copying Bio/Tools/EPCR.pm -> blib/lib/Bio/Tools/EPCR.pm Copying Bio/Location/NarrowestCoordPolicy.pm -> blib/lib/Bio/Location/NarrowestCoordPolicy.pm Copying Bio/Tools/pSW.pm -> blib/lib/Bio/Tools/pSW.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/Biblio/Proceeding.pm -> blib/lib/Bio/Biblio/Proceeding.pm Copying Bio/Tools/Run/GenericParameters.pm -> blib/lib/Bio/Tools/Run/GenericParameters.pm Copying Bio/TreeIO/newick.pm -> blib/lib/Bio/TreeIO/newick.pm Copying Bio/Biblio/Book.pm -> blib/lib/Bio/Biblio/Book.pm Copying Bio/SeqFeature/Gene/GeneStructure.pm -> blib/lib/Bio/SeqFeature/Gene/GeneStructure.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/Biblio/IO/pubmed2ref.pm -> blib/lib/Bio/Biblio/IO/pubmed2ref.pm Copying Bio/SeqIO/game.pm -> blib/lib/Bio/SeqIO/game.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/Biblio/IO/medlinexml.pm -> blib/lib/Bio/Biblio/IO/medlinexml.pm Copying Bio/Coordinate/GeneMapper.pm -> blib/lib/Bio/Coordinate/GeneMapper.pm Copying Bio/SeqIO/flybase_chadoxml.pm -> blib/lib/Bio/SeqIO/flybase_chadoxml.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/SeqIO/ace.pm -> blib/lib/Bio/SeqIO/ace.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/tree/tree2pag.PLS -> blib/script/tree2pag.PLS Deleting blib/script/tree2pag.PLS.bak blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.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/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/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/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/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-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/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/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/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/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/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/utilities/search2gff.PLS -> blib/script/search2gff.PLS Deleting blib/script/search2gff.PLS.bak blib/script/search2gff.PLS -> blib/script/bp_search2gff.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/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/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/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/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/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/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS Deleting blib/script/taxonomy2tree.PLS.bak blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.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/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/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS Deleting blib/script/seqretsplit.PLS.bak blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.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 Copying Bio/DB/HIV/lanl-schema.xml -> blib/lib/Bio/DB/HIV/lanl-schema.xml Writing config notes to blib/lib/Bio/ConfigData.pm Manifying blib/script/bp_translate_seq.pl -> blib/bindoc/bp_translate_seq.pl.1 Manifying blib/script/bp_chaos_plot.pl -> blib/bindoc/bp_chaos_plot.pl.1 Manifying blib/script/bp_flanks.pl -> blib/bindoc/bp_flanks.pl.1 Manifying blib/script/bp_mask_by_search.pl -> blib/bindoc/bp_mask_by_search.pl.1 Manifying blib/script/bp_hmmer_to_table.pl -> blib/bindoc/bp_hmmer_to_table.pl.1 Manifying blib/script/bp_filter_search.pl -> blib/bindoc/bp_filter_search.pl.1 Manifying blib/script/bp_seqretsplit.pl -> blib/bindoc/bp_seqretsplit.pl.1 Manifying blib/script/bp_bulk_load_gff.pl -> blib/bindoc/bp_bulk_load_gff.pl.1 Manifying blib/script/bp_dbsplit.pl -> blib/bindoc/bp_dbsplit.pl.1 Manifying blib/script/bp_search2BSML.pl -> blib/bindoc/bp_search2BSML.pl.1 Manifying blib/script/bp_search2tribe.pl -> blib/bindoc/bp_search2tribe.pl.1 Manifying blib/script/bp_biofetch_genbank_proxy.pl -> blib/bindoc/bp_biofetch_genbank_proxy.pl.1 Manifying blib/script/bp_search2gff.pl -> blib/bindoc/bp_search2gff.pl.1 Manifying blib/script/bp_seqconvert.pl -> blib/bindoc/bp_seqconvert.pl.1 Manifying blib/script/bp_meta_gff.pl -> blib/bindoc/bp_meta_gff.pl.1 Manifying blib/script/bp_make_mrna_protein.pl -> blib/bindoc/bp_make_mrna_protein.pl.1 Manifying blib/script/bp_local_taxonomydb_query.pl -> blib/bindoc/bp_local_taxonomydb_query.pl.1 Manifying blib/script/bp_sreformat.pl -> blib/bindoc/bp_sreformat.pl.1 Manifying blib/script/bp_search2table.pl -> blib/bindoc/bp_search2table.pl.1 Manifying blib/script/bp_taxid4species.pl -> blib/bindoc/bp_taxid4species.pl.1 Manifying blib/script/bp_biblio.pl -> blib/bindoc/bp_biblio.pl.1 Manifying blib/script/bp_gccalc.pl -> blib/bindoc/bp_gccalc.pl.1 Manifying blib/script/bp_hivq.pl -> blib/bindoc/bp_hivq.pl.1 Manifying blib/script/bp_download_query_genbank.pl -> blib/bindoc/bp_download_query_genbank.pl.1 Manifying blib/script/bp_remote_blast.pl -> blib/bindoc/bp_remote_blast.pl.1 Manifying blib/script/bp_aacomp.pl -> blib/bindoc/bp_aacomp.pl.1 Manifying blib/script/bp_mrtrans.pl -> blib/bindoc/bp_mrtrans.pl.1 Manifying blib/script/bp_split_seq.pl -> blib/bindoc/bp_split_seq.pl.1 Manifying blib/script/bp_mutate.pl -> blib/bindoc/bp_mutate.pl.1 Manifying blib/script/bp_genbank2gff3.pl -> blib/bindoc/bp_genbank2gff3.pl.1 Manifying blib/script/bp_search2alnblocks.pl -> blib/bindoc/bp_search2alnblocks.pl.1 Manifying blib/script/bp_process_sgd.pl -> blib/bindoc/bp_process_sgd.pl.1 Manifying blib/script/bp_einfo.pl -> blib/bindoc/bp_einfo.pl.1 Manifying blib/script/bp_genbank2gff.pl -> blib/bindoc/bp_genbank2gff.pl.1 Manifying blib/script/bp_fast_load_gff.pl -> blib/bindoc/bp_fast_load_gff.pl.1 Manifying blib/script/bp_fetch.pl -> blib/bindoc/bp_fetch.pl.1 Manifying blib/script/bp_index.pl -> blib/bindoc/bp_index.pl.1 Manifying blib/script/bp_taxonomy2tree.pl -> blib/bindoc/bp_taxonomy2tree.pl.1 Manifying blib/script/bp_nexus2nh.pl -> blib/bindoc/bp_nexus2nh.pl.1 Manifying blib/script/bp_oligo_count.pl -> blib/bindoc/bp_oligo_count.pl.1 Manifying blib/script/bp_bioflat_index.pl -> blib/bindoc/bp_bioflat_index.pl.1 Manifying blib/script/bp_biogetseq.pl -> blib/bindoc/bp_biogetseq.pl.1 Manifying blib/script/bp_extract_feature_seq.pl -> blib/bindoc/bp_extract_feature_seq.pl.1 Manifying blib/script/bp_tree2pag.pl -> blib/bindoc/bp_tree2pag.pl.1 Manifying blib/script/bp_unflatten_seq.pl -> blib/bindoc/bp_unflatten_seq.pl.1 Manifying blib/script/bp_parse_hmmsearch.pl -> blib/bindoc/bp_parse_hmmsearch.pl.1 Manifying blib/script/bp_pairwise_kaks.pl -> blib/bindoc/bp_pairwise_kaks.pl.1 Manifying blib/script/bp_query_entrez_taxa.pl -> blib/bindoc/bp_query_entrez_taxa.pl.1 Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1 Manifying blib/script/bp_seq_length.pl -> blib/bindoc/bp_seq_length.pl.1 Manifying blib/script/bp_load_gff.pl -> blib/bindoc/bp_load_gff.pl.1 Manifying blib/script/bp_fastam9_to_table.pl -> blib/bindoc/bp_fastam9_to_table.pl.1 Manifying blib/script/bp_process_wormbase.pl -> blib/bindoc/bp_process_wormbase.pl.1 Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1 Manifying blib/script/bp_composite_LD.pl -> blib/bindoc/bp_composite_LD.pl.1 Manifying blib/script/bp_classify_hits_kingdom.pl -> blib/bindoc/bp_classify_hits_kingdom.pl.1 Manifying blib/script/bp_blast2tree.pl -> blib/bindoc/bp_blast2tree.pl.1 Manifying blib/script/bp_revtrans-motif.pl -> blib/bindoc/bp_revtrans-motif.pl.1 Manifying blib/script/bp_heterogeneity_test.pl -> blib/bindoc/bp_heterogeneity_test.pl.1 Manifying blib/script/bp_generate_histogram.pl -> blib/bindoc/bp_generate_histogram.pl.1 Manifying blib/script/bp_process_gadfly.pl -> blib/bindoc/bp_process_gadfly.pl.1 Manifying blib/lib/Bio/SeqIO/interpro.pm -> blib/libdoc/Bio::SeqIO::interpro.3 Manifying blib/lib/Bio/Tools/SiRNA/Ruleset/tuschl.pm -> blib/libdoc/Bio::Tools::SiRNA::Ruleset::tuschl.3 Manifying blib/lib/Bio/Expression/FeatureGroup.pm -> blib/libdoc/Bio::Expression::FeatureGroup.3 Manifying blib/lib/Bio/OntologyIO/dagflat.pm -> blib/libdoc/Bio::OntologyIO::dagflat.3 Manifying blib/lib/Bio/Seq/SeqFactory.pm -> blib/libdoc/Bio::Seq::SeqFactory.3 Manifying blib/lib/Bio/Location/CoordinatePolicyI.pm -> blib/libdoc/Bio::Location::CoordinatePolicyI.3 Manifying blib/lib/Bio/Root/Storable.pm -> blib/libdoc/Bio::Root::Storable.3 Manifying blib/lib/Bio/Location/Atomic.pm -> blib/libdoc/Bio::Location::Atomic.3 Manifying blib/lib/Bio/SearchIO/SearchWriterI.pm -> blib/libdoc/Bio::SearchIO::SearchWriterI.3 Manifying blib/lib/Bio/FeatureIO.pm -> blib/libdoc/Bio::FeatureIO.3 Manifying blib/lib/Bio/Biblio/IO.pm -> blib/libdoc/Bio::Biblio::IO.3 Manifying blib/lib/Bio/Variation/RNAChange.pm -> blib/libdoc/Bio::Variation::RNAChange.3 Manifying blib/lib/Bio/Root/Exception.pm -> blib/libdoc/Bio::Root::Exception.3 Manifying blib/lib/Bio/Factory/LocationFactoryI.pm -> blib/libdoc/Bio::Factory::LocationFactoryI.3 Manifying blib/lib/Bio/Biblio/Ref.pm -> blib/libdoc/Bio::Biblio::Ref.3 Manifying blib/lib/Bio/Search/HSP/WABAHSP.pm -> blib/libdoc/Bio::Search::HSP::WABAHSP.3 Manifying blib/lib/Bio/SeqIO/embl.pm -> blib/libdoc/Bio::SeqIO::embl.3 Manifying blib/lib/Bio/Factory/DriverFactory.pm -> blib/libdoc/Bio::Factory::DriverFactory.3 Manifying blib/lib/Bio/Tools/Genemark.pm -> blib/libdoc/Bio::Tools::Genemark.3 Manifying blib/lib/Bio/Biblio/MedlineArticle.pm -> blib/libdoc/Bio::Biblio::MedlineArticle.3 Manifying blib/lib/Bio/LiveSeq/ChainI.pm -> blib/libdoc/Bio::LiveSeq::ChainI.3 Manifying blib/lib/Bio/Tools/PrositeScan.pm -> blib/libdoc/Bio::Tools::PrositeScan.3 Manifying blib/lib/Bio/LiveSeq/Intron.pm -> blib/libdoc/Bio::LiveSeq::Intron.3 Manifying blib/lib/Bio/Matrix/IO/scoring.pm -> blib/libdoc/Bio::Matrix::IO::scoring.3 Manifying blib/lib/Bio/Seq/LargeLocatableSeq.pm -> blib/libdoc/Bio::Seq::LargeLocatableSeq.3 Manifying blib/lib/Bio/AlignIO/msf.pm -> blib/libdoc/Bio::AlignIO::msf.3 Manifying blib/lib/Bio/Tools/Glimmer.pm -> blib/libdoc/Bio::Tools::Glimmer.3 Manifying blib/lib/Bio/SeqIO/flybase_chadoxml.pm -> blib/libdoc/Bio::SeqIO::flybase_chadoxml.3 Manifying blib/lib/Bio/Map/RelativeI.pm -> blib/libdoc/Bio::Map::RelativeI.3 Manifying blib/lib/Bio/Tools/Profile.pm -> blib/libdoc/Bio::Tools::Profile.3 Manifying blib/lib/Bio/LiveSeq/Mutator.pm -> blib/libdoc/Bio::LiveSeq::Mutator.3 Manifying blib/lib/Bio/Tools/Primer/Pair.pm -> blib/libdoc/Bio::Tools::Primer::Pair.3 Manifying blib/lib/Bio/Annotation/TypeManager.pm -> blib/libdoc/Bio::Annotation::TypeManager.3 Manifying blib/lib/Bio/Expression/ProbeI.pm -> blib/libdoc/Bio::Expression::ProbeI.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/alignment.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::alignment.3 Manifying blib/lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm -> blib/libdoc/Bio::SearchIO::IteratedSearchResultEventBuilder.3 Manifying blib/lib/Bio/Map/LinkagePosition.pm -> blib/libdoc/Bio::Map::LinkagePosition.3 Manifying blib/lib/Bio/Tools/Primer/Assessor/Base.pm -> blib/libdoc/Bio::Tools::Primer::Assessor::Base.3 Manifying blib/lib/Bio/ClusterIO/unigene.pm -> blib/libdoc/Bio::ClusterIO::unigene.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/biofetch_oracle.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::biofetch_oracle.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/pg.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::pg.3 Manifying blib/lib/Bio/DB/GFF/Util/Binning.pm -> blib/libdoc/Bio::DB::GFF::Util::Binning.3 Manifying blib/lib/Bio/Index/Abstract.pm -> blib/libdoc/Bio::Index::Abstract.3 Manifying blib/lib/Bio/PopGen/GenotypeI.pm -> blib/libdoc/Bio::PopGen::GenotypeI.3 Manifying blib/lib/Bio/Cluster/ClusterFactory.pm -> blib/libdoc/Bio::Cluster::ClusterFactory.3 Manifying blib/lib/Bio/Tools/pSW.pm -> blib/libdoc/Bio::Tools::pSW.3 Manifying blib/lib/Bio/FeatureIO/interpro.pm -> blib/libdoc/Bio::FeatureIO::interpro.3 Manifying blib/lib/Bio/SeqFeature/Gene/TranscriptI.pm -> blib/libdoc/Bio::SeqFeature::Gene::TranscriptI.3 Manifying blib/lib/Bio/TreeIO/tabtree.pm -> blib/libdoc/Bio::TreeIO::tabtree.3 Manifying blib/lib/Bio/DB/SeqFeature/Store.pm -> blib/libdoc/Bio::DB::SeqFeature::Store.3 Manifying blib/lib/Bio/SeqFeature/Gene/NC_Feature.pm -> blib/libdoc/Bio::SeqFeature::Gene::NC_Feature.3 Manifying blib/lib/Bio/Biblio/Provider.pm -> blib/libdoc/Bio::Biblio::Provider.3 Manifying blib/lib/Bio/Phenotype/PhenotypeI.pm -> blib/libdoc/Bio::Phenotype::PhenotypeI.3 Manifying blib/lib/Bio/SeqIO/bsml_sax.pm -> blib/libdoc/Bio::SeqIO::bsml_sax.3 Manifying blib/lib/Bio/Map/OrderedPosition.pm -> blib/libdoc/Bio::Map::OrderedPosition.3 Manifying blib/lib/Bio/Search/BlastUtils.pm -> blib/libdoc/Bio::Search::BlastUtils.3 Manifying blib/lib/Bio/SearchIO/blastxml.pm -> blib/libdoc/Bio::SearchIO::blastxml.3 Manifying blib/lib/Bio/DB/Expression/geo.pm -> blib/libdoc/Bio::DB::Expression::geo.3 Manifying blib/lib/Bio/Tools/FootPrinter.pm -> blib/libdoc/Bio::Tools::FootPrinter.3 Manifying blib/lib/Bio/Coordinate/ResultI.pm -> blib/libdoc/Bio::Coordinate::ResultI.3 Manifying blib/lib/Bio/Factory/ApplicationFactoryI.pm -> blib/libdoc/Bio::Factory::ApplicationFactoryI.3 Manifying blib/lib/Bio/SeqIO/scf.pm -> blib/libdoc/Bio::SeqIO::scf.3 Manifying blib/lib/Bio/Tools/EUtilities/Info.pm -> blib/libdoc/Bio::Tools::EUtilities::Info.3 Manifying blib/lib/Bio/PopGen/PopStats.pm -> blib/libdoc/Bio::PopGen::PopStats.3 Manifying blib/lib/Bio/SeqEvolution/Factory.pm -> blib/libdoc/Bio::SeqEvolution::Factory.3 Manifying blib/lib/Bio/DB/Query/GenBank.pm -> blib/libdoc/Bio::DB::Query::GenBank.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::FeatureFileLoader.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_unigene.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_unigene.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/DBI/SQLite.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::DBI::SQLite.3 Manifying blib/lib/Bio/Tools/Analysis/Protein/Domcut.pm -> blib/libdoc/Bio::Tools::Analysis::Protein::Domcut.3 Manifying blib/lib/Bio/SearchIO/blast.pm -> blib/libdoc/Bio::SearchIO::blast.3 Manifying blib/lib/Bio/Structure/Model.pm -> blib/libdoc/Bio::Structure::Model.3 Manifying blib/lib/Bio/Tools/Hmmpfam.pm -> blib/libdoc/Bio::Tools::Hmmpfam.3 Manifying blib/lib/Bio/CodonUsage/Table.pm -> blib/libdoc/Bio::CodonUsage::Table.3 Manifying blib/lib/Bio/Factory/SequenceStreamI.pm -> blib/libdoc/Bio::Factory::SequenceStreamI.3 Manifying blib/lib/Bio/LiveSeq/Prim_Transcript.pm -> blib/libdoc/Bio::LiveSeq::Prim_Transcript.3 Manifying blib/lib/Bio/MolEvol/CodonModel.pm -> blib/libdoc/Bio::MolEvol::CodonModel.3 Manifying blib/lib/Bio/Annotation/TagTree.pm -> blib/libdoc/Bio::Annotation::TagTree.3 Manifying blib/lib/Bio/DB/EMBL.pm -> blib/libdoc/Bio::DB::EMBL.3 Manifying blib/lib/Bio/Map/Microsatellite.pm -> blib/libdoc/Bio::Map::Microsatellite.3 Manifying blib/lib/Bio/Tools/Alignment/Trim.pm -> blib/libdoc/Bio::Tools::Alignment::Trim.3 Manifying blib/lib/Bio/Tools/Geneid.pm -> blib/libdoc/Bio::Tools::Geneid.3 Manifying blib/lib/Bio/Restriction/IO/prototype.pm -> blib/libdoc/Bio::Restriction::IO::prototype.3 Manifying blib/lib/Bio/Structure/Entry.pm -> blib/libdoc/Bio::Structure::Entry.3 Manifying blib/lib/Bio/Map/Contig.pm -> blib/libdoc/Bio::Map::Contig.3 Manifying blib/lib/Bio/Range.pm -> blib/libdoc/Bio::Range.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_refgene.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_refgene.3 Manifying blib/lib/Bio/Assembly/Contig.pm -> blib/libdoc/Bio::Assembly::Contig.3 Manifying blib/lib/Bio/Tools/AnalysisResult.pm -> blib/libdoc/Bio::Tools::AnalysisResult.3 Manifying blib/lib/Bio/IdentifiableI.pm -> blib/libdoc/Bio::IdentifiableI.3 Manifying blib/lib/Bio/Map/Mappable.pm -> blib/libdoc/Bio::Map::Mappable.3 Manifying blib/lib/Bio/Search/Tiling/MapTiling.pm -> blib/libdoc/Bio::Search::Tiling::MapTiling.3 Manifying blib/lib/Bio/Matrix/PSM/ProtPsm.pm -> blib/libdoc/Bio::Matrix::PSM::ProtPsm.3 Manifying blib/lib/Bio/Taxonomy/Taxon.pm -> blib/libdoc/Bio::Taxonomy::Taxon.3 Manifying blib/lib/Bio/DB/SeqFeature/NormalizedFeature.pm -> blib/libdoc/Bio::DB::SeqFeature::NormalizedFeature.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/orf.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::orf.3 Manifying blib/lib/Bio/TreeIO/svggraph.pm -> blib/libdoc/Bio::TreeIO::svggraph.3 Manifying blib/lib/Bio/PopGen/IO/hapmap.pm -> blib/libdoc/Bio::PopGen::IO::hapmap.3 Manifying blib/lib/Bio/Restriction/IO/withrefm.pm -> blib/libdoc/Bio::Restriction::IO::withrefm.3 Manifying blib/lib/Bio/Tree/DistanceFactory.pm -> blib/libdoc/Bio::Tree::DistanceFactory.3 Manifying blib/lib/Bio/SeqFeature/Gene/Exon.pm -> blib/libdoc/Bio::SeqFeature::Gene::Exon.3 Manifying blib/lib/Bio/DB/Query/WebQuery.pm -> blib/libdoc/Bio::DB::Query::WebQuery.3 Manifying blib/lib/Bio/Search/Result/CrossMatchResult.pm -> blib/libdoc/Bio::Search::Result::CrossMatchResult.3 Manifying blib/lib/Bio/DB/Universal.pm -> blib/libdoc/Bio::DB::Universal.3 Manifying blib/lib/Bio/Tree/NodeI.pm -> blib/libdoc/Bio::Tree::NodeI.3 Manifying blib/lib/Bio/Tools/Phylo/Gerp.pm -> blib/libdoc/Bio::Tools::Phylo::Gerp.3 Manifying blib/lib/Bio/SeqIO/MultiFile.pm -> blib/libdoc/Bio::SeqIO::MultiFile.3 Manifying blib/lib/Bio/Seq/SeqFastaSpeedFactory.pm -> blib/libdoc/Bio::Seq::SeqFastaSpeedFactory.3 Manifying blib/lib/Bio/Tools/EUtilities/Link.pm -> blib/libdoc/Bio::Tools::EUtilities::Link.3 Manifying blib/lib/Bio/Tools/Tmhmm.pm -> blib/libdoc/Bio::Tools::Tmhmm.3 Manifying blib/lib/Bio/Restriction/Enzyme/MultiSite.pm -> blib/libdoc/Bio::Restriction::Enzyme::MultiSite.3 Manifying blib/lib/Bio/Tools/EUtilities/Cookie.pm -> blib/libdoc/Bio::Tools::EUtilities::Cookie.3 Manifying blib/lib/Bio/OntologyIO/InterProParser.pm -> blib/libdoc/Bio::OntologyIO::InterProParser.3 Manifying blib/lib/Bio/SeqIO/chadoxml.pm -> blib/libdoc/Bio::SeqIO::chadoxml.3 Manifying blib/lib/Bio/Index/Qual.pm -> blib/libdoc/Bio::Index::Qual.3 Manifying blib/lib/Bio/Matrix/PSM/IO/masta.pm -> blib/libdoc/Bio::Matrix::PSM::IO::masta.3 Manifying blib/lib/Bio/Annotation/Reference.pm -> blib/libdoc/Bio::Annotation::Reference.3 Manifying blib/lib/Bio/DB/SeqFeature/NormalizedFeatureI.pm -> blib/libdoc/Bio::DB::SeqFeature::NormalizedFeatureI.3 Manifying blib/lib/Bio/Variation/IO.pm -> blib/libdoc/Bio::Variation::IO.3 Manifying blib/lib/Bio/SearchIO/XML/PsiBlastHandler.pm -> blib/libdoc/Bio::SearchIO::XML::PsiBlastHandler.3 Manifying blib/lib/Bio/Matrix/PSM/IO/meme.pm -> blib/libdoc/Bio::Matrix::PSM::IO::meme.3 Manifying blib/lib/Bio/Seq/MetaI.pm -> blib/libdoc/Bio::Seq::MetaI.3 Manifying blib/lib/Bio/TreeIO/pag.pm -> blib/libdoc/Bio::TreeIO::pag.3 Manifying blib/lib/Bio/LiveSeq/IO/Loader.pm -> blib/libdoc/Bio::LiveSeq::IO::Loader.3 Manifying blib/lib/Bio/AlignIO/arp.pm -> blib/libdoc/Bio::AlignIO::arp.3 Manifying blib/lib/Bio/Ontology/SimpleOntologyEngine.pm -> blib/libdoc/Bio::Ontology::SimpleOntologyEngine.3 Manifying blib/lib/Bio/Tools/Analysis/Protein/NetPhos.pm -> blib/libdoc/Bio::Tools::Analysis::Protein::NetPhos.3 Manifying blib/lib/Bio/Ontology/TermI.pm -> blib/libdoc/Bio::Ontology::TermI.3 Manifying blib/lib/Bio/SeqFeature/PositionProxy.pm -> blib/libdoc/Bio::SeqFeature::PositionProxy.3 Manifying blib/lib/Bio/SeqEvolution/DNAPoint.pm -> blib/libdoc/Bio::SeqEvolution::DNAPoint.3 Manifying blib/lib/Bio/SeqIO/ace.pm -> blib/libdoc/Bio::SeqIO::ace.3 Manifying blib/lib/Bio/Map/CytoPosition.pm -> blib/libdoc/Bio::Map::CytoPosition.3 Manifying blib/lib/Bio/Tools/ERPIN.pm -> blib/libdoc/Bio::Tools::ERPIN.3 Manifying blib/lib/Bio/Cluster/UniGene.pm -> blib/libdoc/Bio::Cluster::UniGene.3 Manifying blib/lib/Bio/DB/LocationI.pm -> blib/libdoc/Bio::DB::LocationI.3 Manifying blib/lib/Bio/SeqI.pm -> blib/libdoc/Bio::SeqI.3 Manifying blib/lib/Bio/Tools/SeqPattern/Backtranslate.pm -> blib/libdoc/Bio::Tools::SeqPattern::Backtranslate.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/DBI/Iterator.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::DBI::Iterator.3 Manifying blib/lib/Bio/DB/SeqFeature.pm -> blib/libdoc/Bio::DB::SeqFeature.3 Manifying blib/lib/Bio/Search/Hit/GenericHit.pm -> blib/libdoc/Bio::Search::Hit::GenericHit.3 Manifying blib/lib/Bio/Tools/EUtilities/EUtilParameters.pm -> blib/libdoc/Bio::Tools::EUtilities::EUtilParameters.3 Manifying blib/lib/Bio/Matrix/PSM/IO/mast.pm -> blib/libdoc/Bio::Matrix::PSM::IO::mast.3 Manifying blib/lib/Bio/SearchIO/blasttable.pm -> blib/libdoc/Bio::SearchIO::blasttable.3 Manifying blib/lib/Bio/Tools/Genewise.pm -> blib/libdoc/Bio::Tools::Genewise.3 Manifying blib/lib/Bio/Tools/Primer3.pm -> blib/libdoc/Bio::Tools::Primer3.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/berkeleydb.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::berkeleydb.3 Manifying blib/lib/Bio/Map/EntityI.pm -> blib/libdoc/Bio::Map::EntityI.3 Manifying blib/lib/Bio/Tools/Spidey/Results.pm -> blib/libdoc/Bio::Tools::Spidey::Results.3 Manifying blib/lib/Bio/SearchIO/waba.pm -> blib/libdoc/Bio::SearchIO::waba.3 Manifying blib/lib/Bio/DB/SeqFeature/NormalizedTableFeatureI.pm -> blib/libdoc/Bio::DB::SeqFeature::NormalizedTableFeatureI.3 Manifying blib/lib/Bio/Biblio/IO/pubmed2ref.pm -> blib/libdoc/Bio::Biblio::IO::pubmed2ref.3 Manifying blib/lib/Bio/Species.pm -> blib/libdoc/Bio::Species.3 Manifying blib/lib/Bio/Matrix/PSM/InstanceSite.pm -> blib/libdoc/Bio::Matrix::PSM::InstanceSite.3 Manifying blib/lib/Bio/Variation/AAReverseMutate.pm -> blib/libdoc/Bio::Variation::AAReverseMutate.3 Manifying blib/lib/Bio/Tools/SiRNA/Ruleset/saigo.pm -> blib/libdoc/Bio::Tools::SiRNA::Ruleset::saigo.3 Manifying blib/lib/Bio/Tools/Sim4/Exon.pm -> blib/libdoc/Bio::Tools::Sim4::Exon.3 Manifying blib/lib/Bio/Tools/Run/StandAloneWUBlast.pm -> blib/libdoc/Bio::Tools::Run::StandAloneWUBlast.3 Manifying blib/lib/Bio/Restriction/EnzymeCollection.pm -> blib/libdoc/Bio::Restriction::EnzymeCollection.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/memory.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::memory.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/processed_transcript.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::processed_transcript.3 Manifying blib/lib/Bio/DB/Ace.pm -> blib/libdoc/Bio::DB::Ace.3 Manifying blib/lib/Bio/LiveSeq/DNA.pm -> blib/libdoc/Bio::LiveSeq::DNA.3 Manifying blib/lib/Bio/Tools/HMMER/Results.pm -> blib/libdoc/Bio::Tools::HMMER::Results.3 Manifying blib/lib/Bio/Seq.pm -> blib/libdoc/Bio::Seq.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_softberry.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_softberry.3 Manifying blib/lib/Bio/Ontology/OBOEngine.pm -> blib/libdoc/Bio::Ontology::OBOEngine.3 Manifying blib/lib/Bio/SeqIO/ztr.pm -> blib/libdoc/Bio::SeqIO::ztr.3 Manifying blib/lib/Bio/MapIO.pm -> blib/libdoc/Bio::MapIO.3 Manifying blib/lib/Bio/DB/DBFetch.pm -> blib/libdoc/Bio::DB::DBFetch.3 Manifying blib/lib/Bio/Root/Test.pm -> blib/libdoc/Bio::Root::Test.3 Manifying blib/lib/Bio/Biblio/BookArticle.pm -> blib/libdoc/Bio::Biblio::BookArticle.3 Manifying blib/lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm -> blib/libdoc/Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler.3 Manifying blib/lib/Bio/Tools/Coil.pm -> blib/libdoc/Bio::Tools::Coil.3 Manifying blib/lib/Bio/PopGen/Population.pm -> blib/libdoc/Bio::PopGen::Population.3 Manifying blib/lib/Bio/Matrix/PSM/PsmHeaderI.pm -> blib/libdoc/Bio::Matrix::PSM::PsmHeaderI.3 Manifying blib/lib/Bio/Restriction/EnzymeI.pm -> blib/libdoc/Bio::Restriction::EnzymeI.3 Manifying blib/lib/Bio/SeqFeature/Gene/GeneStructureI.pm -> blib/libdoc/Bio::SeqFeature::Gene::GeneStructureI.3 Manifying blib/lib/Bio/Biblio/MedlineBook.pm -> blib/libdoc/Bio::Biblio::MedlineBook.3 Manifying blib/lib/Bio/Biblio/Proceeding.pm -> blib/libdoc/Bio::Biblio::Proceeding.3 Manifying blib/lib/Bio/Index/Fastq.pm -> blib/libdoc/Bio::Index::Fastq.3 Manifying blib/lib/Bio/SeqUtils.pm -> blib/libdoc/Bio::SeqUtils.3 Manifying blib/lib/Bio/DB/Failover.pm -> blib/libdoc/Bio::DB::Failover.3 Manifying blib/lib/Bio/SeqIO/asciitree.pm -> blib/libdoc/Bio::SeqIO::asciitree.3 Manifying blib/lib/Bio/Matrix/PSM/SiteMatrixI.pm -> blib/libdoc/Bio::Matrix::PSM::SiteMatrixI.3 Manifying blib/lib/Bio/Tools/Gel.pm -> blib/libdoc/Bio::Tools::Gel.3 Manifying blib/lib/Bio/DB/Registry.pm -> blib/libdoc/Bio::DB::Registry.3 Manifying blib/lib/Bio/SeqIO/game/featHandler.pm -> blib/libdoc/Bio::SeqIO::game::featHandler.3 Manifying blib/lib/Bio/Search/HSP/BlastHSP.pm -> blib/libdoc/Bio::Search::HSP::BlastHSP.3 Manifying blib/lib/Bio/Factory/SequenceFactoryI.pm -> blib/libdoc/Bio::Factory::SequenceFactoryI.3 Manifying blib/lib/Bio/Biblio/TechReport.pm -> blib/libdoc/Bio::Biblio::TechReport.3 Manifying blib/lib/Bio/Tools/Blat.pm -> blib/libdoc/Bio::Tools::Blat.3 Manifying blib/lib/Bio/Tools/Protparam.pm -> blib/libdoc/Bio::Tools::Protparam.3 Manifying blib/lib/Bio/PhyloNetwork.pm -> blib/libdoc/Bio::PhyloNetwork.3 Manifying blib/lib/Bio/SeqIO/metafasta.pm -> blib/libdoc/Bio::SeqIO::metafasta.3 Manifying blib/lib/Bio/Expression/Sample.pm -> blib/libdoc/Bio::Expression::Sample.3 Manifying blib/lib/Bio/Map/CytoMarker.pm -> blib/libdoc/Bio::Map::CytoMarker.3 Manifying blib/lib/Bio/Tools/TargetP.pm -> blib/libdoc/Bio::Tools::TargetP.3 Manifying blib/lib/Bio/DB/NCBIHelper.pm -> blib/libdoc/Bio::DB::NCBIHelper.3 Manifying blib/lib/Bio/SeqIO/table.pm -> blib/libdoc/Bio::SeqIO::table.3 Manifying blib/lib/Bio/Root/Root.pm -> blib/libdoc/Bio::Root::Root.3 Manifying blib/lib/Bio/Tools/Spidey/Exon.pm -> blib/libdoc/Bio::Tools::Spidey::Exon.3 Manifying blib/lib/Bio/Tools/EUtilities/EUtilDataI.pm -> blib/libdoc/Bio::Tools::EUtilities::EUtilDataI.3 Manifying blib/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm -> blib/libdoc/Bio::AlignIO::Handler::GenericAlignHandler.3 Manifying blib/lib/Bio/Event/EventGeneratorI.pm -> blib/libdoc/Bio::Event::EventGeneratorI.3 Manifying blib/lib/Bio/SearchIO/exonerate.pm -> blib/libdoc/Bio::SearchIO::exonerate.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/ace.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::ace.3 Manifying blib/lib/Bio/DB/QueryI.pm -> blib/libdoc/Bio::DB::QueryI.3 Manifying blib/lib/Bio/Factory/SeqAnalysisParserFactory.pm -> blib/libdoc/Bio::Factory::SeqAnalysisParserFactory.3 Manifying blib/lib/Bio/AlignIO/maf.pm -> blib/libdoc/Bio::AlignIO::maf.3 Manifying blib/lib/Bio/Tools/Run/StandAloneNCBIBlast.pm -> blib/libdoc/Bio::Tools::Run::StandAloneNCBIBlast.3 Manifying blib/lib/Bio/Tools/Analysis/Protein/Sopma.pm -> blib/libdoc/Bio::Tools::Analysis::Protein::Sopma.3 Manifying blib/lib/Bio/Search/Hit/BlastHit.pm -> blib/libdoc/Bio::Search::Hit::BlastHit.3 Manifying blib/lib/Bio/DB/SeqHound.pm -> blib/libdoc/Bio::DB::SeqHound.3 Manifying blib/lib/Bio/SeqIO/game/gameHandler.pm -> blib/libdoc/Bio::SeqIO::game::gameHandler.3 Manifying blib/lib/Bio/SeqFeature/Generic.pm -> blib/libdoc/Bio::SeqFeature::Generic.3 Manifying blib/lib/Bio/Search/SearchUtils.pm -> blib/libdoc/Bio::Search::SearchUtils.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::mysqlopt.3 Manifying blib/lib/Bio/Factory/ObjectBuilderI.pm -> blib/libdoc/Bio::Factory::ObjectBuilderI.3 Manifying blib/lib/Bio/Map/Relative.pm -> blib/libdoc/Bio::Map::Relative.3 Manifying blib/lib/Bio/Map/Position.pm -> blib/libdoc/Bio::Map::Position.3 Manifying blib/lib/Bio/Symbol/DNAAlphabet.pm -> blib/libdoc/Bio::Symbol::DNAAlphabet.3 Manifying blib/lib/Bio/Root/Utilities.pm -> blib/libdoc/Bio::Root::Utilities.3 Manifying blib/lib/Bio/Matrix/MatrixI.pm -> blib/libdoc/Bio::Matrix::MatrixI.3 Manifying blib/lib/Bio/AlignIO/largemultifasta.pm -> blib/libdoc/Bio::AlignIO::largemultifasta.3 Manifying blib/lib/Bio/DB/MeSH.pm -> blib/libdoc/Bio::DB::MeSH.3 Manifying blib/lib/Bio/SeqIO/pir.pm -> blib/libdoc/Bio::SeqIO::pir.3 Manifying blib/lib/Bio/Variation/IO/flat.pm -> blib/libdoc/Bio::Variation::IO::flat.3 Manifying blib/lib/Bio/Coordinate/GeneMapper.pm -> blib/libdoc/Bio::Coordinate::GeneMapper.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_twinscan.3 Manifying blib/lib/Bio/SearchIO/fasta.pm -> blib/libdoc/Bio::SearchIO::fasta.3 Manifying blib/lib/Bio/SeqFeature/Computation.pm -> blib/libdoc/Bio::SeqFeature::Computation.3 Manifying blib/lib/Bio/Annotation/Target.pm -> blib/libdoc/Bio::Annotation::Target.3 Manifying blib/lib/Bio/Tools/ipcress.pm -> blib/libdoc/Bio::Tools::ipcress.3 Manifying blib/lib/Bio/ClusterIO/dbsnp.pm -> blib/libdoc/Bio::ClusterIO::dbsnp.3 Manifying blib/lib/Bio/Search/HSP/PSLHSP.pm -> blib/libdoc/Bio::Search::HSP::PSLHSP.3 Manifying blib/lib/Bio/ClusterI.pm -> blib/libdoc/Bio::ClusterI.3 Manifying blib/lib/Bio/DB/GFF/Typename.pm -> blib/libdoc/Bio::DB::GFF::Typename.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/coding.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::coding.3 Manifying blib/lib/Bio/Index/Blast.pm -> blib/libdoc/Bio::Index::Blast.3 Manifying blib/lib/Bio/Tree/NodeNHX.pm -> blib/libdoc/Bio::Tree::NodeNHX.3 Manifying blib/lib/Bio/Biblio/Organisation.pm -> blib/libdoc/Bio::Biblio::Organisation.3 Manifying blib/lib/Bio/Ontology/OBOterm.pm -> blib/libdoc/Bio::Ontology::OBOterm.3 Manifying blib/lib/Bio/Structure/Residue.pm -> blib/libdoc/Bio::Structure::Residue.3 Manifying blib/lib/Bio/AnalysisResultI.pm -> blib/libdoc/Bio::AnalysisResultI.3 Manifying blib/lib/Bio/Coordinate/Result/Gap.pm -> blib/libdoc/Bio::Coordinate::Result::Gap.3 Manifying blib/lib/Bio/DB/Expression.pm -> blib/libdoc/Bio::DB::Expression.3 Manifying blib/lib/Bio/SeqIO/excel.pm -> blib/libdoc/Bio::SeqIO::excel.3 Manifying blib/lib/Bio/Tree/Compatible.pm -> blib/libdoc/Bio::Tree::Compatible.3 Manifying blib/lib/Bio/AlignIO/emboss.pm -> blib/libdoc/Bio::AlignIO::emboss.3 Manifying blib/lib/Bio/Search/HSP/HmmpfamHSP.pm -> blib/libdoc/Bio::Search::HSP::HmmpfamHSP.3 Manifying blib/lib/Bio/Tools/Prints.pm -> blib/libdoc/Bio::Tools::Prints.3 Manifying blib/lib/Bio/Search/Iteration/GenericIteration.pm -> blib/libdoc/Bio::Search::Iteration::GenericIteration.3 Manifying blib/lib/Bio/SeqFeature/Primer.pm -> blib/libdoc/Bio::SeqFeature::Primer.3 Manifying blib/lib/Bio/Cluster/SequenceFamily.pm -> blib/libdoc/Bio::Cluster::SequenceFamily.3 Manifying blib/lib/Bio/Assembly/ScaffoldI.pm -> blib/libdoc/Bio::Assembly::ScaffoldI.3 Manifying blib/lib/Bio/Assembly/Singlet.pm -> blib/libdoc/Bio::Assembly::Singlet.3 Manifying blib/lib/Bio/Search/HSP/HSPI.pm -> blib/libdoc/Bio::Search::HSP::HSPI.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/DBI/mysql.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::DBI::mysql.3 Manifying blib/lib/Bio/SeqIO/game/gameSubs.pm -> blib/libdoc/Bio::SeqIO::game::gameSubs.3 Manifying blib/lib/Bio/Biblio/MedlineJournalArticle.pm -> blib/libdoc/Bio::Biblio::MedlineJournalArticle.3 Manifying blib/lib/Bio/Das/FeatureTypeI.pm -> blib/libdoc/Bio::Das::FeatureTypeI.3 Manifying blib/lib/Bio/PhyloNetwork/FactoryX.pm -> blib/libdoc/Bio::PhyloNetwork::FactoryX.3 Manifying blib/lib/Bio/Search/HSP/HSPFactory.pm -> blib/libdoc/Bio::Search::HSP::HSPFactory.3 Manifying blib/lib/Bio/SeqIO/gbdriver.pm -> blib/libdoc/Bio::SeqIO::gbdriver.3 Manifying blib/lib/Bio/Symbol/Symbol.pm -> blib/libdoc/Bio::Symbol::Symbol.3 Manifying blib/lib/Bio/Tools/Prediction/Exon.pm -> blib/libdoc/Bio::Tools::Prediction::Exon.3 Manifying blib/lib/Bio/DB/BiblioI.pm -> blib/libdoc/Bio::DB::BiblioI.3 Manifying blib/lib/Bio/Tools/Analysis/Protein/GOR4.pm -> blib/libdoc/Bio::Tools::Analysis::Protein::GOR4.3 Manifying blib/lib/Bio/Map/Marker.pm -> blib/libdoc/Bio::Map::Marker.3 Manifying blib/lib/Bio/Root/Version.pm -> blib/libdoc/Bio::Root::Version.3 Manifying blib/lib/Bio/SeqIO.pm -> blib/libdoc/Bio::SeqIO.3 Manifying blib/lib/Bio/Location/FuzzyLocationI.pm -> blib/libdoc/Bio::Location::FuzzyLocationI.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_genscan.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_genscan.3 Manifying blib/lib/Bio/PopGen/IO/phase.pm -> blib/libdoc/Bio::PopGen::IO::phase.3 Manifying blib/lib/Bio/Align/DNAStatistics.pm -> blib/libdoc/Bio::Align::DNAStatistics.3 Manifying blib/lib/Bio/Biblio/PubmedJournalArticle.pm -> blib/libdoc/Bio::Biblio::PubmedJournalArticle.3 Manifying blib/lib/Bio/Tools/EUtilities/Summary.pm -> blib/libdoc/Bio::Tools::EUtilities::Summary.3 Manifying blib/lib/Bio/Tools/Eponine.pm -> blib/libdoc/Bio::Tools::Eponine.3 Manifying blib/lib/Bio/Variation/Allele.pm -> blib/libdoc/Bio::Variation::Allele.3 Manifying blib/lib/Bio/Phenotype/Phenotype.pm -> blib/libdoc/Bio::Phenotype::Phenotype.3 Manifying blib/lib/Bio/Factory/SeqAnalysisParserFactoryI.pm -> blib/libdoc/Bio::Factory::SeqAnalysisParserFactoryI.3 Manifying blib/lib/Bio/SeqIO/swiss.pm -> blib/libdoc/Bio::SeqIO::swiss.3 Manifying blib/lib/Bio/DB/ReferenceI.pm -> blib/libdoc/Bio::DB::ReferenceI.3 Manifying blib/lib/Bio/ClusterIO.pm -> blib/libdoc/Bio::ClusterIO.3 Manifying blib/lib/Bio/DB/Taxonomy/entrez.pm -> blib/libdoc/Bio::DB::Taxonomy::entrez.3 Manifying blib/lib/Bio/Map/GenePosition.pm -> blib/libdoc/Bio::Map::GenePosition.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_sanger22.3 Manifying blib/lib/Bio/Map/FPCMarker.pm -> blib/libdoc/Bio::Map::FPCMarker.3 Manifying blib/lib/Bio/AlignIO/mase.pm -> blib/libdoc/Bio::AlignIO::mase.3 Manifying blib/lib/Bio/OntologyIO/soflat.pm -> blib/libdoc/Bio::OntologyIO::soflat.3 Manifying blib/lib/Bio/MapIO/fpc.pm -> blib/libdoc/Bio::MapIO::fpc.3 Manifying blib/lib/Bio/Coordinate/Result/Match.pm -> blib/libdoc/Bio::Coordinate::Result::Match.3 Manifying blib/lib/Bio/Search/Hit/PsiBlastHit.pm -> blib/libdoc/Bio::Search::Hit::PsiBlastHit.3 Manifying blib/lib/Bio/Restriction/IO/bairoch.pm -> blib/libdoc/Bio::Restriction::IO::bairoch.3 Manifying blib/lib/Bio/PopGen/IO/csv.pm -> blib/libdoc/Bio::PopGen::IO::csv.3 Manifying blib/lib/Bio/Biblio/IO/medlinexml.pm -> blib/libdoc/Bio::Biblio::IO::medlinexml.3 Manifying blib/lib/Bio/Search/Result/WABAResult.pm -> blib/libdoc/Bio::Search::Result::WABAResult.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/none.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::none.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/berkeleydb3.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::berkeleydb3.3 Manifying blib/lib/Bio/Search/Result/HmmpfamResult.pm -> blib/libdoc/Bio::Search::Result::HmmpfamResult.3 Manifying blib/lib/Bio/DB/GenBank.pm -> blib/libdoc/Bio::DB::GenBank.3 Manifying blib/lib/Bio/AlignIO/psi.pm -> blib/libdoc/Bio::AlignIO::psi.3 Manifying blib/lib/Bio/SeqIO/agave.pm -> blib/libdoc/Bio::SeqIO::agave.3 Manifying blib/lib/Bio/SeqIO/swissdriver.pm -> blib/libdoc/Bio::SeqIO::swissdriver.3 Manifying blib/lib/Bio/Variation/VariantI.pm -> blib/libdoc/Bio::Variation::VariantI.3 Manifying blib/lib/Bio/SeqFeature/Similarity.pm -> blib/libdoc/Bio::SeqFeature::Similarity.3 Manifying blib/lib/Bio/DescribableI.pm -> blib/libdoc/Bio::DescribableI.3 Manifying blib/lib/Bio/Biblio/IO/medline2ref.pm -> blib/libdoc/Bio::Biblio::IO::medline2ref.3 Manifying blib/lib/Bio/Ontology/OntologyStore.pm -> blib/libdoc/Bio::Ontology::OntologyStore.3 Manifying blib/lib/Bio/SeqFeature/Gene/Promoter.pm -> blib/libdoc/Bio::SeqFeature::Gene::Promoter.3 Manifying blib/lib/Bio/PhyloNetwork/Factory.pm -> blib/libdoc/Bio::PhyloNetwork::Factory.3 Manifying blib/lib/Bio/HandlerBaseI.pm -> blib/libdoc/Bio::HandlerBaseI.3 Manifying blib/lib/Bio/Ontology/Path.pm -> blib/libdoc/Bio::Ontology::Path.3 Manifying blib/lib/Bio/Ontology/TermFactory.pm -> blib/libdoc/Bio::Ontology::TermFactory.3 Manifying blib/lib/Bio/Restriction/Analysis.pm -> blib/libdoc/Bio::Restriction::Analysis.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_acembly.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_acembly.3 Manifying blib/lib/Bio/Factory/ObjectFactoryI.pm -> blib/libdoc/Bio::Factory::ObjectFactoryI.3 Manifying blib/lib/Bio/Annotation/SimpleValue.pm -> blib/libdoc/Bio::Annotation::SimpleValue.3 Manifying blib/lib/Bio/Align/StatisticsI.pm -> blib/libdoc/Bio::Align::StatisticsI.3 Manifying blib/lib/Bio/Tree/TreeFunctionsI.pm -> blib/libdoc/Bio::Tree::TreeFunctionsI.3 Manifying blib/lib/Bio/Restriction/IO/itype2.pm -> blib/libdoc/Bio::Restriction::IO::itype2.3 Manifying blib/lib/Bio/SeqIO/entrezgene.pm -> blib/libdoc/Bio::SeqIO::entrezgene.3 Manifying blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm -> blib/libdoc/Bio::Ontology::SimpleGOEngine::GraphAdaptor02.3 Manifying blib/lib/Bio/SeqIO/tigrxml.pm -> blib/libdoc/Bio::SeqIO::tigrxml.3 Manifying blib/lib/Bio/TreeIO/nexus.pm -> blib/libdoc/Bio::TreeIO::nexus.3 Manifying blib/lib/Bio/Tools/RandomDistFunctions.pm -> blib/libdoc/Bio::Tools::RandomDistFunctions.3 Manifying blib/lib/Bio/DB/Flat.pm -> blib/libdoc/Bio::DB::Flat.3 Manifying blib/lib/Bio/SeqIO/phd.pm -> blib/libdoc/Bio::SeqIO::phd.3 Manifying blib/lib/Bio/Tools/Fgenesh.pm -> blib/libdoc/Bio::Tools::Fgenesh.3 Manifying blib/lib/Bio/Tools/EUtilities/Summary/DocSum.pm -> blib/libdoc/Bio::Tools::EUtilities::Summary::DocSum.3 Manifying blib/lib/Bio/Matrix/PhylipDist.pm -> blib/libdoc/Bio::Matrix::PhylipDist.3 Manifying blib/lib/Bio/DB/CUTG.pm -> blib/libdoc/Bio::DB::CUTG.3 Manifying blib/lib/Bio/Map/CytoMap.pm -> blib/libdoc/Bio::Map::CytoMap.3 Manifying blib/lib/Bio/DB/TFBS/transfac_pro.pm -> blib/libdoc/Bio::DB::TFBS::transfac_pro.3 Manifying blib/lib/Bio/Expression/Platform.pm -> blib/libdoc/Bio::Expression::Platform.3 Manifying blib/lib/Bio/DB/GFF/RelSegment.pm -> blib/libdoc/Bio::DB::GFF::RelSegment.3 Manifying blib/lib/Bio/Tools/ECnumber.pm -> blib/libdoc/Bio::Tools::ECnumber.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/memory/feature_serializer.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::memory::feature_serializer.3 Manifying blib/lib/Bio/Tools/Alignment/Consed.pm -> blib/libdoc/Bio::Tools::Alignment::Consed.3 Manifying blib/lib/Bio/OntologyIO/obo.pm -> blib/libdoc/Bio::OntologyIO::obo.3 Manifying blib/lib/Bio/Tree/Tree.pm -> blib/libdoc/Bio::Tree::Tree.3 Manifying blib/lib/Bio/FeatureHolderI.pm -> blib/libdoc/Bio::FeatureHolderI.3 Manifying blib/lib/Bio/Tree/AlleleNode.pm -> blib/libdoc/Bio::Tree::AlleleNode.3 Manifying blib/lib/Bio/Tools/IUPAC.pm -> blib/libdoc/Bio::Tools::IUPAC.3 Manifying blib/lib/Bio/LiveSeq/Range.pm -> blib/libdoc/Bio::LiveSeq::Range.3 Manifying blib/lib/Bio/Tree/AnnotatableNode.pm -> blib/libdoc/Bio::Tree::AnnotatableNode.3 Manifying blib/lib/Bio/SearchIO/Writer/GbrowseGFF.pm -> blib/libdoc/Bio::SearchIO::Writer::GbrowseGFF.3 Manifying blib/lib/Bio/PrimarySeqI.pm -> blib/libdoc/Bio::PrimarySeqI.3 Manifying blib/lib/Bio/Tools/isPcr.pm -> blib/libdoc/Bio::Tools::isPcr.3 Manifying blib/lib/Bio/Tools/EPCR.pm -> blib/libdoc/Bio::Tools::EPCR.3 Manifying blib/lib/Bio/Index/Stockholm.pm -> blib/libdoc/Bio::Index::Stockholm.3 Manifying blib/lib/Bio/Tools/Phylo/Molphy/Result.pm -> blib/libdoc/Bio::Tools::Phylo::Molphy::Result.3 Manifying blib/lib/Bio/Align/AlignI.pm -> blib/libdoc/Bio::Align::AlignI.3 Manifying blib/lib/Bio/Seq/LargePrimarySeq.pm -> blib/libdoc/Bio::Seq::LargePrimarySeq.3 Manifying blib/lib/Bio/AlignIO/proda.pm -> blib/libdoc/Bio::AlignIO::proda.3 Manifying blib/lib/Bio/Tools/Genomewise.pm -> blib/libdoc/Bio::Tools::Genomewise.3 Manifying blib/lib/Bio/PhyloNetwork/muVector.pm -> blib/libdoc/Bio::PhyloNetwork::muVector.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/pg_fts.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::pg_fts.3 Manifying blib/lib/Bio/DB/Flat/BDB/swiss.pm -> blib/libdoc/Bio::DB::Flat::BDB::swiss.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/memory.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::memory.3 Manifying blib/lib/Bio/SeqIO/game.pm -> blib/libdoc/Bio::SeqIO::game.3 Manifying blib/lib/Bio/SeqIO/FTHelper.pm -> blib/libdoc/Bio::SeqIO::FTHelper.3 Manifying blib/lib/Bio/LocatableSeq.pm -> blib/libdoc/Bio::LocatableSeq.3 Manifying blib/lib/Bio/Tools/EUtilities/Info/FieldInfo.pm -> blib/libdoc/Bio::Tools::EUtilities::Info::FieldInfo.3 Manifying blib/lib/Bio/Search/HSP/GenericHSP.pm -> blib/libdoc/Bio::Search::HSP::GenericHSP.3 Manifying blib/lib/Bio/SearchIO/XML/BlastHandler.pm -> blib/libdoc/Bio::SearchIO::XML::BlastHandler.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/berkeleydb.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::berkeleydb.3 Manifying blib/lib/Bio/SearchIO/Writer/BSMLResultWriter.pm -> blib/libdoc/Bio::SearchIO::Writer::BSMLResultWriter.3 Manifying blib/lib/Bio/FeatureIO/gff.pm -> blib/libdoc/Bio::FeatureIO::gff.3 Manifying blib/lib/Bio/Tools/CodonTable.pm -> blib/libdoc/Bio::Tools::CodonTable.3 Manifying blib/lib/Bio/AlignIO/bl2seq.pm -> blib/libdoc/Bio::AlignIO::bl2seq.3 Manifying blib/lib/Bio/SeqIO/fasta.pm -> blib/libdoc/Bio::SeqIO::fasta.3 Manifying blib/lib/Bio/Cluster/FamilyI.pm -> blib/libdoc/Bio::Cluster::FamilyI.3 Manifying blib/lib/Bio/Ontology/Term.pm -> blib/libdoc/Bio::Ontology::Term.3 Manifying blib/lib/Bio/Location/Fuzzy.pm -> blib/libdoc/Bio::Location::Fuzzy.3 Manifying blib/lib/Bio/Factory/FTLocationFactory.pm -> blib/libdoc/Bio::Factory::FTLocationFactory.3 Manifying blib/lib/Bio/TreeIO/TreeEventBuilder.pm -> blib/libdoc/Bio::TreeIO::TreeEventBuilder.3 Manifying blib/lib/Bio/DB/GFF/Aggregator.pm -> blib/libdoc/Bio::DB::GFF::Aggregator.3 Manifying blib/lib/Bio/LiveSeq/Repeat_Region.pm -> blib/libdoc/Bio::LiveSeq::Repeat_Region.3 Manifying blib/lib/Bio/Restriction/Enzyme/MultiCut.pm -> blib/libdoc/Bio::Restriction::Enzyme::MultiCut.3 Manifying blib/lib/Bio/Matrix/PSM/IO.pm -> blib/libdoc/Bio::Matrix::PSM::IO.3 Manifying blib/lib/Bio/Map/MappableI.pm -> blib/libdoc/Bio::Map::MappableI.3 Manifying blib/lib/Bio/Phenotype/OMIM/OMIMentry.pm -> blib/libdoc/Bio::Phenotype::OMIM::OMIMentry.3 Manifying blib/lib/Bio/Seq/TraceI.pm -> blib/libdoc/Bio::Seq::TraceI.3 Manifying blib/lib/Bio/Map/PositionI.pm -> blib/libdoc/Bio::Map::PositionI.3 Manifying blib/lib/Bio/AlignIO/stockholm.pm -> blib/libdoc/Bio::AlignIO::stockholm.3 Manifying blib/lib/Bio/AlignIO/selex.pm -> blib/libdoc/Bio::AlignIO::selex.3 Manifying blib/lib/Bio/DB/GenericWebAgent.pm -> blib/libdoc/Bio::DB::GenericWebAgent.3 Manifying blib/lib/Bio/SeqFeature/SiRNA/Oligo.pm -> blib/libdoc/Bio::SeqFeature::SiRNA::Oligo.3 Manifying blib/lib/Bio/Ontology/OntologyI.pm -> blib/libdoc/Bio::Ontology::OntologyI.3 Manifying blib/lib/Bio/Das/SegmentI.pm -> blib/libdoc/Bio::Das::SegmentI.3 Manifying blib/lib/Bio/WebAgent.pm -> blib/libdoc/Bio::WebAgent.3 Manifying blib/lib/Bio/TreeIO/cluster.pm -> blib/libdoc/Bio::TreeIO::cluster.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/bdb.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::bdb.3 Manifying blib/lib/Bio/Seq/BaseSeqProcessor.pm -> blib/libdoc/Bio::Seq::BaseSeqProcessor.3 Manifying blib/lib/Bio/DB/GFF/Util/Rearrange.pm -> blib/libdoc/Bio::DB::GFF::Util::Rearrange.3 Manifying blib/lib/Bio/AnalysisI.pm -> blib/libdoc/Bio::AnalysisI.3 Manifying blib/lib/Bio/OntologyIO/simplehierarchy.pm -> blib/libdoc/Bio::OntologyIO::simplehierarchy.3 Manifying blib/lib/Bio/DB/HIV/HIVAnnotProcessor.pm -> blib/libdoc/Bio::DB::HIV::HIVAnnotProcessor.3 Manifying blib/lib/Bio/Search/HSP/PsiBlastHSP.pm -> blib/libdoc/Bio::Search::HSP::PsiBlastHSP.3 Manifying blib/lib/Bio/AlignIO/phylip.pm -> blib/libdoc/Bio::AlignIO::phylip.3 Manifying blib/lib/Bio/Ontology/DocumentRegistry.pm -> blib/libdoc/Bio::Ontology::DocumentRegistry.3 Manifying blib/lib/Bio/Coordinate/Chain.pm -> blib/libdoc/Bio::Coordinate::Chain.3 Manifying blib/lib/Bio/Matrix/PSM/Psm.pm -> blib/libdoc/Bio::Matrix::PSM::Psm.3 Manifying blib/lib/Bio/OntologyIO/Handlers/InterProHandler.pm -> blib/libdoc/Bio::OntologyIO::Handlers::InterProHandler.3 Manifying blib/lib/Bio/Align/PairwiseStatistics.pm -> blib/libdoc/Bio::Align::PairwiseStatistics.3 Manifying blib/lib/Bio/Tools/SiRNA.pm -> blib/libdoc/Bio::Tools::SiRNA.3 Manifying blib/lib/Bio/Ontology/OntologyEngineI.pm -> blib/libdoc/Bio::Ontology::OntologyEngineI.3 Manifying blib/lib/Bio/AlignIO/pfam.pm -> blib/libdoc/Bio::AlignIO::pfam.3 Manifying blib/lib/Bio/Taxonomy/FactoryI.pm -> blib/libdoc/Bio::Taxonomy::FactoryI.3 Manifying blib/lib/Bio/SeqFeature/Lite.pm -> blib/libdoc/Bio::SeqFeature::Lite.3 Manifying blib/lib/Bio/TreeIO/lintree.pm -> blib/libdoc/Bio::TreeIO::lintree.3 Manifying blib/lib/Bio/Tools/EUtilities/Query/GlobalQuery.pm -> blib/libdoc/Bio::Tools::EUtilities::Query::GlobalQuery.3 Manifying blib/lib/Bio/Tools/Infernal.pm -> blib/libdoc/Bio::Tools::Infernal.3 Manifying blib/lib/Bio/SearchIO/hmmer_pull.pm -> blib/libdoc/Bio::SearchIO::hmmer_pull.3 Manifying blib/lib/Bio/DB/SeqVersion.pm -> blib/libdoc/Bio::DB::SeqVersion.3 Manifying blib/lib/Bio/Tools/Phylo/PAML.pm -> blib/libdoc/Bio::Tools::Phylo::PAML.3 Manifying blib/lib/Bio/Search/StatisticsI.pm -> blib/libdoc/Bio::Search::StatisticsI.3 Manifying blib/lib/Bio/SimpleAlign.pm -> blib/libdoc/Bio::SimpleAlign.3 Manifying blib/lib/Bio/Factory/TreeFactoryI.pm -> blib/libdoc/Bio::Factory::TreeFactoryI.3 Manifying blib/lib/Bio/Tools/RepeatMasker.pm -> blib/libdoc/Bio::Tools::RepeatMasker.3 Manifying blib/lib/Bio/Map/GeneMap.pm -> blib/libdoc/Bio::Map::GeneMap.3 Manifying blib/lib/Bio/DB/RandomAccessI.pm -> blib/libdoc/Bio::DB::RandomAccessI.3 Manifying blib/lib/Bio/PopGen/Marker.pm -> blib/libdoc/Bio::PopGen::Marker.3 Manifying blib/lib/Bio/Matrix/Generic.pm -> blib/libdoc/Bio::Matrix::Generic.3 Manifying blib/lib/Bio/Root/HTTPget.pm -> blib/libdoc/Bio::Root::HTTPget.3 Manifying blib/lib/Bio/Index/SwissPfam.pm -> blib/libdoc/Bio::Index::SwissPfam.3 Manifying blib/lib/Bio/TreeIO.pm -> blib/libdoc/Bio::TreeIO.3 Manifying blib/lib/Bio/Search/Hit/PullHitI.pm -> blib/libdoc/Bio::Search::Hit::PullHitI.3 Manifying blib/lib/Bio/Tools/EUtilities/Query.pm -> blib/libdoc/Bio::Tools::EUtilities::Query.3 Manifying blib/lib/Bio/PopGen/Individual.pm -> blib/libdoc/Bio::PopGen::Individual.3 Manifying blib/lib/Bio/Tools/GuessSeqFormat.pm -> blib/libdoc/Bio::Tools::GuessSeqFormat.3 Manifying blib/lib/Bio/AlignIO/xmfa.pm -> blib/libdoc/Bio::AlignIO::xmfa.3 Manifying blib/lib/Bio/Map/LinkageMap.pm -> blib/libdoc/Bio::Map::LinkageMap.3 Manifying blib/lib/Bio/SearchIO/rnamotif.pm -> blib/libdoc/Bio::SearchIO::rnamotif.3 Manifying blib/lib/Bio/SeqFeature/Gene/ExonI.pm -> blib/libdoc/Bio::SeqFeature::Gene::ExonI.3 Manifying blib/lib/Bio/Biblio/Thesis.pm -> blib/libdoc/Bio::Biblio::Thesis.3 Manifying blib/lib/Bio/Search/GenericStatistics.pm -> blib/libdoc/Bio::Search::GenericStatistics.3 Manifying blib/lib/Bio/SeqIO/alf.pm -> blib/libdoc/Bio::SeqIO::alf.3 Manifying blib/lib/Bio/Factory/SequenceProcessorI.pm -> blib/libdoc/Bio::Factory::SequenceProcessorI.3 Manifying blib/lib/Bio/Search/Processor.pm -> blib/libdoc/Bio::Search::Processor.3 Manifying blib/lib/Bio/AnalysisParserI.pm -> blib/libdoc/Bio::AnalysisParserI.3 Manifying blib/lib/Bio/Search/Result/BlastPullResult.pm -> blib/libdoc/Bio::Search::Result::BlastPullResult.3 Manifying blib/lib/Bio/Phenotype/OMIM/OMIMparser.pm -> blib/libdoc/Bio::Phenotype::OMIM::OMIMparser.3 Manifying blib/lib/Bio/Biblio/Book.pm -> blib/libdoc/Bio::Biblio::Book.3 Manifying blib/lib/Bio/DB/Biblio/eutils.pm -> blib/libdoc/Bio::DB::Biblio::eutils.3 Manifying blib/lib/Bio/DBLinkContainerI.pm -> blib/libdoc/Bio::DBLinkContainerI.3 Manifying blib/lib/Bio/Index/AbstractSeq.pm -> blib/libdoc/Bio::Index::AbstractSeq.3 Manifying blib/lib/Bio/Location/Split.pm -> blib/libdoc/Bio::Location::Split.3 Manifying blib/lib/Bio/Symbol/ProteinAlphabet.pm -> blib/libdoc/Bio::Symbol::ProteinAlphabet.3 Manifying blib/lib/Bio/Annotation/StructuredValue.pm -> blib/libdoc/Bio::Annotation::StructuredValue.3 Manifying blib/lib/Bio/SeqFeature/Gene/GeneStructure.pm -> blib/libdoc/Bio::SeqFeature::Gene::GeneStructure.3 Manifying blib/lib/Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm -> blib/libdoc/Bio::Phenotype::OMIM::OMIMentryAllelicVariant.3 Manifying blib/lib/Bio/Tools/EMBOSS/Palindrome.pm -> blib/libdoc/Bio::Tools::EMBOSS::Palindrome.3 Manifying blib/lib/Bio/SearchIO/cross_match.pm -> blib/libdoc/Bio::SearchIO::cross_match.3 Manifying blib/lib/Bio/Map/GeneRelative.pm -> blib/libdoc/Bio::Map::GeneRelative.3 Manifying blib/lib/Bio/Map/MarkerI.pm -> blib/libdoc/Bio::Map::MarkerI.3 Manifying blib/lib/Bio/SeqIO/tinyseq.pm -> blib/libdoc/Bio::SeqIO::tinyseq.3 Manifying blib/lib/Bio/SearchIO/erpin.pm -> blib/libdoc/Bio::SearchIO::erpin.3 Manifying blib/lib/Bio/Ontology/PathI.pm -> blib/libdoc/Bio::Ontology::PathI.3 Manifying blib/lib/Bio/Expression/DataSet.pm -> blib/libdoc/Bio::Expression::DataSet.3 Manifying blib/lib/Bio/PopGen/Simulation/Coalescent.pm -> blib/libdoc/Bio::PopGen::Simulation::Coalescent.3 Manifying blib/lib/Bio/DB/SeqVersion/gi.pm -> blib/libdoc/Bio::DB::SeqVersion::gi.3 Manifying blib/lib/Bio/Tools/TandemRepeatsFinder.pm -> blib/libdoc/Bio::Tools::TandemRepeatsFinder.3 Manifying blib/lib/Bio/Taxonomy.pm -> blib/libdoc/Bio::Taxonomy.3 Manifying blib/lib/Bio/Tools/Analysis/Protein/Mitoprot.pm -> blib/libdoc/Bio::Tools::Analysis::Protein::Mitoprot.3 Manifying blib/lib/Bio/Search/DatabaseI.pm -> blib/libdoc/Bio::Search::DatabaseI.3 Manifying blib/lib/Bio/Tools/Phylo/Gumby.pm -> blib/libdoc/Bio::Tools::Phylo::Gumby.3 Manifying blib/lib/Bio/DasI.pm -> blib/libdoc/Bio::DasI.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::LoadHelper.3 Manifying blib/lib/Bio/SeqIO/tigr.pm -> blib/libdoc/Bio::SeqIO::tigr.3 Manifying blib/lib/Bio/Index/GenBank.pm -> blib/libdoc/Bio::Index::GenBank.3 Manifying blib/lib/Bio/FeatureIO/ptt.pm -> blib/libdoc/Bio::FeatureIO::ptt.3 Manifying blib/lib/Bio/PhyloNetwork/RandomFactory.pm -> blib/libdoc/Bio::PhyloNetwork::RandomFactory.3 Manifying blib/lib/Bio/DB/Biblio/soap.pm -> blib/libdoc/Bio::DB::Biblio::soap.3 Manifying blib/lib/Bio/SearchIO/hmmer.pm -> blib/libdoc/Bio::SearchIO::hmmer.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/Loader.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::Loader.3 Manifying blib/lib/Bio/Tools/tRNAscanSE.pm -> blib/libdoc/Bio::Tools::tRNAscanSE.3 Manifying blib/lib/Bio/Assembly/IO/tigr.pm -> blib/libdoc/Bio::Assembly::IO::tigr.3 Manifying blib/lib/Bio/Biblio/JournalArticle.pm -> blib/libdoc/Bio::Biblio::JournalArticle.3 Manifying blib/lib/Bio/Tools/Sim4/Results.pm -> blib/libdoc/Bio::Tools::Sim4::Results.3 Manifying blib/lib/Bio/Index/Hmmer.pm -> blib/libdoc/Bio::Index::Hmmer.3 Manifying blib/lib/Bio/MapIO/mapmaker.pm -> blib/libdoc/Bio::MapIO::mapmaker.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/biofetch.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::biofetch.3 Manifying blib/lib/Bio/Tools/Prediction/Gene.pm -> blib/libdoc/Bio::Tools::Prediction::Gene.3 Manifying blib/lib/Bio/Root/Test/Warn.pm -> blib/libdoc/Bio::Root::Test::Warn.3 Manifying blib/lib/Bio/AlignIO/meme.pm -> blib/libdoc/Bio::AlignIO::meme.3 Manifying blib/lib/Bio/Tools/SeqPattern.pm -> blib/libdoc/Bio::Tools::SeqPattern.3 Manifying blib/lib/Bio/Seq/RichSeq.pm -> blib/libdoc/Bio::Seq::RichSeq.3 Manifying blib/lib/Bio/Tools/EUtilities/Summary/ItemContainerI.pm -> blib/libdoc/Bio::Tools::EUtilities::Summary::ItemContainerI.3 Manifying blib/lib/Bio/Search/HSP/HMMERHSP.pm -> blib/libdoc/Bio::Search::HSP::HMMERHSP.3 Manifying blib/lib/Bio/SeqIO/ctf.pm -> blib/libdoc/Bio::SeqIO::ctf.3 Manifying blib/lib/Bio/DB/Taxonomy/list.pm -> blib/libdoc/Bio::DB::Taxonomy::list.3 Manifying blib/lib/Bio/Location/NarrowestCoordPolicy.pm -> blib/libdoc/Bio::Location::NarrowestCoordPolicy.3 Manifying blib/lib/Bio/Tools/Sigcleave.pm -> blib/libdoc/Bio::Tools::Sigcleave.3 Manifying blib/lib/Bio/DB/Taxonomy.pm -> blib/libdoc/Bio::DB::Taxonomy.3 Manifying blib/lib/Bio/Assembly/Tools/ContigSpectrum.pm -> blib/libdoc/Bio::Assembly::Tools::ContigSpectrum.3 Manifying blib/lib/Bio/Ontology/GOterm.pm -> blib/libdoc/Bio::Ontology::GOterm.3 Manifying blib/lib/Bio/DB/Flat/BDB/embl.pm -> blib/libdoc/Bio::DB::Flat::BDB::embl.3 Manifying blib/lib/Bio/Tools/MZEF.pm -> blib/libdoc/Bio::Tools::MZEF.3 Manifying blib/lib/Bio/Phenotype/MeSH/Twig.pm -> blib/libdoc/Bio::Phenotype::MeSH::Twig.3 Manifying blib/lib/Bio/Tools/Primer/Feature.pm -> blib/libdoc/Bio::Tools::Primer::Feature.3 Manifying blib/lib/Bio/DB/GFF/Featname.pm -> blib/libdoc/Bio::DB::GFF::Featname.3 Manifying blib/lib/Bio/LiveSeq/SeqI.pm -> blib/libdoc/Bio::LiveSeq::SeqI.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/oracleace.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::oracleace.3 Manifying blib/lib/Bio/SeqFeature/FeaturePair.pm -> blib/libdoc/Bio::SeqFeature::FeaturePair.3 Manifying blib/lib/Bio/LiveSeq/Repeat_Unit.pm -> blib/libdoc/Bio::LiveSeq::Repeat_Unit.3 Manifying blib/lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm -> blib/libdoc/Bio::SeqIO::Handler::GenericRichSeqHandler.3 Manifying blib/lib/Bio/OntologyIO.pm -> blib/libdoc/Bio::OntologyIO.3 Manifying blib/lib/Bio/Variation/SNP.pm -> blib/libdoc/Bio::Variation::SNP.3 Manifying blib/lib/Bio/PhyloNetwork/TreeFactory.pm -> blib/libdoc/Bio::PhyloNetwork::TreeFactory.3 Manifying blib/lib/Bio/Tools/pICalculator.pm -> blib/libdoc/Bio::Tools::pICalculator.3 Manifying blib/lib/Bio/DB/GenPept.pm -> blib/libdoc/Bio::DB::GenPept.3 Manifying blib/lib/Bio/Matrix/PSM/SiteMatrix.pm -> blib/libdoc/Bio::Matrix::PSM::SiteMatrix.3 Manifying blib/lib/Bio/DB/GFF.pm -> blib/libdoc/Bio::DB::GFF.3 Manifying blib/lib/Bio/Ontology/RelationshipFactory.pm -> blib/libdoc/Bio::Ontology::RelationshipFactory.3 Manifying blib/lib/Bio/Biblio/WebResource.pm -> blib/libdoc/Bio::Biblio::WebResource.3 Manifying blib/lib/Bio/ParameterBaseI.pm -> blib/libdoc/Bio::ParameterBaseI.3 Manifying blib/lib/Bio/Search/Hit/HitFactory.pm -> blib/libdoc/Bio::Search::Hit::HitFactory.3 Manifying blib/lib/Bio/DB/SeqFeature/Segment.pm -> blib/libdoc/Bio::DB::SeqFeature::Segment.3 Manifying blib/lib/Bio/Index/Fasta.pm -> blib/libdoc/Bio::Index::Fasta.3 Manifying blib/lib/Bio/FeatureIO/bed.pm -> blib/libdoc/Bio::FeatureIO::bed.3 Manifying blib/lib/Bio/ConfigData.pm -> blib/libdoc/Bio::ConfigData.3 Manifying blib/lib/Bio/Ontology/InterProTerm.pm -> blib/libdoc/Bio::Ontology::InterProTerm.3 Manifying blib/lib/Bio/PopGen/Simulation/GeneticDrift.pm -> blib/libdoc/Bio::PopGen::Simulation::GeneticDrift.3 Manifying blib/lib/Bio/AlignIO/metafasta.pm -> blib/libdoc/Bio::AlignIO::metafasta.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::caching_handle.3 Manifying blib/lib/Bio/Restriction/Enzyme.pm -> blib/libdoc/Bio::Restriction::Enzyme.3 Manifying blib/lib/Bio/Tools/QRNA.pm -> blib/libdoc/Bio::Tools::QRNA.3 Manifying blib/lib/Bio/Tools/Phylo/PAML/Result.pm -> blib/libdoc/Bio::Tools::Phylo::PAML::Result.3 Manifying blib/lib/Bio/Location/AvWithinCoordPolicy.pm -> blib/libdoc/Bio::Location::AvWithinCoordPolicy.3 Manifying blib/lib/Bio/Symbol/AlphabetI.pm -> blib/libdoc/Bio::Symbol::AlphabetI.3 Manifying blib/lib/Bio/Tools/Genscan.pm -> blib/libdoc/Bio::Tools::Genscan.3 Manifying blib/lib/Bio/Annotation/Relation.pm -> blib/libdoc/Bio::Annotation::Relation.3 Manifying blib/lib/Bio/Tree/Draw/Cladogram.pm -> blib/libdoc/Bio::Tree::Draw::Cladogram.3 Manifying blib/lib/Bio/Biblio/IO/pubmedxml.pm -> blib/libdoc/Bio::Biblio::IO::pubmedxml.3 Manifying blib/lib/Bio/DB/GFF/Homol.pm -> blib/libdoc/Bio::DB::GFF::Homol.3 Manifying blib/lib/Bio/SearchIO/FastHitEventBuilder.pm -> blib/libdoc/Bio::SearchIO::FastHitEventBuilder.3 Manifying blib/lib/Bio/SeqFeature/SiRNA/Pair.pm -> blib/libdoc/Bio::SeqFeature::SiRNA::Pair.3 Manifying blib/lib/Bio/Factory/MapFactoryI.pm -> blib/libdoc/Bio::Factory::MapFactoryI.3 Manifying blib/lib/Bio/SeqEvolution/EvolutionI.pm -> blib/libdoc/Bio::SeqEvolution::EvolutionI.3 Manifying blib/lib/Bio/Tools/OddCodes.pm -> blib/libdoc/Bio::Tools::OddCodes.3 Manifying blib/lib/Bio/SearchIO/psl.pm -> blib/libdoc/Bio::SearchIO::psl.3 Manifying blib/lib/Bio/Map/TranscriptionFactor.pm -> blib/libdoc/Bio::Map::TranscriptionFactor.3 Manifying blib/lib/Bio/RangeI.pm -> blib/libdoc/Bio::RangeI.3 Manifying blib/lib/Bio/SeqAnalysisParserI.pm -> blib/libdoc/Bio::SeqAnalysisParserI.3 Manifying blib/lib/Bio/Map/Clone.pm -> blib/libdoc/Bio::Map::Clone.3 Manifying blib/lib/Bio/SeqIO/chaos.pm -> blib/libdoc/Bio::SeqIO::chaos.3 Manifying blib/lib/Bio/Restriction/IO.pm -> blib/libdoc/Bio::Restriction::IO.3 Manifying blib/lib/Bio/DB/TFBS.pm -> blib/libdoc/Bio::DB::TFBS.3 Manifying blib/lib/Bio/Structure/IO/pdb.pm -> blib/libdoc/Bio::Structure::IO::pdb.3 Manifying blib/lib/Bio/Align/Utilities.pm -> blib/libdoc/Bio::Align::Utilities.3 Manifying blib/lib/Bio/LiveSeq/Transcript.pm -> blib/libdoc/Bio::LiveSeq::Transcript.3 Manifying blib/lib/Bio/AlignIO/po.pm -> blib/libdoc/Bio::AlignIO::po.3 Manifying blib/lib/Bio/Index/EMBL.pm -> blib/libdoc/Bio::Index::EMBL.3 Manifying blib/lib/Bio/Expression/FeatureI.pm -> blib/libdoc/Bio::Expression::FeatureI.3 Manifying blib/lib/Bio/Seq/QualI.pm -> blib/libdoc/Bio::Seq::QualI.3 Manifying blib/lib/Bio/TreeIO/nhx.pm -> blib/libdoc/Bio::TreeIO::nhx.3 Manifying blib/lib/Bio/Tools/Promoterwise.pm -> blib/libdoc/Bio::Tools::Promoterwise.3 Manifying blib/lib/Bio/PopGen/IO.pm -> blib/libdoc/Bio::PopGen::IO.3 Manifying blib/lib/Bio/Assembly/Scaffold.pm -> blib/libdoc/Bio::Assembly::Scaffold.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/memory/iterator.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::memory::iterator.3 Manifying blib/lib/Bio/SeqIO/locuslink.pm -> blib/libdoc/Bio::SeqIO::locuslink.3 Manifying blib/lib/Bio/Tools/Est2Genome.pm -> blib/libdoc/Bio::Tools::Est2Genome.3 Manifying blib/lib/Bio/Structure/Atom.pm -> blib/libdoc/Bio::Structure::Atom.3 Manifying blib/lib/Bio/Search/GenericDatabase.pm -> blib/libdoc/Bio::Search::GenericDatabase.3 Manifying blib/lib/Bio/Search/HSP/PullHSPI.pm -> blib/libdoc/Bio::Search::HSP::PullHSPI.3 Manifying blib/lib/Bio/DB/GFF/Segment.pm -> blib/libdoc/Bio::DB::GFF::Segment.3 Manifying blib/lib/Bio/Root/RootI.pm -> blib/libdoc/Bio::Root::RootI.3 Manifying blib/lib/Bio/Tools/EUtilities/HistoryI.pm -> blib/libdoc/Bio::Tools::EUtilities::HistoryI.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/iterator.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::iterator.3 Manifying blib/lib/Bio/Assembly/ContigAnalysis.pm -> blib/libdoc/Bio::Assembly::ContigAnalysis.3 Manifying blib/lib/Bio/SeqIO/genbank.pm -> blib/libdoc/Bio::SeqIO::genbank.3 Manifying blib/lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm -> blib/libdoc/Bio::OntologyIO::Handlers::BaseSAXHandler.3 Manifying blib/lib/Bio/Search/Hit/HmmpfamHit.pm -> blib/libdoc/Bio::Search::Hit::HmmpfamHit.3 Manifying blib/lib/Bio/Tools/HMMER/Set.pm -> blib/libdoc/Bio::Tools::HMMER::Set.3 Manifying blib/lib/Bio/CodonUsage/IO.pm -> blib/libdoc/Bio::CodonUsage::IO.3 Manifying blib/lib/Bio/Variation/IO/xml.pm -> blib/libdoc/Bio::Variation::IO::xml.3 Manifying blib/lib/Bio/Matrix/PSM/PsmI.pm -> blib/libdoc/Bio::Matrix::PSM::PsmI.3 Manifying blib/lib/Bio/Biblio/Service.pm -> blib/libdoc/Bio::Biblio::Service.3 Manifying blib/lib/Bio/Seq/RichSeqI.pm -> blib/libdoc/Bio::Seq::RichSeqI.3 Manifying blib/lib/Bio/Biblio/PubmedBookArticle.pm -> blib/libdoc/Bio::Biblio::PubmedBookArticle.3 Manifying blib/lib/Bio/TreeIO/phyloxml.pm -> blib/libdoc/Bio::TreeIO::phyloxml.3 Manifying blib/lib/Bio/Search/Hit/Fasta.pm -> blib/libdoc/Bio::Search::Hit::Fasta.3 Manifying blib/lib/Bio/Tools/EUtilities/Summary/Item.pm -> blib/libdoc/Bio::Tools::EUtilities::Summary::Item.3 Manifying blib/lib/Bio/Coordinate/MapperI.pm -> blib/libdoc/Bio::Coordinate::MapperI.3 Manifying blib/lib/Bio/SearchIO/infernal.pm -> blib/libdoc/Bio::SearchIO::infernal.3 Manifying blib/lib/Bio/Map/MapI.pm -> blib/libdoc/Bio::Map::MapI.3 Manifying blib/lib/Bio/SeqIO/gcg.pm -> blib/libdoc/Bio::SeqIO::gcg.3 Manifying blib/lib/Bio/SearchIO/Writer/HSPTableWriter.pm -> blib/libdoc/Bio::SearchIO::Writer::HSPTableWriter.3 Manifying blib/lib/Bio/Seq/PrimaryQual.pm -> blib/libdoc/Bio::Seq::PrimaryQual.3 Manifying blib/lib/Bio/Tools/Signalp.pm -> blib/libdoc/Bio::Tools::Signalp.3 Manifying blib/lib/Bio/FeatureIO/vecscreen_simple.pm -> blib/libdoc/Bio::FeatureIO::vecscreen_simple.3 Manifying blib/lib/Bio/Tools/EUtilities/Info/LinkInfo.pm -> blib/libdoc/Bio::Tools::EUtilities::Info::LinkInfo.3 Manifying blib/lib/Bio/DB/Flat/BDB.pm -> blib/libdoc/Bio::DB::Flat::BDB.3 Manifying blib/lib/Bio/Seq/Meta.pm -> blib/libdoc/Bio::Seq::Meta.3 Manifying blib/lib/Bio/SeqFeature/Gene/Intron.pm -> blib/libdoc/Bio::SeqFeature::Gene::Intron.3 Manifying blib/lib/Bio/Seq/SequenceTrace.pm -> blib/libdoc/Bio::Seq::SequenceTrace.3 Manifying blib/lib/Bio/Annotation/Collection.pm -> blib/libdoc/Bio::Annotation::Collection.3 Manifying blib/lib/Bio/SearchIO/Writer/HitTableWriter.pm -> blib/libdoc/Bio::SearchIO::Writer::HitTableWriter.3 Manifying blib/lib/Bio/SearchIO/Writer/ResultTableWriter.pm -> blib/libdoc/Bio::SearchIO::Writer::ResultTableWriter.3 Manifying blib/lib/Bio/Seq/PrimedSeq.pm -> blib/libdoc/Bio::Seq::PrimedSeq.3 Manifying blib/lib/Bio/Tools/Phylo/Molphy.pm -> blib/libdoc/Bio::Tools::Phylo::Molphy.3 Manifying blib/lib/Bio/AnnotationCollectionI.pm -> blib/libdoc/Bio::AnnotationCollectionI.3 Manifying blib/lib/Bio/Location/SplitLocationI.pm -> blib/libdoc/Bio::Location::SplitLocationI.3 Manifying blib/lib/Bio/Tree/RandomFactory.pm -> blib/libdoc/Bio::Tree::RandomFactory.3 Manifying blib/lib/Bio/Biblio/Patent.pm -> blib/libdoc/Bio::Biblio::Patent.3 Manifying blib/lib/Bio/Tree/TreeI.pm -> blib/libdoc/Bio::Tree::TreeI.3 Manifying blib/lib/Bio/Biblio/BiblioBase.pm -> blib/libdoc/Bio::Biblio::BiblioBase.3 Manifying blib/lib/Bio/Tools/Run/StandAloneBlast.pm -> blib/libdoc/Bio::Tools::Run::StandAloneBlast.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/transcript.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::transcript.3 Manifying blib/lib/Bio/PullParserI.pm -> blib/libdoc/Bio::PullParserI.3 Manifying blib/lib/Bio/Tools/Analysis/Protein/Scansite.pm -> blib/libdoc/Bio::Tools::Analysis::Protein::Scansite.3 Manifying blib/lib/Bio/Biblio/MedlineBookArticle.pm -> blib/libdoc/Bio::Biblio::MedlineBookArticle.3 Manifying blib/lib/Bio/DB/Taxonomy/flatfile.pm -> blib/libdoc/Bio::DB::Taxonomy::flatfile.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/mysql.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::mysql.3 Manifying blib/lib/Bio/SeqFeature/SimilarityPair.pm -> blib/libdoc/Bio::SeqFeature::SimilarityPair.3 Manifying blib/lib/Bio/Index/BlastTable.pm -> blib/libdoc/Bio::Index::BlastTable.3 Manifying blib/lib/Bio/Search/HSP/BlastPullHSP.pm -> blib/libdoc/Bio::Search::HSP::BlastPullHSP.3 Manifying blib/lib/Bio/SeqIO/pln.pm -> blib/libdoc/Bio::SeqIO::pln.3 Manifying blib/lib/Bio/Expression/Contact.pm -> blib/libdoc/Bio::Expression::Contact.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_ensgene.3 Manifying blib/lib/Bio/Event/EventHandlerI.pm -> blib/libdoc/Bio::Event::EventHandlerI.3 Manifying blib/lib/Bio/LocationI.pm -> blib/libdoc/Bio::LocationI.3 Manifying blib/lib/Bio/Variation/AAChange.pm -> blib/libdoc/Bio::Variation::AAChange.3 Manifying 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blib/libdoc/Bio::Seq::EncodedSeq.3 Manifying blib/lib/Bio/Tree/Statistics.pm -> blib/libdoc/Bio::Tree::Statistics.3 Manifying blib/lib/Bio/Tools/Match.pm -> blib/libdoc/Bio::Tools::Match.3 Manifying blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm -> blib/libdoc/Bio::SearchIO::Writer::HTMLResultWriter.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::berkeleydb::iterator.3 Manifying blib/lib/Bio/Tools/Primer/AssessorI.pm -> blib/libdoc/Bio::Tools::Primer::AssessorI.3 Manifying blib/lib/Bio/Root/Build.pm -> blib/libdoc/Bio::Root::Build.3 Manifying blib/lib/Bio/Map/PositionWithSequence.pm -> blib/libdoc/Bio::Map::PositionWithSequence.3 Manifying blib/lib/Bio/Matrix/IO/phylip.pm -> blib/libdoc/Bio::Matrix::IO::phylip.3 Manifying blib/lib/Bio/DB/SeqI.pm -> blib/libdoc/Bio::DB::SeqI.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::mysqlcmap.3 Manifying blib/lib/Bio/SeqFeature/Tools/FeatureNamer.pm -> blib/libdoc/Bio::SeqFeature::Tools::FeatureNamer.3 Manifying blib/lib/Bio/Coordinate/Pair.pm -> blib/libdoc/Bio::Coordinate::Pair.3 Manifying blib/lib/Bio/SeqFeature/Annotated.pm -> blib/libdoc/Bio::SeqFeature::Annotated.3 Manifying blib/lib/Bio/DB/Query/HIVQuery.pm -> blib/libdoc/Bio::DB::Query::HIVQuery.3 Manifying blib/lib/Bio/Structure/SecStr/DSSP/Res.pm -> blib/libdoc/Bio::Structure::SecStr::DSSP::Res.3 Manifying blib/lib/Bio/Tools/Phylo/PAML/ModelResult.pm -> blib/libdoc/Bio::Tools::Phylo::PAML::ModelResult.3 Manifying blib/lib/Bio/PopGen/PopulationI.pm -> blib/libdoc/Bio::PopGen::PopulationI.3 Manifying blib/lib/Bio/LiveSeq/Translation.pm -> blib/libdoc/Bio::LiveSeq::Translation.3 Manifying blib/lib/Bio/SeqIO/embldriver.pm -> blib/libdoc/Bio::SeqIO::embldriver.3 Manifying blib/lib/Bio/SearchIO/gmap_f9.pm -> blib/libdoc/Bio::SearchIO::gmap_f9.3 Manifying blib/lib/Bio/SearchIO/SearchResultEventBuilder.pm -> blib/libdoc/Bio::SearchIO::SearchResultEventBuilder.3 Manifying blib/lib/Bio/Factory/ObjectFactory.pm -> blib/libdoc/Bio::Factory::ObjectFactory.3 Manifying blib/lib/Bio/DB/SwissProt.pm -> blib/libdoc/Bio::DB::SwissProt.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/gene.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::gene.3 Manifying blib/lib/Bio/Phenotype/Correlate.pm -> blib/libdoc/Bio::Phenotype::Correlate.3 Manifying blib/lib/Bio/Tools/Run/ParametersI.pm -> blib/libdoc/Bio::Tools::Run::ParametersI.3 Manifying blib/lib/Bio/SeqIO/largefasta.pm -> blib/libdoc/Bio::SeqIO::largefasta.3 Manifying blib/lib/Bio/AlignIO.pm -> blib/libdoc/Bio::AlignIO.3 Manifying blib/lib/Bio/Search/Tiling/MapTileUtils.pm -> blib/libdoc/Bio::Search::Tiling::MapTileUtils.3 Manifying blib/lib/Bio/SeqIO/chaosxml.pm -> blib/libdoc/Bio::SeqIO::chaosxml.3 Manifying blib/lib/Bio/PhyloNetwork/TreeFactoryMulti.pm -> blib/libdoc/Bio::PhyloNetwork::TreeFactoryMulti.3 Manifying blib/lib/Bio/Taxonomy/Node.pm -> blib/libdoc/Bio::Taxonomy::Node.3 Manifying blib/lib/Bio/Search/Result/ResultI.pm -> blib/libdoc/Bio::Search::Result::ResultI.3 Manifying blib/lib/Bio/SearchIO/axt.pm -> blib/libdoc/Bio::SearchIO::axt.3 Manifying blib/lib/Bio/DB/UpdateableSeqI.pm -> blib/libdoc/Bio::DB::UpdateableSeqI.3 Manifying blib/lib/Bio/SeqFeature/Tools/IDHandler.pm -> blib/libdoc/Bio::SeqFeature::Tools::IDHandler.3 Manifying blib/lib/Bio/Expression/FeatureGroup/FeatureGroupMas50.pm -> blib/libdoc/Bio::Expression::FeatureGroup::FeatureGroupMas50.3 Manifying blib/lib/Bio/DB/Flat/BDB/genbank.pm -> blib/libdoc/Bio::DB::Flat::BDB::genbank.3 Manifying blib/lib/Bio/SearchIO/blast_pull.pm -> blib/libdoc/Bio::SearchIO::blast_pull.3 Manifying blib/lib/Bio/DB/Flat/BinarySearch.pm -> blib/libdoc/Bio::DB::Flat::BinarySearch.3 Manifying blib/lib/Bio/Map/PositionHandlerI.pm -> blib/libdoc/Bio::Map::PositionHandlerI.3 Manifying blib/lib/Bio/Tools/EUtilities/Link/UrlLink.pm -> blib/libdoc/Bio::Tools::EUtilities::Link::UrlLink.3 Manifying blib/lib/Bio/SearchIO/megablast.pm -> blib/libdoc/Bio::SearchIO::megablast.3 Manifying blib/lib/Bio/Annotation/DBLink.pm -> blib/libdoc/Bio::Annotation::DBLink.3 Manifying blib/lib/Bio/Tree/Node.pm -> blib/libdoc/Bio::Tree::Node.3 Manifying blib/lib/Bio/LiveSeq/Exon.pm -> blib/libdoc/Bio::LiveSeq::Exon.3 Manifying blib/lib/Bio/Tools/EUtilities.pm -> blib/libdoc/Bio::Tools::EUtilities.3 Manifying blib/lib/Bio/SeqIO/exp.pm -> blib/libdoc/Bio::SeqIO::exp.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/match.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::match.3 Manifying blib/lib/Bio/SeqIO/bsml.pm -> blib/libdoc/Bio::SeqIO::bsml.3 Manifying blib/lib/Bio/AlignIO/prodom.pm -> blib/libdoc/Bio::AlignIO::prodom.3 Manifying blib/lib/Bio/Tools/ESTScan.pm -> blib/libdoc/Bio::Tools::ESTScan.3 Manifying blib/lib/Bio/Cluster/UniGeneI.pm -> blib/libdoc/Bio::Cluster::UniGeneI.3 Manifying blib/lib/Bio/Tools/Signalp/ExtendedSignalp.pm -> blib/libdoc/Bio::Tools::Signalp::ExtendedSignalp.3 Manifying blib/lib/Bio/Biblio/Journal.pm -> blib/libdoc/Bio::Biblio::Journal.3 Manifying blib/lib/Bio/Matrix/Scoring.pm -> blib/libdoc/Bio::Matrix::Scoring.3 Manifying blib/lib/Bio/Structure/Chain.pm -> blib/libdoc/Bio::Structure::Chain.3 Manifying blib/lib/Bio/Phenotype/Measure.pm -> blib/libdoc/Bio::Phenotype::Measure.3 Manifying blib/lib/Bio/UpdateableSeqI.pm -> blib/libdoc/Bio::UpdateableSeqI.3 Manifying blib/lib/Bio/DB/HIV/HIVQueryHelper.pm -> blib/libdoc/Bio::DB::HIV::HIVQueryHelper.3 Manifying blib/lib/Bio/Search/Tiling/TilingI.pm -> blib/libdoc/Bio::Search::Tiling::TilingI.3 Manifying blib/lib/Bio/SearchDist.pm -> blib/libdoc/Bio::SearchDist.3 Manifying blib/lib/Bio/Coordinate/Graph.pm -> blib/libdoc/Bio::Coordinate::Graph.3 Manifying blib/lib/Bio/IdCollectionI.pm -> blib/libdoc/Bio::IdCollectionI.3 Manifying blib/lib/Bio/Search/Hit/HitI.pm -> blib/libdoc/Bio::Search::Hit::HitI.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi.3 Manifying blib/lib/Bio/Search/Result/BlastResult.pm -> blib/libdoc/Bio::Search::Result::BlastResult.3 Manifying blib/lib/Bio/Seq/LargeSeq.pm -> blib/libdoc/Bio::Seq::LargeSeq.3 Manifying blib/lib/Bio/Expression/FeatureSet/FeatureSetMas50.pm -> blib/libdoc/Bio::Expression::FeatureSet::FeatureSetMas50.3 Manifying blib/lib/Bio/SeqIO/game/seqHandler.pm -> blib/libdoc/Bio::SeqIO::game::seqHandler.3 Manifying blib/lib/Bio/Align/ProteinStatistics.pm -> blib/libdoc/Bio::Align::ProteinStatistics.3 Manifying blib/lib/Bio/DB/GFF/Feature.pm -> blib/libdoc/Bio::DB::GFF::Feature.3 Manifying blib/lib/Bio/Annotation/Comment.pm -> blib/libdoc/Bio::Annotation::Comment.3 Manifying blib/lib/Bio/Coordinate/Result.pm -> blib/libdoc/Bio::Coordinate::Result.3 Manifying blib/lib/Bio/SeqFeature/Gene/Poly_A_site.pm -> blib/libdoc/Bio::SeqFeature::Gene::Poly_A_site.3 Manifying blib/lib/Bio/Root/IO.pm -> blib/libdoc/Bio::Root::IO.3 Manifying blib/lib/Bio/Search/Hit/HMMERHit.pm -> blib/libdoc/Bio::Search::Hit::HMMERHit.3 Manifying blib/lib/Bio/DB/Fasta.pm -> blib/libdoc/Bio::DB::Fasta.3 Manifying blib/lib/Bio/DB/Biblio/biofetch.pm -> blib/libdoc/Bio::DB::Biblio::biofetch.3 Manifying blib/lib/Bio/Seq/Quality.pm -> blib/libdoc/Bio::Seq::Quality.3 Manifying blib/lib/Bio/SeqIO/strider.pm -> blib/libdoc/Bio::SeqIO::strider.3 Manifying blib/lib/Bio/PhyloNetwork/TreeFactoryX.pm -> blib/libdoc/Bio::PhyloNetwork::TreeFactoryX.3 Manifying blib/lib/Bio/Matrix/Mlagan.pm -> blib/libdoc/Bio::Matrix::Mlagan.3 Manifying blib/lib/Bio/SearchIO/sim4.pm -> blib/libdoc/Bio::SearchIO::sim4.3 Manifying blib/lib/Bio/Assembly/IO.pm -> blib/libdoc/Bio::Assembly::IO.3 Manifying blib/lib/Bio/SeqFeature/Gene/UTR.pm -> blib/libdoc/Bio::SeqFeature::Gene::UTR.3 Manifying blib/lib/Bio/Index/Swissprot.pm -> blib/libdoc/Bio::Index::Swissprot.3 Manifying blib/lib/Bio/Tools/SeqStats.pm -> blib/libdoc/Bio::Tools::SeqStats.3 Manifying blib/lib/Bio/Structure/StructureI.pm -> blib/libdoc/Bio::Structure::StructureI.3 Manifying 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blib/lib/Bio/Symbol/Alphabet.pm -> blib/libdoc/Bio::Symbol::Alphabet.3 Manifying blib/lib/Bio/Coordinate/ExtrapolatingPair.pm -> blib/libdoc/Bio::Coordinate::ExtrapolatingPair.3 Manifying blib/lib/Bio/Search/Result/PullResultI.pm -> blib/libdoc/Bio::Search::Result::PullResultI.3 Manifying blib/lib/Bio/SeqIO/tab.pm -> blib/libdoc/Bio::SeqIO::tab.3 Manifying blib/lib/Bio/Coordinate/Collection.pm -> blib/libdoc/Bio::Coordinate::Collection.3 Manifying blib/lib/Bio/LiveSeq/Gene.pm -> blib/libdoc/Bio::LiveSeq::Gene.3 Manifying blib/lib/Bio/Annotation/AnnotationFactory.pm -> blib/libdoc/Bio::Annotation::AnnotationFactory.3 Manifying blib/lib/Bio/Search/Hit/BlastPullHit.pm -> blib/libdoc/Bio::Search::Hit::BlastPullHit.3 Manifying blib/lib/Bio/OntologyIO/goflat.pm -> blib/libdoc/Bio::OntologyIO::goflat.3 Manifying blib/lib/Bio/Location/Simple.pm -> blib/libdoc/Bio::Location::Simple.3 Manifying blib/lib/Bio/Tools/Phylo/Phylip/ProtDist.pm -> blib/libdoc/Bio::Tools::Phylo::Phylip::ProtDist.3 Manifying blib/lib/Bio/SeqFeature/Collection.pm -> blib/libdoc/Bio::SeqFeature::Collection.3 Manifying blib/lib/Bio/Biblio.pm -> blib/libdoc/Bio::Biblio.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo.3 Manifying blib/lib/Bio/DB/GFF/Aggregator/clone.pm -> blib/libdoc/Bio::DB::GFF::Aggregator::clone.3 Manifying blib/lib/Bio/SeqFeature/Gene/Transcript.pm -> blib/libdoc/Bio::SeqFeature::Gene::Transcript.3 Manifying blib/lib/Bio/SeqFeatureI.pm -> blib/libdoc/Bio::SeqFeatureI.3 Manifying blib/lib/Bio/PopGen/IndividualI.pm -> blib/libdoc/Bio::PopGen::IndividualI.3 Manifying blib/lib/Bio/Tools/Lucy.pm -> blib/libdoc/Bio::Tools::Lucy.3 Manifying blib/lib/Bio/Tools/Run/WrapperBase.pm -> blib/libdoc/Bio::Tools::Run::WrapperBase.3 Manifying blib/lib/Bio/SeqFeature/Tools/TypeMapper.pm -> blib/libdoc/Bio::SeqFeature::Tools::TypeMapper.3 Manifying blib/lib/Bio/Biblio/MedlineJournal.pm -> blib/libdoc/Bio::Biblio::MedlineJournal.3 Manifying blib/lib/Bio/SeqIO/kegg.pm -> blib/libdoc/Bio::SeqIO::kegg.3 Manifying blib/lib/Bio/Matrix/PSM/ProtMatrix.pm -> blib/libdoc/Bio::Matrix::PSM::ProtMatrix.3 Manifying blib/lib/Bio/AlignIO/fasta.pm -> blib/libdoc/Bio::AlignIO::fasta.3 Manifying blib/lib/Bio/Matrix/PSM/PsmHeader.pm -> blib/libdoc/Bio::Matrix::PSM::PsmHeader.3 Manifying blib/lib/Bio/SeqFeature/Tools/Unflattener.pm -> blib/libdoc/Bio::SeqFeature::Tools::Unflattener.3 Manifying blib/lib/Bio/Location/WidestCoordPolicy.pm -> blib/libdoc/Bio::Location::WidestCoordPolicy.3 Manifying blib/lib/Bio/Search/Result/GenericResult.pm -> blib/libdoc/Bio::Search::Result::GenericResult.3 Manifying blib/lib/Bio/Map/PositionHandler.pm -> blib/libdoc/Bio::Map::PositionHandler.3 Manifying blib/lib/Bio/Tools/GFF.pm -> blib/libdoc/Bio::Tools::GFF.3 Manifying blib/lib/Bio/Ontology/Ontology.pm -> blib/libdoc/Bio::Ontology::Ontology.3 Manifying blib/lib/Bio/Biblio/PubmedArticle.pm -> blib/libdoc/Bio::Biblio::PubmedArticle.3 Manifying blib/lib/Bio/SearchIO/Writer/TextResultWriter.pm -> blib/libdoc/Bio::SearchIO::Writer::TextResultWriter.3 Manifying blib/lib/Bio/Seq/LargeSeqI.pm -> blib/libdoc/Bio::Seq::LargeSeqI.3 Manifying blib/lib/Bio/AlignIO/nexus.pm -> blib/libdoc/Bio::AlignIO::nexus.3 Manifying blib/lib/Bio/SearchIO/EventHandlerI.pm -> blib/libdoc/Bio::SearchIO::EventHandlerI.3 Manifying blib/lib/Bio/Tools/Seg.pm -> blib/libdoc/Bio::Tools::Seg.3 Manifying blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm -> blib/libdoc/Bio::DB::GFF::Adaptor::dbi::mysqlace.3 Manifying blib/lib/Bio/DB/BioFetch.pm -> blib/libdoc/Bio::DB::BioFetch.3 Manifying blib/lib/Bio/Assembly/IO/phrap.pm -> blib/libdoc/Bio::Assembly::IO::phrap.3 Manifying blib/lib/Bio/Taxon.pm -> blib/libdoc/Bio::Taxon.3 Manifying blib/lib/Bio/Tools/RNAMotif.pm -> blib/libdoc/Bio::Tools::RNAMotif.3 Manifying blib/lib/Bio/Ontology/RelationshipI.pm -> blib/libdoc/Bio::Ontology::RelationshipI.3 Manifying blib/lib/Bio/Factory/AnalysisI.pm -> blib/libdoc/Bio::Factory::AnalysisI.3 Manifying blib/lib/Bio/PopGen/Genotype.pm -> blib/libdoc/Bio::PopGen::Genotype.3 Manifying blib/lib/Bio/Map/OrderedPositionWithDistance.pm -> blib/libdoc/Bio::Map::OrderedPositionWithDistance.3 Manifying blib/lib/Bio/Coordinate/Utils.pm -> blib/libdoc/Bio::Coordinate::Utils.3 Manifying blib/lib/Bio/Tools/EUtilities/History.pm -> blib/libdoc/Bio::Tools::EUtilities::History.3 Manifying blib/lib/Bio/PopGen/Statistics.pm -> blib/libdoc/Bio::PopGen::Statistics.3 Manifying blib/lib/Bio/DB/EntrezGene.pm -> blib/libdoc/Bio::DB::EntrezGene.3 Manifying blib/lib/Bio/AnnotationI.pm -> blib/libdoc/Bio::AnnotationI.3 Manifying blib/lib/Bio/Ontology/Relationship.pm -> blib/libdoc/Bio::Ontology::Relationship.3 Manifying blib/lib/Bio/Tools/Analysis/Protein/HNN.pm -> blib/libdoc/Bio::Tools::Analysis::Protein::HNN.3 Manifying blib/lib/Bio/Seq/SeqBuilder.pm -> blib/libdoc/Bio::Seq::SeqBuilder.3 Manifying blib/lib/Bio/Tools/SeqWords.pm -> blib/libdoc/Bio::Tools::SeqWords.3 Manifying blib/lib/Bio/SeqIO/raw.pm -> blib/libdoc/Bio::SeqIO::raw.3 Manifying blib/lib/Bio/SeqFeature/TypedSeqFeatureI.pm -> blib/libdoc/Bio::SeqFeature::TypedSeqFeatureI.3 Manifying blib/lib/Bio/Search/Iteration/IterationI.pm -> blib/libdoc/Bio::Search::Iteration::IterationI.3 Manifying blib/lib/Bio/Search/Result/ResultFactory.pm -> blib/libdoc/Bio::Search::Result::ResultFactory.3 Manifying blib/lib/Bio/LiveSeq/Chain.pm -> blib/libdoc/Bio::LiveSeq::Chain.3 Manifying blib/lib/Bio/PopGen/HtSNP.pm -> blib/libdoc/Bio::PopGen::HtSNP.3 Manifying blib/lib/Bio/LiveSeq/Mutation.pm -> blib/libdoc/Bio::LiveSeq::Mutation.3 Manifying blib/lib/Bio/Map/SimpleMap.pm -> blib/libdoc/Bio::Map::SimpleMap.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/GFF2Loader.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::GFF2Loader.3 Manifying blib/lib/Bio/DB/SeqFeature/Store/DBI/Pg.pm -> blib/libdoc/Bio::DB::SeqFeature::Store::DBI::Pg.3 Manifying blib/lib/Bio/Search/Hit/ModelHit.pm -> blib/libdoc/Bio::Search::Hit::ModelHit.3 Manifying blib/lib/Bio/Tools/HMMER/Domain.pm -> blib/libdoc/Bio::Tools::HMMER::Domain.3 Manifying blib/lib/Bio/Matrix/PSM/InstanceSiteI.pm -> blib/libdoc/Bio::Matrix::PSM::InstanceSiteI.3 Manifying blib/lib/Bio/Structure/SecStr/STRIDE/Res.pm -> blib/libdoc/Bio::Structure::SecStr::STRIDE::Res.3 Manifying blib/lib/Bio/Map/Physical.pm -> blib/libdoc/Bio::Map::Physical.3 Manifying blib/lib/Bio/DB/InMemoryCache.pm -> blib/libdoc/Bio::DB::InMemoryCache.3 Manifying blib/lib/Bio/Perl.pm -> blib/libdoc/Bio::Perl.3 Manifying blib/lib/Bio/SeqIO/game/gameWriter.pm -> blib/libdoc/Bio::SeqIO::game::gameWriter.3 Manifying blib/lib/Bio/SeqIO/abi.pm -> blib/libdoc/Bio::SeqIO::abi.3 Manifying blib/lib/Bio/LiveSeq/AARange.pm -> blib/libdoc/Bio::LiveSeq::AARange.3 Manifying blib/lib/Bio/PrimarySeq.pm -> blib/libdoc/Bio::PrimarySeq.3 Manifying blib/lib/Bio/DB/Flat/BDB/fasta.pm -> blib/libdoc/Bio::DB::Flat::BDB::fasta.3 Manifying blib/lib/Bio/Tools/Run/GenericParameters.pm -> blib/libdoc/Bio::Tools::Run::GenericParameters.3 Manifying blib/lib/Bio/SeqIO/lasergene.pm -> blib/libdoc/Bio::SeqIO::lasergene.3 Manifying blib/lib/Bio/PopGen/IO/prettybase.pm -> blib/libdoc/Bio::PopGen::IO::prettybase.3 Manifying blib/lib/Bio/Assembly/IO/ace.pm -> blib/libdoc/Bio::Assembly::IO::ace.3 Manifying blib/lib/Bio/Symbol/SymbolI.pm -> blib/libdoc/Bio::Symbol::SymbolI.3 Manifying blib/lib/Bio/SimpleAnalysisI.pm -> blib/libdoc/Bio::SimpleAnalysisI.3 Manifying blib/lib/Bio/Matrix/PSM/IO/transfac.pm -> blib/libdoc/Bio::Matrix::PSM::IO::transfac.3 Manifying blib/lib/Bio/LiveSeq/IO/BioPerl.pm -> blib/libdoc/Bio::LiveSeq::IO::BioPerl.3 Manifying blib/lib/Bio/Annotation/OntologyTerm.pm -> blib/libdoc/Bio::Annotation::OntologyTerm.3 Manifying blib/lib/Bio/Tools/Run/RemoteBlast.pm -> blib/libdoc/Bio::Tools::Run::RemoteBlast.3 Manifying blib/lib/Bio/Phenotype/MeSH/Term.pm -> blib/libdoc/Bio::Phenotype::MeSH::Term.3 Manifying blib/lib/Bio/Tools/Pseudowise.pm -> blib/libdoc/Bio::Tools::Pseudowise.3 Manifying blib/lib/Bio/DB/HIV.pm -> blib/libdoc/Bio::DB::HIV.3 Manifying blib/lib/Bio/SeqFeature/AnnotationAdaptor.pm -> blib/libdoc/Bio::SeqFeature::AnnotationAdaptor.3 Manifying blib/lib/Bio/Matrix/IO.pm -> blib/libdoc/Bio::Matrix::IO.3 Manifying blib/lib/Bio/Map/Gene.pm -> blib/libdoc/Bio::Map::Gene.3 Manifying blib/lib/Bio/Map/Prediction.pm -> blib/libdoc/Bio::Map::Prediction.3 Manifying blib/lib/Bio/Biblio/Person.pm -> blib/libdoc/Bio::Biblio::Person.3 Manifying blib/lib/Bio/Search/BlastStatistics.pm -> blib/libdoc/Bio::Search::BlastStatistics.3 Manifying blib/lib/Bio/PopGen/MarkerI.pm -> blib/libdoc/Bio::PopGen::MarkerI.3 Manifying blib/lib/Bio/Tools/Grail.pm -> blib/libdoc/Bio::Tools::Grail.3 Manifying blib/lib/Bio/Search/HSP/ModelHSP.pm -> blib/libdoc/Bio::Search::HSP::ModelHSP.3 Manifying blib/lib/Bio/DB/WebDBSeqI.pm Build: blib/script/bp_bulk_load_gff.pl: cannot resolve L in paragraph 26. 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blib/libhtml/site/lib/Bio/LiveSeq/Intron.html HTMLifying blib/lib/Bio/Matrix/IO/scoring.pm -> blib/libhtml/site/lib/Bio/Matrix/IO/scoring.html HTMLifying blib/lib/Bio/Seq/LargeLocatableSeq.pm -> blib/libhtml/site/lib/Bio/Seq/LargeLocatableSeq.html HTMLifying blib/lib/Bio/AlignIO/msf.pm -> blib/libhtml/site/lib/Bio/AlignIO/msf.html HTMLifying blib/lib/Bio/Tools/Glimmer.pm -> blib/libhtml/site/lib/Bio/Tools/Glimmer.html HTMLifying blib/lib/Bio/SeqIO/flybase_chadoxml.pm -> blib/libhtml/site/lib/Bio/SeqIO/flybase_chadoxml.html HTMLifying blib/lib/Bio/Map/RelativeI.pm -> blib/libhtml/site/lib/Bio/Map/RelativeI.html HTMLifying blib/lib/Bio/Tools/Profile.pm -> blib/libhtml/site/lib/Bio/Tools/Profile.html HTMLifying blib/lib/Bio/LiveSeq/Mutator.pm -> blib/libhtml/site/lib/Bio/LiveSeq/Mutator.html HTMLifying blib/lib/Bio/Tools/Primer/Pair.pm -> blib/libhtml/site/lib/Bio/Tools/Primer/Pair.html HTMLifying blib/lib/Bio/Annotation/TypeManager.pm -> 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blib/libhtml/site/lib/Bio/Factory/ApplicationFactoryI.html HTMLifying blib/lib/Bio/SeqIO/scf.pm -> blib/libhtml/site/lib/Bio/SeqIO/scf.html HTMLifying blib/lib/Bio/Tools/EUtilities/Info.pm -> blib/libhtml/site/lib/Bio/Tools/EUtilities/Info.html HTMLifying blib/lib/Bio/PopGen/PopStats.pm -> blib/libhtml/site/lib/Bio/PopGen/PopStats.html HTMLifying blib/lib/Bio/SeqEvolution/Factory.pm -> blib/libhtml/site/lib/Bio/SeqEvolution/Factory.html HTMLifying blib/lib/Bio/DB/Query/GenBank.pm -> blib/libhtml/site/lib/Bio/DB/Query/GenBank.html HTMLifying blib/lib/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm -> blib/libhtml/site/lib/Bio/DB/SeqFeature/Store/FeatureFileLoader.html HTMLifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_unigene.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Aggregator/ucsc_unigene.html HTMLifying blib/lib/Bio/DB/SeqFeature/Store/DBI/SQLite.pm -> blib/libhtml/site/lib/Bio/DB/SeqFeature/Store/DBI/SQLite.html HTMLifying blib/lib/Bio/Tools/Analysis/Protein/Domcut.pm -> 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blib/libhtml/site/lib/Bio/IdentifiableI.html HTMLifying blib/lib/Bio/Map/Mappable.pm -> blib/libhtml/site/lib/Bio/Map/Mappable.html HTMLifying blib/lib/Bio/Search/Tiling/MapTiling.pm -> blib/libhtml/site/lib/Bio/Search/Tiling/MapTiling.html HTMLifying blib/lib/Bio/Matrix/PSM/ProtPsm.pm -> blib/libhtml/site/lib/Bio/Matrix/PSM/ProtPsm.html HTMLifying blib/lib/Bio/Taxonomy/Taxon.pm -> blib/libhtml/site/lib/Bio/Taxonomy/Taxon.html HTMLifying blib/lib/Bio/DB/SeqFeature/NormalizedFeature.pm -> blib/libhtml/site/lib/Bio/DB/SeqFBuild: blib/lib/Bio/DB/SeqFeature/NormalizedFeature.pm: cannot resolve L in paragraph 160. 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Build: blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm: cannot resolve L in paragraph 8. eneStructureI.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Gene/GeneStructureI.html HTMLifying blib/lib/Bio/Biblio/MedlineBook.pm -> blib/libhtml/site/lib/Bio/Biblio/MedlineBook.html HTMLifying blib/lib/Bio/Biblio/Proceeding.pm -> blib/libhtml/site/lib/Bio/Biblio/Proceeding.html HTMLifying blib/lib/Bio/Index/Fastq.pm -> blib/libhtml/site/lib/Bio/Index/Fastq.html HTMLifying blib/lib/Bio/SeqUtils.pm -> blib/libhtml/site/lib/Bio/SeqUtils.html HTMLifying blib/lib/Bio/DB/Failover.pm -> blib/libhtml/site/lib/Bio/DB/Failover.html HTMLifying blib/lib/Bio/SeqIO/asciitree.pm -> blib/libhtml/site/lib/Bio/SeqIO/asciitree.html HTMLifying blib/lib/Bio/Matrix/PSM/SiteMatrixI.pm -> blib/libhtml/site/lib/Bio/Matrix/PSM/SiteMatrixI.html HTMLifying blib/lib/Bio/Tools/Gel.pm -> blib/libhtml/site/lib/Bio/Tools/Gel.html HTMLifying blib/lib/Bio/DB/Registry.pm -> blib/libhtml/site/lib/Bio/DB/Registry.html HTMLifying blib/lib/Bio/SeqIO/game/featHandler.pm -> blib/libhtml/site/lib/Bio/SeqIO/game/featHandler.html HTMLifying blib/lib/Bio/Search/HSP/BlastHSP.pm -> blib/libhtml/site/lib/Bio/Search/HSP/BlastHSP.html HTMLifying blib/lib/Bio/Factory/SequenceFactoryI.pm -> blib/libhtml/site/lib/Bio/Factory/SequenceFactoryI.html HTMLifying blib/lib/Bio/Biblio/TechReport.pm -> blib/libhtml/site/lib/Bio/Biblio/TechReport.html HTMLifying blib/lib/Bio/Tools/Blat.pm -> blib/libhtml/site/lib/Bio/Tools/Blat.html HTMLifying blib/lib/Bio/Tools/Protparam.pm -> blib/libhtml/site/lib/Bio/Tools/Protparam.html HTMLifying blib/lib/Bio/PhyloNetwork.pm -> blib/libhtml/site/lib/Bio/PhyloNetwork.html HTMLifying blib/lib/Bio/SeqIO/metafasta.pm -> blib/libhtml/site/lib/Bio/SeqIO/metafasta.html HTMLifying blib/lib/Bio/Expression/Sample.pm -> blib/libhtml/site/lib/Bio/Expression/Sample.html HTMLifying blib/lib/Bio/Map/CytoMarker.pm -> blib/libhtml/site/lib/Bio/Map/CytoMarker.html HTMLifying blib/lib/Bio/Tools/TargetP.pm -> blib/libhtml/site/lib/Bio/Tools/TargetP.html HTMLifying blib/lib/Bio/DB/NCBIHelper.pm -> blib/libhtml/site/lib/Bio/DB/NCBIHelper.html HTMLifying blib/lib/Bio/SeqIO/table.pm -> blib/libhtml/site/lib/Bio/SeqIO/table.html HTMLifying blib/lib/Bio/Root/Root.pm -> blib/libhtml/site/lib/Bio/Root/Root.html HTMLifying blib/lib/Bio/Tools/Spidey/Exon.pm -> blib/libhtml/site/lib/Bio/Tools/Spidey/Exon.html HTMLifying blib/lib/Bio/Tools/EUtilities/EUtilDataI.pm -> blib/libhtml/site/lib/Bio/Tools/EUtilities/EUtilDataI.html HTMLifying blib/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm -> blib/libhtml/site/lib/Bio/AlignIO/Handler/GenericAlignHandler.html HTMLifying blib/lib/Bio/Event/EventGeneratorI.pm -> blib/libhtml/site/lib/Bio/Event/EventGeneratorI.html HTMLifying blib/lib/Bio/SearchIO/exonerate.pm -> blib/libhtml/site/lib/Bio/SearchIO/exonerate.html HTMLifying blib/lib/Bio/DB/GFF/Adaptor/ace.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Adaptor/ace.html HTMLifying blib/lib/Bio/DB/QueryI.pm -> blib/libhtml/site/lib/Bio/DB/QueryI.html HTMLifying blib/lib/Bio/Factory/SeqAnalysisParserFactory.pm -> blib/libhtml/site/lib/Bio/Factory/SeqAnalysisParserFactory.html HTMLifying blib/lib/Bio/AlignIO/maf.pm -> blib/libhtml/site/lib/Bio/AlignIO/maf.html HTMLifying blib/lib/Bio/Tools/Run/StandAloneNCBIBlast.pm -> blib/libhtml/site/lib/Bio/Tools/Run/StandAloneNCBIBlast.html HTMLifying blib/lib/Bio/Tools/Analysis/Protein/Sopma.pm -> blib/libhtml/site/lib/Bio/Tools/Analysis/Protein/Sopma.html HTMLifying blib/lib/Bio/Search/Hit/BlastHit.pm -> blib/libhtml/site/lib/Bio/Search/Hit/BlastHit.html HTMLifying blib/lib/Bio/DB/SeqHound.pm -> blib/libhtml/site/lib/Bio/DB/SeqHound.html HTMLifying blib/lib/Bio/SeqIO/game/gameHandler.pm -> blib/libhtml/site/lib/Bio/SeqIO/game/gameHandler.html HTMLifying blib/lib/Bio/SeqFeature/Generic.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Generic.html HTMLifying blib/lib/Bio/Search/SearchUtils.pm -> blib/libhtml/site/lib/Bio/Search/SearchUtils.html HTMLifying blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Adaptor/dbi/mysqlopt.html HTMLifying blib/lib/Bio/Factory/ObjectBuilderI.pm -> blib/libhtml/site/lib/Bio/Factory/ObjectBuilderI.html HBuild: blib/lib/Bio/DB/GFF/Typename.pm: cannot resolve L in paragraph 49. 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Build: blib/lib/Bio/SeqIO/swiss.pm: cannot resolve L in paragraph 44. Build: blib/lib/Bio/ClusterIO.pm: cannot resolve L in paragraph 29. Build: blib/lib/Bio/DB/SeqFeature/Store/berkeleydb3.pm: cannot resolve L in paragraph 15. ib/Bio/Das/FeatureTypeI.pm -> blib/libhtml/site/lib/Bio/Das/FeatureTypeI.html HTMLifying blib/lib/Bio/PhyloNetwork/FactoryX.pm -> blib/libhtml/site/lib/Bio/PhyloNetwork/FactoryX.html HTMLifying blib/lib/Bio/Search/HSP/HSPFactory.pm -> blib/libhtml/site/lib/Bio/Search/HSP/HSPFactory.html HTMLifying blib/lib/Bio/SeqIO/gbdriver.pm -> blib/libhtml/site/lib/Bio/SeqIO/gbdriver.html HTMLifying blib/lib/Bio/Symbol/Symbol.pm -> blib/libhtml/site/lib/Bio/Symbol/Symbol.html HTMLifying blib/lib/Bio/Tools/Prediction/Exon.pm -> blib/libhtml/site/lib/Bio/Tools/Prediction/Exon.html HTMLifying blib/lib/Bio/DB/BiblioI.pm -> blib/libhtml/site/lib/Bio/DB/BiblioI.html HTMLifying blib/lib/Bio/Tools/Analysis/Protein/GOR4.pm -> blib/libhtml/site/lib/Bio/Tools/Analysis/Protein/GOR4.html HTMLifying blib/lib/Bio/Map/Marker.pm -> blib/libhtml/site/lib/Bio/Map/Marker.html HTMLifying blib/lib/Bio/Root/Version.pm -> blib/libhtml/site/lib/Bio/Root/Version.html HTMLifying blib/lib/Bio/SeqIO.pm -> blib/libhtml/site/lib/Bio/SeqIO.html HTMLifying blib/lib/Bio/Location/FuzzyLocationI.pm -> blib/libhtml/site/lib/Bio/Location/FuzzyLocationI.html HTMLifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_genscan.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Aggregator/ucsc_genscan.html HTMLifying blib/lib/Bio/PopGen/IO/phase.pm -> blib/libhtml/site/lib/Bio/PopGen/IO/phase.html HTMLifying blib/lib/Bio/Align/DNAStatistics.pm -> blib/libhtml/site/lib/Bio/Align/DNAStatistics.html HTMLifying blib/lib/Bio/Biblio/PubmedJournalArticle.pm -> blib/libhtml/site/lib/Bio/Biblio/PubmedJournalArticle.html HTMLifying blib/lib/Bio/Tools/EUtilities/Summary.pm -> blib/libhtml/site/lib/Bio/Tools/EUtilities/Summary.html HTMLifying blib/lib/Bio/Tools/Eponine.pm -> blib/libhtml/site/lib/Bio/Tools/Eponine.html HTMLifying blib/lib/Bio/Variation/Allele.pm -> blib/libhtml/site/lib/Bio/Variation/Allele.html HTMLifying blib/lib/Bio/Phenotype/Phenotype.pm -> blib/libhtml/site/lib/Bio/Phenotype/Phenotype.html HTMLifying blib/lib/Bio/Factory/SeqAnalysisParserFactoryI.pm -> blib/libhtml/site/lib/Bio/Factory/SeqAnalysisParserFactoryI.html HTMLifying blib/lib/Bio/SeqIO/swiss.pm -> blib/libhtml/site/lib/Bio/SeqIO/swiss.html HTMLifying blib/lib/Bio/DB/ReferenceI.pm -> blib/libhtml/site/lib/Bio/DB/ReferenceI.html HTMLifying blib/lib/Bio/ClusterIO.pm -> blib/libhtml/site/lib/Bio/ClusterIO.html HTMLifying blib/lib/Bio/DB/Taxonomy/entrez.pm -> blib/libhtml/site/lib/Bio/DB/Taxonomy/entrez.html HTMLifying blib/lib/Bio/Map/GenePosition.pm -> blib/libhtml/site/lib/Bio/Map/GenePosition.html HTMLifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22.html HTMLifying blib/lib/Bio/Map/FPCMarker.pm -> blib/libhtml/site/lib/Bio/Map/FPCMarker.html HTMLifying blib/lib/Bio/AlignIO/mase.pm -> blib/libhtml/site/lib/Bio/AlignIO/mase.html HTMLifying blib/lib/Bio/OntologyIO/soflat.pm -> blib/libhtml/site/lib/Bio/OntologyIO/soflat.html HTMLifying blib/lib/Bio/MapIO/fpc.pm -> blib/libhtml/site/lib/Bio/MapIO/fpc.html HTMLifying blib/lib/Bio/Coordinate/Result/Match.pm -> blib/libhtml/site/lib/Bio/Coordinate/Result/Match.html HTMLifying blib/lib/Bio/Search/Hit/PsiBlastHit.pm -> blib/libhtml/site/lib/Bio/Search/Hit/PsiBlastHit.html HTMLifying blib/lib/Bio/Restriction/IO/bairoch.pm -> blib/libhtml/site/lib/Bio/Restriction/IO/bairoch.html HTMLifying blib/lib/Bio/PopGen/IO/csv.pm -> blib/libhtml/site/lib/Bio/PopGen/IO/csv.html HTMLifying blib/lib/Bio/Biblio/IO/medlinexml.pm -> blib/libhtml/site/lib/Bio/Biblio/IO/medlinexml.html HTMLifying blib/lib/Bio/Search/Result/WABAResult.pm -> blib/libhtml/site/lib/Bio/Search/Result/WABAResult.html HTMLifying blib/lib/Bio/DB/GFF/Aggregator/none.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Aggregator/none.html HTMLifying blib/lib/Bio/DB/SeqFeature/Store/berkeleydb3.pm -> blib/libhtml/site/lib/Bio/DB/SeqFeature/Store/berkeleydb3.html HTMLifying blib/lib/Bio/Search/Result/HmmpfamResult.pm -> blib/libhtml/site/lib/Bio/Search/Result/HmmpfamResult.html HTMLifying blib/lib/Bio/DB/GenBank.pm -> blib/libhtml/site/lib/Bio/DB/GenBank.html HTMLifying blib/lib/Bio/AlBuild: blib/lib/Bio/DB/GFF/RelSegment.pm: cannot resolve L in paragraph 251. 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Build: blib/lib/Bio/DB/GFF/Adaptor/dbi/pg_fts.pm: cannot resolve L in paragraph 45. Build: blib/lib/Bio/DB/SeqFeature/Store/memory.pm: cannot resolve L in paragraph 121. 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Build: blib/lib/Bio/DB/SeqFeature/Store/Loader.pm: cannot resolve L in paragraph 178. Build: blib/lib/Bio/DB/GFF/Featname.pm: cannot resolve L in paragraph 44. Build: blib/lib/Bio/DB/GFF/Adaptor/dbi/oracleace.pm: cannot resolve L in paragraph 8. atabaseI.html HTMLifying blib/lib/Bio/Tools/Phylo/Gumby.pm -> blib/libhtml/site/lib/Bio/Tools/Phylo/Gumby.html HTMLifying blib/lib/Bio/DasI.pm -> blib/libhtml/site/lib/Bio/DasI.html HTMLifying blib/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm -> blib/libhtml/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.html HTMLifying blib/lib/Bio/SeqIO/tigr.pm -> blib/libhtml/site/lib/Bio/SeqIO/tigr.html HTMLifying blib/lib/Bio/Index/GenBank.pm -> blib/libhtml/site/lib/Bio/Index/GenBank.html HTMLifying blib/lib/Bio/FeatureIO/ptt.pm -> blib/libhtml/site/lib/Bio/FeatureIO/ptt.html HTMLifying blib/lib/Bio/PhyloNetwork/RandomFactory.pm -> blib/libhtml/site/lib/Bio/PhyloNetwork/RandomFactory.html HTMLifying blib/lib/Bio/DB/Biblio/soap.pm -> blib/libhtml/site/lib/Bio/DB/Biblio/soap.html HTMLifying blib/lib/Bio/SearchIO/hmmer.pm -> blib/libhtml/site/lib/Bio/SearchIO/hmmer.html HTMLifying blib/lib/Bio/DB/SeqFeature/Store/Loader.pm -> blib/libhtml/site/lib/Bio/DB/SeqFeature/Store/Loader.html HTMLifying blib/lib/Bio/Tools/tRNAscanSE.pm -> blib/libhtml/site/lib/Bio/Tools/tRNAscanSE.html HTMLifying blib/lib/Bio/Assembly/IO/tigr.pm -> blib/libhtml/site/lib/Bio/Assembly/IO/tigr.html HTMLifying blib/lib/Bio/Biblio/JournalArticle.pm -> blib/libhtml/site/lib/Bio/Biblio/JournalArticle.html HTMLifying blib/lib/Bio/Tools/Sim4/Results.pm -> blib/libhtml/site/lib/Bio/Tools/Sim4/Results.html HTMLifying blib/lib/Bio/Index/Hmmer.pm -> blib/libhtml/site/lib/Bio/Index/Hmmer.html HTMLifying blib/lib/Bio/MapIO/mapmaker.pm -> blib/libhtml/site/lib/Bio/MapIO/mapmaker.html HTMLifying blib/lib/Bio/DB/GFF/Adaptor/biofetch.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Adaptor/biofetch.html HTMLifying blib/lib/Bio/Tools/Prediction/Gene.pm -> blib/libhtml/site/lib/Bio/Tools/Prediction/Gene.html HTMLifying blib/lib/Bio/Root/Test/Warn.pm -> blib/libhtml/site/lib/Bio/Root/Test/Warn.html HTMLifying blib/lib/Bio/AlignIO/meme.pm -> blib/libhtml/site/lib/Bio/AlignIO/meme.html HTMLifying blib/lib/Bio/Tools/SeqPattern.pm -> blib/libhtml/site/lib/Bio/Tools/SeqPattern.html HTMLifying blib/lib/Bio/Seq/RichSeq.pm -> blib/libhtml/site/lib/Bio/Seq/RichSeq.html HTMLifying blib/lib/Bio/Tools/EUtilities/Summary/ItemContainerI.pm -> blib/libhtml/site/lib/Bio/Tools/EUtilities/Summary/ItemContainerI.html HTMLifying blib/lib/Bio/Search/HSP/HMMERHSP.pm -> blib/libhtml/site/lib/Bio/Search/HSP/HMMERHSP.html HTMLifying blib/lib/Bio/SeqIO/ctf.pm -> blib/libhtml/site/lib/Bio/SeqIO/ctf.html HTMLifying blib/lib/Bio/DB/Taxonomy/list.pm -> blib/libhtml/site/lib/Bio/DB/Taxonomy/list.html HTMLifying blib/lib/Bio/Location/NarrowestCoordPolicy.pm -> blib/libhtml/site/lib/Bio/Location/NarrowestCoordPolicy.html HTMLifying blib/lib/Bio/Tools/Sigcleave.pm -> blib/libhtml/site/lib/Bio/Tools/Sigcleave.html HTMLifying blib/lib/Bio/DB/Taxonomy.pm -> blib/libhtml/site/lib/Bio/DB/Taxonomy.html HTMLifying blib/lib/Bio/Assembly/Tools/ContigSpectrum.pm -> blib/libhtml/site/lib/Bio/Assembly/Tools/ContigSpectrum.html HTMLifying blib/lib/Bio/Ontology/GOterm.pm -> blib/libhtml/site/lib/Bio/Ontology/GOterm.html HTMLifying blib/lib/Bio/DB/Flat/BDB/embl.pm -> blib/libhtml/site/lib/Bio/DB/Flat/BDB/embl.html HTMLifying blib/lib/Bio/Tools/MZEF.pm -> blib/libhtml/site/lib/Bio/Tools/MZEF.html HTMLifying blib/lib/Bio/Phenotype/MeSH/Twig.pm -> blib/libhtml/site/lib/Bio/Phenotype/MeSH/Twig.html HTMLifying blib/lib/Bio/Tools/Primer/Feature.pm -> blib/libhtml/site/lib/Bio/Tools/Primer/Feature.html HTMLifying blib/lib/Bio/DB/GFF/Featname.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Featname.html HTMLifying blib/lib/Bio/LiveSeq/SeqI.pm -> blib/libhtml/site/lib/Bio/LiveSeq/SeqI.html HTMLifying blib/lib/Bio/DB/GFF/Adaptor/dbi/oracleace.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Adaptor/dbi/oracleace.html HTMLifying blib/lib/Bio/SeqFeature/FeaturePair.pm -> blib/libhtml/site/lib/Bio/SeqFeature/FeaturePair.html HTMLifying blib/lib/Bio/LiveSeq/Repeat_Unit.pm -> blib/libhtml/site/lib/Bio/LiveSeq/Repeat_Unit.html HTMLifying blib/lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm -> blib/libhtml/site/lib/Bio/SeqIO/Handler/GenericRichSeqHandler.html HTMLifying blib/lib/BioBuild: blib/lib/Bio/DB/SeqFeature/Segment.pm: cannot resolve L in paragraph 122. 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Build: blib/lib/Bio/DB/GFF/Homol.pm: cannot resolve L in paragraph 28. /OntologyIO.pm -> blib/libhtml/site/lib/Bio/OntologyIO.html HTMLifying blib/lib/Bio/Variation/SNP.pm -> blib/libhtml/site/lib/Bio/Variation/SNP.html HTMLifying blib/lib/Bio/PhyloNetwork/TreeFactory.pm -> blib/libhtml/site/lib/Bio/PhyloNetwork/TreeFactory.html HTMLifying blib/lib/Bio/Tools/pICalculator.pm -> blib/libhtml/site/lib/Bio/Tools/pICalculator.html HTMLifying blib/lib/Bio/DB/GenPept.pm -> blib/libhtml/site/lib/Bio/DB/GenPept.html HTMLifying blib/lib/Bio/Matrix/PSM/SiteMatrix.pm -> blib/libhtml/site/lib/Bio/Matrix/PSM/SiteMatrix.html HTMLifying blib/lib/Bio/DB/GFF.pm -> blib/libhtml/site/lib/Bio/DB/GFF.html HTMLifying blib/lib/Bio/Ontology/RelationshipFactory.pm -> blib/libhtml/site/lib/Bio/Ontology/RelationshipFactory.html HTMLifying blib/lib/Bio/Biblio/WebResource.pm -> blib/libhtml/site/lib/Bio/Biblio/WebResource.html HTMLifying blib/lib/Bio/ParameterBaseI.pm -> blib/libhtml/site/lib/Bio/ParameterBaseI.html HTMLifying blib/lib/Bio/Search/Hit/HitFactory.pm -> blib/libhtml/site/lib/Bio/Search/Hit/HitFactory.html HTMLifying blib/lib/Bio/DB/SeqFeature/Segment.pm -> blib/libhtml/site/lib/Bio/DB/SeqFeature/Segment.html HTMLifying blib/lib/Bio/Index/Fasta.pm -> blib/libhtml/site/lib/Bio/Index/Fasta.html HTMLifying blib/lib/Bio/FeatureIO/bed.pm -> blib/libhtml/site/lib/Bio/FeatureIO/bed.html HTMLifying blib/lib/Bio/ConfigData.pm -> blib/libhtml/site/lib/Bio/ConfigData.html HTMLifying blib/lib/Bio/Ontology/InterProTerm.pm -> blib/libhtml/site/lib/Bio/Ontology/InterProTerm.html HTMLifying blib/lib/Bio/PopGen/Simulation/GeneticDrift.pm -> blib/libhtml/site/lib/Bio/PopGen/Simulation/GeneticDrift.html HTMLifying blib/lib/Bio/AlignIO/metafasta.pm -> blib/libhtml/site/lib/Bio/AlignIO/metafasta.html HTMLifying blib/lib/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Adaptor/dbi/caching_handle.html HTMLifying blib/lib/Bio/Restriction/Enzyme.pm -> blib/libhtml/site/lib/Bio/Restriction/Enzyme.html HTMLifying blib/lib/Bio/Tools/QRNA.pm -> blib/libhtml/site/lib/Bio/Tools/QRNA.html HTMLifying blib/lib/Bio/Tools/Phylo/PAML/Result.pm -> blib/libhtml/site/lib/Bio/Tools/Phylo/PAML/Result.html HTMLifying blib/lib/Bio/Location/AvWithinCoordPolicy.pm -> blib/libhtml/site/lib/Bio/Location/AvWithinCoordPolicy.html HTMLifying blib/lib/Bio/Symbol/AlphabetI.pm -> blib/libhtml/site/lib/Bio/Symbol/AlphabetI.html HTMLifying blib/lib/Bio/Tools/Genscan.pm -> blib/libhtml/site/lib/Bio/Tools/Genscan.html HTMLifying blib/lib/Bio/Annotation/Relation.pm -> blib/libhtml/site/lib/Bio/Annotation/Relation.html HTMLifying blib/lib/Bio/Tree/Draw/Cladogram.pm -> blib/libhtml/site/lib/Bio/Tree/Draw/Cladogram.html HTMLifying blib/lib/Bio/Biblio/IO/pubmedxml.pm -> blib/libhtml/site/lib/Bio/Biblio/IO/pubmedxml.html HTMLifying blib/lib/Bio/DB/GFF/Homol.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Homol.html HTMLifying blib/lib/Bio/SearchIO/FastHitEventBuilder.pm -> blib/libhtml/site/lib/Bio/SearchIO/FastHitEventBuilder.html HTMLifying blib/lib/Bio/SeqFeature/SiRNA/Pair.pm -> blib/libhtml/site/lib/Bio/SeqFeature/SiRNA/Pair.html HTMLifying blib/lib/Bio/Factory/MapFactoryI.pm -> blib/libhtml/site/lib/Bio/Factory/MapFactoryI.html HTMLifying blib/lib/Bio/SeqEvolution/EvolutionI.pm -> blib/libhtml/site/lib/Bio/SeqEvolution/EvolutionI.html HTMLifying blib/lib/Bio/Tools/OddCodes.pm -> blib/libhtml/site/lib/Bio/Tools/OddCodes.html HTMLifying blib/lib/Bio/SearchIO/psl.pm -> blib/libhtml/site/lib/Bio/SearchIO/psl.html HTMLifying blib/lib/Bio/Map/TranscriptionFactor.pm -> blib/libhtml/site/lib/Bio/Map/TranscriptionFactor.html HTMLifying blib/lib/Bio/RangeI.pm -> blib/libhtml/site/lib/Bio/RangeI.html HTMLifying blib/lib/Bio/SeqAnalysisParserI.pm -> blib/libhtml/site/lib/Bio/SeqAnalysisParserI.html HTMLifying blib/lib/Bio/Map/Clone.pm -> blib/libhtml/site/lib/Bio/Map/Clone.html HTMLifying blib/lib/Bio/SeqIO/chaos.pm -> blib/libhtml/site/lib/Bio/SeqIO/chaos.html HTMLifying blib/lib/Bio/Restriction/IO.pm -> blib/libhtml/site/lib/Bio/Restriction/IO.html HTMLifying blib/lib/Bio/DB/TFBS.pm -> blib/libhtml/site/lib/Bio/DB/TFBS.html HTMLifying blib/lib/Bio/StructuBuild: blib/lib/Bio/DB/GFF/Segment.pm: cannot resolve L in paragraph 229. Build: blib/lib/Bio/SeqIO/genbank.pm: cannot resolve L in paragraph 22. 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blib/libhtml/site/lib/Bio/Seq/PrimaryQual.html HTMLifying blib/lib/Bio/Tools/Signalp.pm -> blib/libhtml/site/lib/Bio/Tools/Signalp.html HTMLifying blib/lib/Bio/FeatureIO/vecscreen_simple.pm -Build: blib/lib/Bio/DB/GFF/Adaptor/dbi/mysql.pm: cannot resolve L in paragraph 161. > blib/libhtml/site/lib/Bio/FeatureIO/vecscreen_simple.html HTMLifying blib/lib/Bio/Tools/EUtilities/Info/LinkInfo.pm -> blib/libhtml/site/lib/Bio/Tools/EUtilities/Info/LinkInfo.html HTMLifying blib/lib/Bio/DB/Flat/BDB.pm -> blib/libhtml/site/lib/Bio/DB/Flat/BDB.html HTMLifying blib/lib/Bio/Seq/Meta.pm -> blib/libhtml/site/lib/Bio/Seq/Meta.html HTMLifying blib/lib/Bio/SeqFeature/Gene/Intron.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Gene/Intron.html HTMLifying blib/lib/Bio/Seq/SequenceTrace.pm -> blib/libhtml/site/lib/Bio/Seq/SequenceTrace.html HTMLifying blib/lib/Bio/Annotation/Collection.pm -> blib/libhtml/site/lib/Bio/Annotation/Collection.html HTMLifying blib/lib/Bio/SearchIO/Writer/HitTableWriter.pm -> 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MLifying blib/lib/Bio/Restriction/IO/base.pm -> blib/libhtml/site/lib/Bio/Restriction/IO/base.html HTMLifying blib/lib/Bio/DB/FileCache.pm -> blib/libhtml/site/lib/Bio/DB/FileCache.html HTMLifying blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm -> blib/libhtml/site/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.html HTMLifying blib/lib/Bio/Seq/EncodedSeq.pm -> blib/libhtml/site/lib/Bio/Seq/EncodedSeq.html HTMLifying blib/lib/Bio/Tree/Statistics.pm -> blib/libhtml/site/lib/Bio/Tree/Statistics.html HTMLifying blib/lib/Bio/Tools/Match.pm -> blib/libhtml/site/lib/Bio/Tools/Match.html HTMLifying blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm -> blib/libhtml/site/lib/Bio/SearchIO/Writer/HTMLResultWriter.html HTMLifying blib/lib/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Adaptor/berkeleydb/iterator.html HTMLifying blib/lib/Bio/Tools/Primer/AssessorI.pm -> blib/libhtml/site/lib/Bio/Tools/Primer/AssessorI.html HTMLifying blib/lib/Bio/Root/Build.pm -> blib/libhtml/site/lib/Bio/Root/Build.html HTMLifying blib/lib/Bio/Map/PositionWithSequence.pm -> blib/libhtml/site/lib/Bio/Map/PositionWithSequence.html HTMLifying blib/lib/Bio/Matrix/IO/phylip.pm -> blib/libhtml/site/lib/Bio/Matrix/IO/phylip.html HTMLifying blib/lib/Bio/DB/SeqI.pm -> blib/libhtml/site/lib/Bio/DB/SeqI.html HTMLifying blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.html HTMLifying blib/lib/Bio/SeqFeature/Tools/FeatureNamer.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Tools/FeatureNamer.html HTMLifying blib/lib/Bio/Coordinate/Pair.pm -> blib/libhtml/site/lib/Bio/Coordinate/Pair.html HTMLifying blib/lib/Bio/SeqFeature/Annotated.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Annotated.html HTMLifying blib/lib/Bio/DB/Query/HIVQuery.pm -> blib/libhtml/site/lib/Bio/DB/Query/HIVQuery.html HTMLifying blib/lib/Bio/Structure/SecStr/DSSP/Res.pm -> blib/libhtml/site/lib/Bio/Structure/SecStr/DSSP/Res.html HTMLifying blib/lib/Bio/Tools/Phylo/PAML/ModelResult.pm -> blib/libhtml/site/lib/Bio/Tools/Phylo/PAML/ModelResult.html HTMLifying blib/lib/Bio/PopGen/PopulationI.pm -> blib/libhtml/site/lib/Bio/PopGen/PopulationI.html HTMLifying blib/lib/Bio/LiveSeq/Translation.pm -> blib/libhtml/site/lib/Bio/LiveSeq/Translation.html HTMLifying blib/lib/Bio/SeqIO/embldriver.pm -> blib/libhtml/site/lib/Bio/SeqIO/embldriver.html HTMLifying blib/lib/Bio/SearchIO/gmap_f9.pm -> blib/libhtml/site/lib/Bio/SearchIO/gmap_f9.html HTMLifying blib/lib/Bio/SearchIO/SearchResultEventBuilder.pm -> blib/libhtml/site/lib/Bio/SearchIO/SearchResultEventBuilder.html HTMLifying blib/lib/Bio/Factory/ObjectFactory.pm -> blib/libhtml/site/lib/Bio/Factory/ObjectFactory.html HTMLifying blib/lib/Bio/DB/SwissProt.pm -> blib/libhtml/site/lib/Bio/DB/SwissProt.html HTMLifying blib/lib/Bio/DB/GFF/Aggregator/gene.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Aggregator/gene.html HTMLifying blib/lib/Bio/Phenotype/Correlate.pm -> blib/libhtml/site/lib/Bio/Phenotype/Correlate.html HTMLifying blib/lib/Bio/Tools/Run/ParametersI.pm -> blib/libhtml/site/lib/Bio/Tools/Run/ParametersI.html HTMLifying blib/lib/Bio/SeqIO/largefasta.pm -> blib/libhtml/site/lib/Bio/SeqIO/largefasta.html HTMLifying blib/lib/Bio/AlignIO.pm -> blib/libhtml/site/lib/Bio/AlignIO.html HTMLifying blib/lib/Bio/Search/Tiling/MapTileUtils.pm -> blib/libhtml/site/lib/Bio/Search/Tiling/MapTileUtils.html HTMLifying blib/lib/Bio/SeqIO/chaosxml.pm -> blib/libhtml/site/lib/Bio/SeqIO/chaosxml.html HTMLifying blib/lib/Bio/PhyloNetwork/TreeFactoryMulti.pm -> blib/libhtml/site/lib/Bio/PhyloNetwork/TreeFactoryMulti.html HTMLifying blib/lib/Bio/Taxonomy/Node.pm -> blib/libhtml/site/lib/Bio/Taxonomy/Node.html HTMLifying blib/lib/Bio/Search/Result/ResultI.pm -> blib/libhtml/site/lib/Bio/Search/Result/ResultI.html HTMLifying blib/lib/Bio/SearchIO/axt.pm -> blib/libhtml/site/lib/Bio/SearchIO/axt.html HTMLifying blib/lib/Bio/DB/UpdateableSeqI.pm -> blib/libhtml/site/lib/Bio/DB/UpdateableSeqI.html HTMLifying blib/lib/Bio/SeqFeature/Tools/IDHandler.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Tools/IDHandlerBuild: blib/lib/Bio/Search/Hit/HitI.pm: cannot resolve L in paragraph 126. 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Build: blib/lib/Bio/Search/Hit/BlastPullHit.pm: cannot resolve L in paragraph 74. /DB/Fasta.pm -> blib/libhtml/site/lib/Bio/DB/Fasta.html HTMLifying blib/lib/Bio/DB/Biblio/biofetch.pm -> blib/libhtml/site/lib/Bio/DB/Biblio/biofetch.html HTMLifying blib/lib/Bio/Seq/Quality.pm -> blib/libhtml/site/lib/Bio/Seq/Quality.html HTMLifying blib/lib/Bio/SeqIO/strider.pm -> blib/libhtml/site/lib/Bio/SeqIO/strider.html HTMLifying blib/lib/Bio/PhyloNetwork/TreeFactoryX.pm -> blib/libhtml/site/lib/Bio/PhyloNetwork/TreeFactoryX.html HTMLifying blib/lib/Bio/Matrix/Mlagan.pm -> blib/libhtml/site/lib/Bio/Matrix/Mlagan.html HTMLifying blib/lib/Bio/SearchIO/sim4.pm -> blib/libhtml/site/lib/Bio/SearchIO/sim4.html HTMLifying blib/lib/Bio/Assembly/IO.pm -> blib/libhtml/site/lib/Bio/Assembly/IO.html HTMLifying blib/lib/Bio/SeqFeature/Gene/UTR.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Gene/UTR.html HTMLifying blib/lib/Bio/Index/Swissprot.pm -> blib/libhtml/site/lib/Bio/Index/Swissprot.html HTMLifying blib/lib/Bio/Tools/SeqStats.pm -> blib/libhtml/site/lib/Bio/Tools/SeqStats.html HTMLifying blib/lib/Bio/Structure/StructureI.pm -> blib/libhtml/site/lib/Bio/Structure/StructureI.html HTMLifying blib/lib/Bio/AlignIO/mega.pm -> blib/libhtml/site/lib/Bio/AlignIO/mega.html HTMLifying blib/lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm -> blib/libhtml/site/lib/Bio/SeqIO/tinyseq/tinyseqHandler.html HTMLifying blib/lib/Bio/DB/GFF/Aggregator/so_transcript.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Aggregator/so_transcript.html HTMLifying blib/lib/Bio/Tools/dpAlign.pm -> blib/libhtml/site/lib/Bio/Tools/dpAlign.html HTMLifying blib/lib/Bio/Variation/DNAMutation.pm -> blib/libhtml/site/lib/Bio/Variation/DNAMutation.html HTMLifying blib/lib/Bio/Search/Result/HMMERResult.pm -> blib/libhtml/site/lib/Bio/Search/Result/HMMERResult.html HTMLifying blib/lib/Bio/SeqIO/fastq.pm -> blib/libhtml/site/lib/Bio/SeqIO/fastq.html HTMLifying blib/lib/Bio/PhyloNetwork/GraphViz.pm -> blib/libhtml/site/lib/Bio/PhyloNetwork/GraphViz.html HTMLifying blib/lib/Bio/SearchIO/wise.pm -> blib/libhtml/site/lib/Bio/SearchIO/wise.html HTMLifying blib/lib/Bio/Ontology/RelationshipType.pm -> blib/libhtml/site/lib/Bio/Ontology/RelationshipType.html HTMLifying blib/lib/Bio/Biblio/Article.pm -> blib/libhtml/site/lib/Bio/Biblio/Article.html HTMLifying blib/lib/Bio/Symbol/Alphabet.pm -> blib/libhtml/site/lib/Bio/Symbol/Alphabet.html HTMLifying blib/lib/Bio/Coordinate/ExtrapolatingPair.pm -> blib/libhtml/site/lib/Bio/Coordinate/ExtrapolatingPair.html HTMLifying blib/lib/Bio/Search/Result/PullResultI.pm -> blib/libhtml/site/lib/Bio/Search/Result/PullResultI.html HTMLifying blib/lib/Bio/SeqIO/tab.pm -> blib/libhtml/site/lib/Bio/SeqIO/tab.html HTMLifying blib/lib/Bio/Coordinate/Collection.pm -> blib/libhtml/site/lib/Bio/Coordinate/Collection.html HTMLifying blib/lib/Bio/LiveSeq/Gene.pm -> blib/libhtml/site/lib/Bio/LiveSeq/Gene.html HTMLifying blib/lib/Bio/Annotation/AnnotationFactory.pm -> blib/libhtml/site/lib/Bio/Annotation/AnnotationFactory.html HTMLifying blib/lib/Bio/Search/Hit/BlastPullHit.pm -> blib/libhtml/site/lib/Bio/Search/Hit/BlastPullHit.html HTMLifying blib/lib/Bio/OntologyIO/goflat.pm -> blib/libhtml/site/lib/Bio/OntologyIO/goflat.html HTMLifying blib/lib/Bio/Location/Simple.pm -> blib/libhtml/site/lib/Bio/Location/Simple.html HTMLifying blib/lib/Bio/Tools/Phylo/Phylip/ProtDist.pm -> blib/libhtml/site/lib/Bio/Tools/Phylo/Phylip/ProtDist.html HTMLifying blib/lib/Bio/SeqFeature/Collection.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Collection.html HTMLifying blib/lib/Bio/Biblio.pm -> blib/libhtml/site/lib/Bio/Biblio.html HTMLifying blib/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.html HTMLifying blib/lib/Bio/DB/GFF/Aggregator/clone.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Aggregator/clone.html HTMLifying blib/lib/Bio/SeqFeature/Gene/Transcript.pm -> blib/libhtml/site/lib/Bio/SeqFeature/Gene/Transcript.html HTMLifying blib/lib/Bio/SeqFeatureI.pm -> blib/libhtml/site/lib/Bio/SeqFeatureI.html HTMLifying blib/lib/Bio/PopGen/IndividualI.pm -> blib/libhtml/site/lib/Bio/PopGen/IndividualI.html HTMLifying blib/lib/Bio/Build: blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm: cannot resolve L in paragraph 8. 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blib/lib/Bio/Matrix/PSM/InstanceSiteI.pm -> blib/libhtml/site/lib/Bio/Matrix/PSM/InstanceSiteI.html HTMLifying blib/lib/Bio/Structure/SecStr/STRIDE/Res.pm -> blib/libhtml/site/lib/Bio/Structure/SecStr/STRIDE/Res.html HTMLifying blib/lib/Bio/Map/Physical.pm -> blib/libhtml/site/lib/Bio/Map/Physical.html HTMLifying blib/lib/Bio/DB/InMemoryCache.pm -> blib/libhtml/site/lib/Bio/DB/InMemoryCache.html HTMLifying blib/lib/Bio/Perl.pm -> blib/libhtml/site/lib/Bio/Perl.html HTMLifying blib/lib/Bio/SeqIO/game/gameWriter.pm -> blib/libhtml/site/lib/Bio/SeqIO/game/gameWriter.html HTMLifying blib/lib/Bio/SeqIO/abi.pm -> blib/libhtml/site/lib/Bio/SeqIO/abi.html HTMLifying blib/lib/Bio/LiveSeq/AARange.pm -> blib/libhtml/site/lib/Bio/LiveSeq/AARange.html HTMLifying blib/lib/Bio/PrimarySeq.pm -> blib/libhtml/site/lib/Bio/PrimarySeq.html HTMLifying blib/lib/Bio/DB/Flat/BDB/fasta.pm -> blib/libhtml/site/lib/Bio/DB/Flat/BDB/fasta.html HTMLifying blib/lib/Bio/Tools/Run/GenericParameters.pm -> blib/libhtml/site/lib/Bio/Tools/Run/GenericParameters.html HTMLifying blib/lib/Bio/SeqIO/lasergene.pm -> blib/libhtml/site/lib/Bio/SeqIO/lasergene.html HTMLifying blib/lib/Bio/PopGen/IO/prettybase.pm -> blib/libhtml/site/lib/Bio/PopGen/IO/prettybase.html HTMLifying blib/lib/Bio/Assembly/IO/ace.pm -> blib/libhtml/site/lib/Bio/Assembly/IO/ace.html HTMLifying blib/lib/Bio/Symbol/SymbolI.pm -> blib/libhtml/site/lib/Bio/Symbol/SymbolI.html HTMLifying blib/lib/Bio/SimpleAnalysisI.pm -> blib/libhtml/site/lib/Bio/SimpleAnalysisI.html HTMLifying blib/lib/Bio/Matrix/PSM/IO/transfac.pm -> blib/libhtml/site/lib/Bio/Matrix/PSM/IO/transfac.html HTMLifying blib/lib/Bio/LiveSeq/IO/BioPerl.pm -> blib/libhtml/site/lib/Bio/LiveSeq/IO/BioPerl.html HTMLifying blib/lib/Bio/Annotation/OntologyTerm.pm -> blib/libhtml/site/lib/Bio/Annotation/OntologyTerm.html HTMLifying blib/lib/Bio/Tools/Run/RemoteBlast.pm -> blib/libhtml/site/lib/Bio/Tools/Run/RemoteBlast.html HTMLifying blib/lib/Bio/Phenotype/MeSH/Term.pm -> blib/libhtml/site/lib/Bio/Phenotype/MeSH/Term.html HTMLifying blib/lib/Bio/Tools/Pseudowise.pm -> blib/libhtml/site/lib/Bio/Tools/Pseudowise.html HTMLifying blib/lib/Bio/DB/HIV.pm -> blib/libhtml/site/lib/Bio/DB/HIV.html HTMLifying blib/lib/Bio/SeqFeature/AnnotationAdaptor.pm -> blib/libhtml/site/lib/Bio/SeqFeature/AnnotationAdaptor.html HTMLifying blib/lib/Bio/Matrix/IO.pm -> blib/libhtml/site/lib/Bio/Matrix/IO.html HTMLifying blib/lib/Bio/Map/Gene.pm -> blib/libhtml/site/lib/Bio/Map/Gene.html HTMLifying blib/lib/Bio/Map/Prediction.pm -> blib/libhtml/site/lib/Bio/Map/Prediction.html HTMLifying blib/lib/Bio/Biblio/Person.pm -> blib/libhtml/site/lib/Bio/Biblio/Person.html HTMLifying blib/lib/Bio/Search/BlastStatistics.pm -> blib/libhtml/site/lib/Bio/Search/BlastStatistics.html HTMLifying blib/lib/Bio/PopGen/MarkerI.pm -> blib/libhtml/site/lib/Bio/PopGen/MarkerI.html HTMLifying blib/lib/Bio/Tools/Grail.pm -> blib/libhtml/site/lib/Bio/Tools/Grail.html HTMLifying blib/lib/Bio/Search/HSP/ModelHSP.pm -> blib/libhtml/site/lib/Bio/Search/HSP/ModelHSP.html HTMLifying blib/lib/Bio/DB/WebDBSeqI.pm -> blib/libhtml/site/lib/Bio/DB/WebDBSeqI.html HTMLifying blib/lib/Bio/AlignIO/clustalw.pm -> blib/libBuild: blib/lib/Bio/Structure/IO.pm: cannot resolve L in paragraph 56. html/site/lib/Bio/AlignIO/clustalw.html HTMLifying blib/lib/Bio/TreeIO/newick.pm -> blib/libhtml/site/lib/Bio/TreeIO/newick.html HTMLifying blib/lib/Bio/Tools/EUtilities/Link/LinkSet.pm -> blib/libhtml/site/lib/Bio/Tools/EUtilities/Link/LinkSet.html HTMLifying blib/lib/Bio/PopGen/Utilities.pm -> blib/libhtml/site/lib/Bio/PopGen/Utilities.html HTMLifying blib/lib/Bio/Tools/Analysis/DNA/ESEfinder.pm -> blib/libhtml/site/lib/Bio/Tools/Analysis/DNA/ESEfinder.html HTMLifying blib/lib/Bio/Search/HSP/FastaHSP.pm -> blib/libhtml/site/lib/Bio/Search/HSP/FastaHSP.html HTMLifying blib/lib/Bio/Phenotype/OMIM/MiniMIMentry.pm -> blib/libhtml/site/lib/Bio/Phenotype/OMIM/MiniMIMentry.html HTMLifying blib/lib/Bio/Tools/Analysis/Protein/ELM.pm -> blib/libhtml/site/lib/Bio/Tools/Analysis/Protein/ELM.html HTMLifying blib/lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm -> blib/libhtml/site/lib/Bio/Tools/Analysis/SimpleAnalysisBase.html HTMLifying blib/lib/Bio/FeatureIO/gtf.pm -> blib/libhtml/site/lib/Bio/FeatureIO/gtf.html HTMLifying blib/lib/Bio/AnnotatableI.pm -> blib/libhtml/site/lib/Bio/AnnotatableI.html HTMLifying blib/lib/Bio/DB/RefSeq.pm -> blib/libhtml/site/lib/Bio/DB/RefSeq.html HTMLifying blib/lib/Bio/Seq/Meta/Array.pm -> blib/libhtml/site/lib/Bio/Seq/Meta/Array.html HTMLifying blib/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm -> blib/libhtml/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.html HTMLifying blib/lib/Bio/Structure/IO.pm -> blib/libhtml/site/lib/Bio/Structure/IO.html HTMLifying blib/lib/Bio/Variation/SeqDiff.pm -> blib/libhtml/site/lib/Bio/Variation/SeqDiff.html HTMLifying blib/lib/Bio/Seq/SeqWithQuality.pm -> blib/libhtml/site/lib/Bio/Seq/SeqWithQuality.html HTMLifying blib/lib/Bio/PopGen/TagHaplotype.pm -> blib/libhtml/site/lib/Bio/PopGen/TagHaplotype.html HTMLifying blib/lib/Bio/Matrix/IO/mlagan.pm -> blib/libhtml/site/lib/Bio/Matrix/IO/mlagan.html HTMLifying blib/lib/Bio/DB/GFF/Adaptor/dbi/oracle.pm -> blib/libhtml/site/lib/Bio/DB/GFF/Adaptor/dbi/oracle.html HTMLifying blib/lib/Bio/DB/Qual.pm -> blib/libhtml/site/lib/Bio/DB/Qual.html CJFIELDS/BioPerl-1.6.1.tar.gz make -- OK Running make test >>> make test TEST_VERBOSE=1 /export/home/fly1003/bin/perl Build --makefile_env_macros 1 test Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS Changing sharpbang in blib/script/bp_sreformat.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/seqconvert.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/parse_hmmsearch.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/hivq.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/bp_seqret.PLS to /export/home/fly1003/bin/perlDeleting blib/script/bp_seqret.PLS.bak blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS Changing sharpbang in blib/script/tree2pag.PLS to /export/home/fly1003/bin/perlDeleting blib/script/tree2pag.PLS.bak blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS Changing sharpbang in blib/script/meta_gff.PLS to /export/home/fly1003/bin/perlDeleting blib/script/meta_gff.PLS.bak blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS Changing sharpbang in blib/script/nexus2nh.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/filter_search.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/generate_histogram.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/heterogeneity_test.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/flanks.PLS to /export/home/fly1003/bin/perlDeleting blib/script/flanks.PLS.bak blib/script/flanks.PLS -> blib/script/bp_flanks.pl Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS Changing sharpbang in blib/script/split_seq.PLS to /export/home/fly1003/bin/perlDeleting blib/script/split_seq.PLS.bak blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS Changing sharpbang in blib/script/load_gff.PLS to /export/home/fly1003/bin/perlDeleting blib/script/load_gff.PLS.bak blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS Changing sharpbang in blib/script/biogetseq.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/bp_fetch.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/mutate.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/process_sgd.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/bp_index.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/dbsplit.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/oligo_count.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/hmmer_to_table.PLS to /export/home/fly1003/bin/perlDeleting blib/script/hmmer_to_table.PLS.bak blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS Changing sharpbang in blib/script/process_gadfly.PLS to /export/home/fly1003/bin/perlDeleting blib/script/process_gadfly.PLS.bak blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS Changing sharpbang in blib/script/bp_seqfeature_load.PLS to /export/home/fly1003/bin/perlDeleting blib/script/bp_seqfeature_load.PLS.bak blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS Changing sharpbang in blib/script/fastam9_to_table.PLS to /export/home/fly1003/bin/perlDeleting blib/script/fastam9_to_table.PLS.bak blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS Changing sharpbang in blib/script/biofetch_genbank_proxy.PLS to /export/home/fly1003/bin/perlDeleting blib/script/biofetch_genbank_proxy.PLS.bak blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS Changing sharpbang in blib/script/seq_length.PLS to /export/home/fly1003/bin/perlDeleting blib/script/seq_length.PLS.bak blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS Changing sharpbang in blib/script/extract_feature_seq.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/genbank2gff.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/bulk_load_gff.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/taxid4species.PLS to /export/home/fly1003/bin/perlDeleting blib/script/taxid4species.PLS.bak blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS Changing sharpbang in blib/script/search2gff.PLS to /export/home/fly1003/bin/perlDeleting blib/script/search2gff.PLS.bak blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS Changing sharpbang in blib/script/blast2tree.PLS to /export/home/fly1003/bin/perlDeleting blib/script/blast2tree.PLS.bak blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS Changing sharpbang in blib/script/unflatten_seq.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/make_mrna_protein.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/search2tribe.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/bioflat_index.PLS to /export/home/fly1003/bin/perlDeleting blib/script/bioflat_index.PLS.bak blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS Changing sharpbang in blib/script/pairwise_kaks.PLS to /export/home/fly1003/bin/perlDeleting blib/script/pairwise_kaks.PLS.bak blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS Changing sharpbang in blib/script/query_entrez_taxa.PLS to /export/home/fly1003/bin/perlDeleting blib/script/query_entrez_taxa.PLS.bak blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS Changing sharpbang in blib/script/bp_seqfeature_delete.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/fast_load_gff.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/chaos_plot.PLS to /export/home/fly1003/bin/perlDeleting blib/script/chaos_plot.PLS.bak blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS Changing sharpbang in blib/script/bp_mrtrans.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/search2alnblocks.PLS to /export/home/fly1003/bin/perlDeleting blib/script/search2alnblocks.PLS.bak blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS Changing sharpbang in blib/script/taxonomy2tree.PLS to /export/home/fly1003/bin/perlDeleting blib/script/taxonomy2tree.PLS.bak blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl Copying scripts/Bio-DB-EUtilities/einfo.PLS -> blib/script/einfo.PLS Changing sharpbang in blib/script/einfo.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/download_query_genbank.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/bp_nrdb.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/mask_by_search.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/gccalc.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/classify_hits_kingdom.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/composite_LD.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/aacomp.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/revtrans-motif.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/process_wormbase.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/local_taxonomydb_query.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/biblio.PLS to /export/home/fly1003/bin/perlDeleting blib/script/biblio.PLS.bak blib/script/biblio.PLS -> blib/script/bp_biblio.pl Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS Changing sharpbang in blib/script/remote_blast.PLS to /export/home/fly1003/bin/perlDeleting blib/script/remote_blast.PLS.bak blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS Changing sharpbang in blib/script/seqretsplit.PLS to /export/home/fly1003/bin/perlDeleting blib/script/seqretsplit.PLS.bak blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS Changing sharpbang in blib/script/genbank2gff3.PLS to /export/home/fly1003/bin/perlDeleting blib/script/genbank2gff3.PLS.bak blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS Changing sharpbang in blib/script/search2table.PLS to /export/home/fly1003/bin/perlDeleting blib/script/search2table.PLS.bak blib/script/search2table.PLS -> blib/script/bp_search2table.pl Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS Changing sharpbang in blib/script/search2BSML.PLS to /export/home/fly1003/bin/perlDeleting 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 Changing sharpbang in blib/script/translate_seq.PLS to /export/home/fly1003/bin/perlDeleting blib/script/translate_seq.PLS.bak blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl t/Align/AlignStats.t ......................... 1..43 ok 1 - use Bio::Align::DNAStatistics; ok 2 - use Bio::Align::ProteinStatistics; ok 3 - use Bio::AlignIO; ok 4 - The object isa Bio::Align::AlignI ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 - The object isa Bio::Align::AlignI ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 - The object isa Bio::Align::AlignI ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 - The object isa Bio::Align::AlignI ok 38 - The object isa Bio::Matrix::PhylipDist ok 39 ok 40 ok 41 ok 42 - The object isa Bio::PrimarySeqI ok 43 ok t/Align/AlignUtil.t .......................... 1..33 ok 1 - use Bio::Align::Utilities; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - The object isa Bio::Align::AlignI ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok t/Align/SimpleAlign.t ........................ 1..179 ok 1 - use Bio::SimpleAlign; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqFeature::Generic; ok 4 - use Bio::Location::Simple; ok 5 - use Bio::Location::Split; ok 6 - The object isa Bio::AlignIO ok 7 - pfam input test ok 8 - match_line ok 9 - The object isa Bio::Align::AlignI ok 10 - num_sequences ok 11 - num_sequences ok 12 - select_noncont ok 13 - select_noncont ok 14 - num_sequences ok 15 - select_noncont ok 16 - select_noncont ok 17 - each_seq ok 18 - get_nse ok 19 - id ok 20 - num_gaps ok 21 - each_alphabetically ok 22 - column_from_residue_number ok 23 - display_name get/set ok 24 - display_name get ok 25 - consensus_string ok 26 - consensus_string ok 27 - consensus_string ok 28 ok 29 - each_seq_with_id ok 30 - is_flush ok 31 - id get/set ok 32 - length ok 33 - num_residues ok 34 - num_sequences ok 35 - overall_percentage_identity ok 36 - overall_percentage_identity ok 37 - overall_percentage_identity ok 38 - overall_percentage_identity ok 39 - average_percentage_identity ok 40 ok 41 - set_displayname_count ok 42 ok 43 - set_displayname_flat ok 44 ok 45 - set_displayname_normal ok 46 ok 47 ok 48 - uppercase, map_chars ok 49 - match_line ok 50 - remove_seqs ok 51 - remove_seqs ok 52 - add_seq ok 53 - add_seq ok 54 - get_seq_by_pos ok 55 - get_seq_by_pos ok 56 ok 57 ok 58 ok 59 - purge ok 60 - purge ok 61 - IO::String consensus_iupac ok 62 - IO::String write_aln normal ok 63 - IO::String write_aln slice ok 64 - IO::String write_aln slice ok 65 - IO::String write_aln slice ok 66 - IO::String write_aln slice ok 67 - IO::String write_aln slice ok 68 ok 69 - remove_columns by position ok 70 - remove_columns by position (wrong order) ok 71 - cigar_line ok 72 - cigar_line ok 73 - cigar_line ok 74 - cigar_line ok 75 - sort_alphabetically - before ok 76 ok 77 - sort_alphabetically - after ok 78 - remove_gaps ok 79 - remove_gaps all_gaps_only ok 80 - set_new_reference ok 81 - set_new_reference ok 82 - uniq_seq ok 83 - bug 2099 ok 84 - bug 2099 ok 85 - bug 2793 ok 86 - bug 2793 ok 87 - bug 2793 ok 88 - bug 2793 ok 89 - Bad sequence, bad! ok 90 - added 3 seqs ok 91 - first 2 features added ok 92 - 3rd feature added not ok 93 # TODO This should pass but dies; see bug 2842 # Failed (TODO) test at t/Align/SimpleAlign.t line 421. # died: Bio::Root::Exception ( # ------------- EXCEPTION: Bio::Root::Exception ------------- # MSG: In sequence one residue count gives end value 1. # Overriding value [0] with value 1 for Bio::LocatableSeq::end(). # ? # STACK: Error::throw # STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368 # STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:181 # STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:196 # STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1143 # STACK: try{} block t/Align/SimpleAlign.t:421 # STACK: Sub::Uplevel::uplevel /export/home/fly1003/var/megalib/Sub/Uplevel.pm:133 # STACK: Test::Exception::_try_as_caller /export/home/fly1003/var/megalib/Test/Exception.pm:104 # STACK: Test::Exception::lives_ok /export/home/fly1003/var/megalib/Test/Exception.pm:258 # STACK: t/Align/SimpleAlign.t:421 # ----------------------------------------------------------- # ) ok 94 - slice 1 len ok 95 - correct masked seq ok 96 - correct masked seq ok 97 - correct masked seq not ok 98 # TODO This should pass but dies; see bug 2842 # Failed (TODO) test at t/Align/SimpleAlign.t line 421. # died: Bio::Root::Exception ( # ------------- EXCEPTION: Bio::Root::Exception ------------- # MSG: In sequence one residue count gives end value 3. # Overriding value [2] with value 3 for Bio::LocatableSeq::end(). # ? # STACK: Error::throw # STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368 # STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:181 # STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:196 # STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1143 # STACK: try{} block t/Align/SimpleAlign.t:421 # STACK: Sub::Uplevel::uplevel /export/home/fly1003/var/megalib/Sub/Uplevel.pm:133 # STACK: Test::Exception::_try_as_caller /export/home/fly1003/var/megalib/Test/Exception.pm:104 # STACK: Test::Exception::lives_ok /export/home/fly1003/var/megalib/Test/Exception.pm:258 # STACK: t/Align/SimpleAlign.t:421 # ----------------------------------------------------------- # ) ok 99 - slice 2 len ok 100 - correct masked seq ok 101 - correct masked seq ok 102 - correct masked seq not ok 103 # TODO This should pass but dies; see bug 2842 # Failed (TODO) test at t/Align/SimpleAlign.t line 421. # died: Bio::Root::Exception ( # ------------- EXCEPTION: Bio::Root::Exception ------------- # MSG: In sequence one residue count gives end value 3. # Overriding value [1] with value 3 for Bio::LocatableSeq::end(). # ?? # STACK: Error::throw # STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368 # STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:181 # STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:196 # STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1143 # STACK: try{} block t/Align/SimpleAlign.t:421 # STACK: Sub::Uplevel::uplevel /export/home/fly1003/var/megalib/Sub/Uplevel.pm:133 # STACK: Test::Exception::_try_as_caller /export/home/fly1003/var/megalib/Test/Exception.pm:104 # STACK: Test::Exception::lives_ok /export/home/fly1003/var/megalib/Test/Exception.pm:258 # STACK: t/Align/SimpleAlign.t:421 # ----------------------------------------------------------- # ) ok 104 - slice 3 len ok 105 - correct masked seq ok 106 - correct masked seq ok 107 - correct masked seq not ok 108 # TODO This should pass but dies; see bug 2842 # Failed (TODO) test at t/Align/SimpleAlign.t line 421. # died: Bio::Root::Exception ( # ------------- EXCEPTION: Bio::Root::Exception ------------- # MSG: In sequence one residue count gives end value 6. # Overriding value [4] with value 6 for Bio::LocatableSeq::end(). # ?? # STACK: Error::throw # STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368 # STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:181 # STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:196 # STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1143 # STACK: try{} block t/Align/SimpleAlign.t:421 # STACK: Sub::Uplevel::uplevel /export/home/fly1003/var/megalib/Sub/Uplevel.pm:133 # STACK: Test::Exception::_try_as_caller /export/home/fly1003/var/megalib/Test/Exception.pm:104 # STACK: Test::Exception::lives_ok /export/home/fly1003/var/megalib/Test/Exception.pm:258 # STACK: t/Align/SimpleAlign.t:421 # ----------------------------------------------------------- # ) ok 109 - slice 4 len ok 110 - correct masked seq ok 111 - correct masked seq ok 112 - correct masked seq ok 113 - initial display id ok ok 114 - safe display id ok ok 115 - restored display id ok ok 116 - sort by list ok ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 - BIC:GGATCCATT[C/C]CTACT ok 124 - BIC:GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT ok 125 - BIC:G[G/C]ATCCATT[C/G]CTACT ok 126 - BIC:GGATCCATT[C/G]CTACT ok 127 - BIC:GGATCCATT[C/G]CTAC[T/A] ok 128 - BIC:GGATCCATT[C/G]CTA[C/G][T/A] ok 129 - BIC:GGATCCATT[C/G]CTACT ok 130 - BIC:GGATCCATT{C.C}CTACT ok 131 - BIC:GGAT{C.-}{C.-}ATT{C.C}CT{A.C}CT ok 132 - BIC:G{G.C}ATCCATT{C.G}CTACT ok 133 - BIC:GGATCCATT{C.G}CTACT ok 134 - BIC:GGATCCATT{C.G}CTAC{T.A} ok 135 - BIC:GGATCCATT{C.G}CTA{C.G}{T.A} ok 136 - BIC:GGATCCATT{C.G}CTACT ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 ok 156 ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 - The object isa Bio::SimpleAlign ok 175 - consensus string looks ok ok 176 - looks like correct unmasked alignment (from clustalw) ok 177 - looks like correct masked alignment (from clustalw) ok 178 ok 179 - align after looks ok ok t/Align/TreeBuild.t .......................... 1..13 ok 1 - use Bio::Align::DNAStatistics; ok 2 - use Bio::Align::ProteinStatistics; ok 3 - use Bio::Align::Utilities; ok 4 - use Bio::AlignIO; ok 5 - use Bio::Tree::DistanceFactory; ok 6 - use Bio::TreeIO; ok 7 - SimpleAlign object parsed out isa Bio::SimpleAlign ok 8 - Protein distance matrix retrieved isa Bio::Matrix::MatrixI ok 9 - Tree object gotten back isa Bio::Tree::TreeI ok 10 - NJ calculated Branch length ok 11 - NJ calculated Branch length ok 12 - Make sure two nodes are sister ok 13 - 10 replicates formulated ok t/Align/Utilities.t .......................... 1..13 ok 1 - use Bio::Align::Utilities; ok 2 - use Bio::SimpleAlign; ok 3 - use Bio::PrimarySeq; ok 4 - use Bio::LocatableSeq; ok 5 - use Bio::AlignIO; ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok t/AlignIO/AlignIO.t .......................... 1..28 ok 1 - use Bio::AlignIO; ok 2 - input filehandle method test : metafasta ok 3 - input filehandle method test : po ok 4 - input filehandle method test : nexus ok 5 - input filehandle method test : clustalw ok 6 - input filehandle method test : prodom ok 7 - input filehandle method test : fasta ok 8 - input filehandle method test : arp ok 9 - input filehandle method test : xmfa ok 10 - input filehandle method test : mase ok 11 - input filehandle method test : psi ok 12 - input filehandle method test : phylip ok 13 - input filehandle method test : pfam ok 14 - input filehandle method test : selex ok 15 - input filehandle method test : stockholm ok 16 - input filehandle method test : msf ok 17 - filehandle output test : metafasta ok 18 - filehandle output test : po ok 19 - filehandle output test : nexus ok 20 - filehandle output test : clustalw ok 21 - filehandle output test : fasta ok 22 - filehandle output test : xmfa ok 23 - filehandle output test : psi ok 24 - filehandle output test : phylip ok 25 - filehandle output test : pfam ok 26 - filehandle output test : selex ok 27 - filehandle output test : stockholm ok 28 - filehandle output test : msf ok t/AlignIO/arp.t .............................. 1..48 ok 1 - use Bio::AlignIO::arp; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 - ARP get_nse() ok 5 ok 6 - ARP num_sequences() ok 7 - ARP id() ok 8 - ARP description() ok 9 - The object isa Bio::AnnotationCollectionI ok 10 - The object isa Bio::AnnotationI ok 11 ok 12 ok 13 ok 14 ok 15 - The object isa Bio::AlignIO ok 16 - The object isa Bio::Align::AlignI ok 17 - ARP get_nse() ok 18 - ARP num_sequences() ok 19 - ARP id() ok 20 - ARP description() ok 21 - The object isa Bio::AnnotationCollectionI ok 22 - The object isa Bio::AnnotationI ok 23 ok 24 ok 25 ok 26 ok 27 - The object isa Bio::Align::AlignI ok 28 - ARP get_nse() ok 29 - ARP num_sequences() ok 30 - ARP id() ok 31 - ARP description() ok 32 - The object isa Bio::AnnotationCollectionI ok 33 - The object isa Bio::AnnotationI ok 34 ok 35 ok 36 ok 37 ok 38 - The object isa Bio::Align::AlignI ok 39 - ARP get_nse() ok 40 - ARP num_sequences() ok 41 - ARP id() ok 42 - ARP description() ok 43 - The object isa Bio::AnnotationCollectionI ok 44 - The object isa Bio::AnnotationI ok 45 ok 46 ok 47 ok 48 ok t/AlignIO/bl2seq.t ........................... 1..3 ok 1 - use Bio::AlignIO::bl2seq; ok 2 - The object isa Bio::Align::AlignI ok 3 - BLAST bl2seq format test ok t/AlignIO/clustalw.t ......................... 1..6 ok 1 - use Bio::AlignIO::clustalw; ok 2 - The object isa Bio::Align::AlignI ok 3 - clustalw consensus_string test ok 4 - clustalw (.aln) output test ok 5 - The object isa Bio::Align::AlignI ok 6 - clustalw (.aln) input test ok t/AlignIO/emboss.t ........................... 1..37 ok 1 - use Bio::AlignIO::emboss; ok 2 - The object isa Bio::Align::AlignI ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 - The object isa Bio::Align::AlignI ok 11 ok 12 ok 13 ok 14 - The object isa Bio::Align::AlignI ok 15 ok 16 ok 17 ok 18 - The object isa Bio::Align::AlignI ok 19 ok 20 ok 21 - The object isa Bio::Align::AlignI ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 - The object isa Bio::Align::AlignI ok 33 ok 34 ok 35 ok 36 ok 37 ok t/AlignIO/fasta.t ............................ 1..10 ok 1 - use Bio::AlignIO::fasta; ok 2 - The object isa Bio::Align::AlignI ok 3 - fasta input test ok 4 - fasta input test for description ok 5 - fasta input test for id ok 6 - fasta input test for end ok 7 - fasta input test for description ok 8 - fasta output test ok 9 - filehandle input test ok 10 - filehandle output test ok t/AlignIO/largemultifasta.t .................. 1..7 ok 1 - use Bio::AlignIO::largemultifasta; ok 2 - The object isa Bio::Align::AlignI ok 3 - fasta input test ok 4 - fasta input test for description ok 5 - fasta input test for id ok 6 - fasta input test for description ok 7 - fasta output test ok t/AlignIO/maf.t .............................. 1..11 ok 1 - use Bio::AlignIO::maf; ok 2 - The object isa Bio::Align::AlignI ok 3 - maf input test ok 4 ok 5 - The object isa Bio::Align::AlignI ok 6 - maf input test ok 7 ok 8 - maf input test ok 9 ok 10 - maf input test ok 11 ok t/AlignIO/mase.t ............................. 1..3 ok 1 - use Bio::AlignIO::mase; ok 2 - The object isa Bio::Align::AlignI ok 3 - mase input test ok t/AlignIO/mega.t ............................. 1..6 ok 1 - use Bio::AlignIO::mega; ok 2 - The object isa Bio::Align::AlignI ok 3 ok 4 ok 5 ok 6 - mega output test ok t/AlignIO/meme.t ............................. 1..14 ok 1 - use Bio::AlignIO::meme; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 ok 5 ok 6 ok 7 ok 8 - The object isa Bio::AlignIO ok 9 - The object isa Bio::Align::AlignI ok 10 ok 11 ok 12 ok 13 ok 14 ok t/AlignIO/metafasta.t ........................ 1..4 ok 1 - use Bio::AlignIO::metafasta; ok 2 - The object isa Bio::Align::AlignI ok 3 - consensus_string on metafasta ok 4 - symbol_chars() using metafasta ok t/AlignIO/msf.t .............................. 1..4 ok 1 - use Bio::AlignIO::msf; ok 2 - The object isa Bio::Align::AlignI ok 3 - msf input test ok 4 - msf output test ok t/AlignIO/nexus.t ............................ 1..43 ok 1 - use Bio::AlignIO::nexus; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 ok 5 - nexus output test ok 6 - The object isa Bio::AlignIO ok 7 - The object isa Bio::Align::AlignI ok 8 - The object isa Bio::AlignIO ok 9 - The object isa Bio::Align::AlignI ok 10 - The object isa Bio::AlignIO ok 11 - The object isa Bio::Align::AlignI ok 12 - The object isa Bio::AlignIO ok 13 - The object isa Bio::Align::AlignI ok 14 - The object isa Bio::AlignIO ok 15 - The object isa Bio::Align::AlignI ok 16 - The object isa Bio::AlignIO ok 17 - The object isa Bio::Align::AlignI ok 18 - The object isa Bio::AlignIO ok 19 - The object isa Bio::Align::AlignI ok 20 - The object isa Bio::AlignIO ok 21 - The object isa Bio::Align::AlignI ok 22 - The object isa Bio::AlignIO ok 23 - The object isa Bio::Align::AlignI ok 24 - The object isa Bio::AlignIO ok 25 - The object isa Bio::Align::AlignI ok 26 - The object isa Bio::AlignIO ok 27 - The object isa Bio::Align::AlignI ok 28 - The object isa Bio::AlignIO ok 29 - The object isa Bio::Align::AlignI ok 30 - The object isa Bio::AlignIO ok 31 - The object isa Bio::Align::AlignI ok 32 - The object isa Bio::AlignIO ok 33 - The object isa Bio::Align::AlignI ok 34 - The object isa Bio::AlignIO ok 35 - The object isa Bio::Align::AlignI ok 36 - The object isa Bio::AlignIO ok 37 - The object isa Bio::Align::AlignI ok 38 - The object isa Bio::AlignIO ok 39 - The object isa Bio::Align::AlignI ok 40 - The object isa Bio::AlignIO ok 41 - The object isa Bio::Align::AlignI ok 42 - The object isa Bio::AlignIO ok 43 - The object isa Bio::Align::AlignI ok t/AlignIO/pfam.t ............................. 1..5 ok 1 - use Bio::AlignIO::pfam; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 ok 5 - pfam output test ok t/AlignIO/phylip.t ........................... 1..11 ok 1 - use Bio::AlignIO::phylip; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 ok 5 - phylip output test ok 6 - The object isa Bio::Align::AlignI ok 7 ok 8 - The object isa Bio::AlignIO ok 9 - The object isa Bio::Align::AlignI ok 10 ok 11 ok t/AlignIO/po.t ............................... 1..11 ok 1 - use Bio::AlignIO::po; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 ok 5 - The object isa Bio::AlignIO ok 6 - The object isa Bio::Align::AlignI ok 7 - po output test ok 8 - The object isa Bio::AlignIO ok 9 - The object isa Bio::Align::AlignI ok 10 ok 11 ok t/AlignIO/prodom.t ........................... 1..3 ok 1 - use Bio::AlignIO::prodom; ok 2 - The object isa Bio::Align::AlignI ok 3 - prodom input test ok t/AlignIO/psi.t .............................. 1..5 ok 1 - use Bio::AlignIO::psi; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 ok 5 ok t/AlignIO/selex.t ............................ 1..4 ok 1 - use Bio::AlignIO::selex; ok 2 - The object isa Bio::Align::AlignI ok 3 - selex format test ok 4 - selex output test ok t/AlignIO/stockholm.t ........................ 1..83 ok 1 - use Bio::AlignIO::stockholm; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 - The object isa Bio::Annotation::Comment ok 10 - Stockholm annotation ok 11 - Stockholm annotation ok 12 - stockholm output test ok 13 - The object isa Bio::Align::AlignI ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 - Stockholm annotation isa Bio::Annotation::Reference ok 21 - Stockholm annotation ok 22 - Stockholm annotation ok 23 - Stockholm annotation ok 24 - Stockholm annotation ok 25 - The object isa Bio::Seq::MetaI ok 26 - Rfam meta data ok 27 - Rfam meta data ok 28 ok 29 - The object isa Bio::Align::AlignI ok 30 ok 31 ok 32 ok 33 ok 34 - The object isa Bio::Seq::MetaI ok 35 - Rfam meta data ok 36 - Rfam meta data ok 37 - The object isa Bio::AlignIO ok 38 ok 39 - The object isa Bio::Align::AlignI ok 40 ok 41 ok 42 ok 43 ok 44 - The object isa Bio::Annotation::SimpleValue ok 45 - Pfam annotation ok 46 ok 47 - The object isa Bio::Align::AlignI ok 48 ok 49 ok 50 ok 51 ok 52 - The object isa Bio::Align::AlignI ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 - The object isa Bio::Seq::MetaI ok 59 - Pfam aln meta data ok 60 - Pfam aln meta data ok 61 - Pfam aln meta data ok 62 - Pfam aln meta data ok 63 - Pfam aln meta data ok 64 - Pfam aln meta data ok 65 - Pfam seq meta data ok 66 - Pfam seq meta data ok 67 - Pfam seq meta data ok 68 - Pfam seq meta data ok 69 ok 70 - The object isa Bio::SeqFeatureI ok 71 - The object isa Bio::Seq::Meta ok 72 - The object isa Bio::AnnotationI ok 73 - The object isa Bio::Annotation::DBLink ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok t/AlignIO/xmfa.t ............................. 1..16 ok 1 - use Bio::AlignIO::xmfa; ok 2 - The object isa Bio::Align::AlignI ok 3 - xmfa input test ok 4 - xmfa input test for description ok 5 - xmfa input test for id ok 6 - xmfa input test for end ok 7 - xmfa input test for end ok 8 - xmfa alignment score ok 9 - The object isa Bio::Align::AlignI ok 10 - xmfa input test ok 11 - xmfa input test for description ok 12 - xmfa input test for id ok 13 - xmfa input test for end ok 14 - xmfa input test for end ok 15 - xmfa alignment score ok 16 - xmfa output test ok t/Alphabet.t ................................. 1..100 ok 1 - use Bio::Symbol::Alphabet; ok 2 - use Bio::Symbol::Symbol; ok 3 - use Bio::Symbol::DNAAlphabet; ok 4 - use Bio::Symbol::ProteinAlphabet; ok 5 - The object isa Bio::Symbol::Alphabet ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 - The object isa Bio::Symbol::AlphabetI ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 - The object isa Bio::Symbol::AlphabetI ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok t/Annotation/Annotation.t .................... 1..158 ok 1 - use Bio::Annotation::Collection; ok 2 - use Bio::Annotation::DBLink; ok 3 - use Bio::Annotation::Comment; ok 4 - use Bio::Annotation::Reference; ok 5 - use Bio::Annotation::SimpleValue; ok 6 - use Bio::Annotation::Target; ok 7 - use Bio::Annotation::AnnotationFactory; ok 8 - use Bio::Annotation::StructuredValue; ok 9 - use Bio::Annotation::TagTree; ok 10 - use Bio::Annotation::Tree; ok 11 - use Bio::Seq; ok 12 - use Bio::SimpleAlign; ok 13 - use Bio::Cluster::UniGene; ok 14 - The object isa Bio::AnnotationI ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 - The object isa Bio::AnnotationI ok 22 ok 23 ok 24 ok 25 - The object isa Bio::AnnotationCollectionI ok 26 ok 27 ok 28 - The object isa Bio::AnnotationI ok 29 ok 30 - The object isa Bio::AnnotationI ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 - The object isa Bio::AnnotationI ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 - The object isa Bio::AnnotationCollectionI ok 69 ok 70 ok 71 ok 72 ok 73 - The object isa Bio::Annotation::StructuredValue ok 74 ok 75 ok 76 ok 77 ok 78 - use Bio::Annotation::OntologyTerm; ok 79 - The object isa Bio::Ontology::Term ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 - The object isa Bio::AnnotatableI ok 86 - isa SeqFeatureI isa Bio::SeqFeatureI ok 87 - isa AnnotatableI isa Bio::AnnotatableI ok 88 - isa SeqFeatureI isa Bio::SeqFeatureI ok 89 - isa AnnotatableI isa Bio::AnnotatableI ok 90 - The object isa Bio::AnnotatableI ok 91 - The object isa Bio::AnnotatableI ok 92 - The object isa Bio::Factory::ObjectFactoryI ok 93 - The object isa Bio::Annotation::SimpleValue ok 94 ok 95 - The object isa Bio::Annotation::OntologyTerm ok 96 - Bio::Annotation::Comment ok 97 - The object isa Bio::Annotation::Comment ok 98 ok 99 - Bio::Annotation::Comment ok 100 - The object isa Bio::Annotation::Comment ok 101 - Bio::Annotation::Comment ok 102 - The object isa Bio::Annotation::Comment ok 103 ok 104 - The object isa Bio::Annotation::Target ok 105 ok 106 ok 107 - The object isa Bio::AnnotationI ok 108 - tree_id() ok 109 - tagname() ok 110 - The object isa Bio::AnnotatableI ok 111 - add tree to AlignI ok 112 - get seq from node id ok 113 ok 114 - The object isa Bio::Annotation::Tree ok 115 - The object isa Bio::AnnotationI ok 116 - default itext ok 117 - roundtrip ok 118 - itext ok 119 - spxr ok 120 - indent ok 121 - xml ok 122 - The object isa Data::Stag::StagI ok 123 ok 124 - child changes ok 125 - The object isa Data::Stag::StagI ok 126 ok 127 - child changes ok 128 - The object isa Data::Stag::StagI ok 129 ok 130 - child changes ok 131 - child changes in parent node ok 132 - no tags ok 133 - before Stag node ok 134 - after Stag node ok 135 - both stag nodes ok 136 - different instances ok 137 - before TagTree ok 138 - after TagTree ok 139 - both stag nodes ok 140 - different instances ok 141 - before TagTree ok 142 - after TagTree ok 143 - stag nodes ok 144 - same instance ok 145 - before TagTree ok 146 - after TagTree ok 147 - stag nodes ok 148 - different instance ok 149 - The object isa Bio::AnnotationI ok 150 - The object isa Data::Stag::StagI ok 151 - child changes ok 152 - The object isa Data::Stag::StagI ok 153 - child changes ok 154 - The object isa Data::Stag::StagI ok 155 - child changes ok 156 ok 157 ok 158 - The object isa Bio::Annotation::TagTree ok t/Annotation/AnnotationAdaptor.t ............. 1..23 ok 1 - use Bio::SeqFeature::Generic; ok 2 - use Bio::SeqFeature::AnnotationAdaptor; ok 3 - use Bio::Annotation::DBLink; ok 4 - use Bio::Annotation::Comment; ok 5 - use Bio::Annotation::SimpleValue; ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok t/Assembly/Assembly.t ........................ skipped: The optional module DB_File (or dependencies thereof) was not installed Bio::Assembly::IO: could not load tigr - for more details on supported formats please see the Assembly::IO docs Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::Assembly::IO::tigr. Can't locate DB_File.pm in @INC (@INC contains: . /export/home/fly1003/var/cpan/build/BioPerl-1.6.1-RKMIUZ/blib/lib /export/home/fly1003/var/cpan/build/BioPerl-1.6.1-RKMIUZ/blib/arch /export/home/fly1003/var/cpan/build/BioPerl-1.6.1-RKMIUZ /export/home/fly1003/var/megalib /export/home/fly1003/ap1003/site/lib /export/home/fly1003/ap1003/lib) at Bio/SeqFeature/Collection.pm line 147. BEGIN failed--compilation aborted at Bio/SeqFeature/Collection.pm line 147. Compilation failed in require at Bio/Assembly/Contig.pm line 223. BEGIN failed--compilation aborted at Bio/Assembly/Contig.pm line 223. Compilation failed in require at Bio/Assembly/IO/tigr.pm line 236. BEGIN failed--compilation aborted at Bio/Assembly/IO/tigr.pm line 236. Compilation failed in require at Bio/Root/Root.pm line 439. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441 STACK: Bio::Assembly::IO::_load_format_module Bio/Assembly/IO.pm:192 STACK: Bio::Assembly::IO::new Bio/Assembly/IO.pm:133 STACK: t/Assembly/ContigSpectrum.t:11 ----------------------------------------------------------- # Failed test 'The thing isa Bio::Assembly::IO' # at t/Assembly/ContigSpectrum.t line 15. # The thing isn't defined Can't call method "next_assembly" on an undefined value at t/Assembly/ContigSpectrum.t line 16. # Looks like you planned 134 tests but ran 3. # Looks like you failed 1 test of 3 run. # Looks like your test exited with 2 just after 3. t/Assembly/ContigSpectrum.t .................. 1..134 ok 1 - use Bio::Assembly::IO; ok 2 - use Bio::Assembly::Tools::ContigSpectrum; not ok 3 - The thing isa Bio::Assembly::IO Dubious, test returned 2 (wstat 512, 0x200) Failed 132/134 subtests t/Biblio/Biblio.t ............................ 1..24 ok 1 - use Bio::Biblio; ok 2 - use Bio::Biblio::IO; ok 3 ok 4 ok 5 - citation 1 ok 6 - citation 2 ok 7 - citation 3 ok 8 - in callback ok 9 - in callback ok 10 - in callback ok 11 - calling callback ok 12 - citation 1 ok 13 - citation 2 ok 14 - citation 1 ok 15 - citation 2 ok 16 ok 17 - citation 1 ok 18 - citation 2 ok 19 - citation 3 ok 20 - citation 4 ok 21 - filehandle test ok 22 - filehandle test ok 23 - filehandle test ok 24 - filehandle test ok t/Biblio/References.t ........................ 1..537 ok 1 - use Bio::Biblio::Article; ok 2 - use Bio::Biblio::Book; ok 3 - use Bio::Biblio::BookArticle; ok 4 - use Bio::Biblio::Journal; ok 5 - use Bio::Biblio::JournalArticle; ok 6 - use Bio::Biblio::MedlineArticle; ok 7 - use Bio::Biblio::MedlineBook; ok 8 - use Bio::Biblio::MedlineBookArticle; ok 9 - use Bio::Biblio::MedlineJournal; ok 10 - use Bio::Biblio::MedlineJournalArticle; ok 11 - use Bio::Biblio::Organisation; ok 12 - use Bio::Biblio::Patent; ok 13 - use Bio::Biblio::Person; ok 14 - use Bio::Biblio::Proceeding; ok 15 - use Bio::Biblio::Provider; ok 16 - use Bio::Biblio::Ref; ok 17 - use Bio::Biblio::Service; ok 18 - use Bio::Biblio::TechReport; ok 19 - use Bio::Biblio::Thesis; ok 20 - use Bio::Biblio::WebResource; ok 21 - use Bio::Biblio::PubmedArticle; ok 22 - use Bio::Biblio::PubmedBookArticle; ok 23 - use Bio::Biblio::PubmedJournalArticle; ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 - set 'abstract' ok 48 - get 'abstract' ok 49 - set 'abstract_language' ok 50 - get 'abstract_language' ok 51 - set 'abstract_type' ok 52 - get 'abstract_type' ok 53 - set 'author_list_complete' ok 54 - get 'author_list_complete' ok 55 - set 'cross_references_list_complete' ok 56 - get 'cross_references_list_complete' ok 57 - set 'date' ok 58 - get 'date' ok 59 - set 'date_completed' ok 60 - get 'date_completed' ok 61 - set 'date_created' ok 62 - get 'date_created' ok 63 - set 'date_revised' ok 64 - get 'date_revised' ok 65 - set 'format' ok 66 - get 'format' ok 67 - set 'identifier' ok 68 - get 'identifier' ok 69 - set 'language' ok 70 - get 'language' ok 71 - set 'last_modified_date' ok 72 - get 'last_modified_date' ok 73 - set 'repository_subset' ok 74 - get 'repository_subset' ok 75 - set 'rights' ok 76 - get 'rights' ok 77 - set 'spatial_location' ok 78 - get 'spatial_location' ok 79 - set 'subject_headings_source' ok 80 - get 'subject_headings_source' ok 81 - set 'temporal_period' ok 82 - get 'temporal_period' ok 83 - set 'title' ok 84 - get 'title' ok 85 - set 'toc' ok 86 - get 'toc' ok 87 - set 'toc_type' ok 88 - get 'toc_type' ok 89 - set 'type' ok 90 - get 'type' ok 91 - set 'first_page' ok 92 - get 'first_page' ok 93 - set 'last_page' ok 94 - get 'last_page' ok 95 - set 'issue' ok 96 - get 'issue' ok 97 - set 'issue_supplement' ok 98 - get 'issue_supplement' ok 99 - set 'volume' ok 100 - get 'volume' ok 101 - set 'affiliation' ok 102 - get 'affiliation' ok 103 - set 'citation_owner' ok 104 - get 'citation_owner' ok 105 - set 'date_of_electronic_publication' ok 106 - get 'date_of_electronic_publication' ok 107 - set 'gene_symbols' ok 108 - get 'gene_symbols' ok 109 - set 'grant_list_complete' ok 110 - get 'grant_list_complete' ok 111 - set 'medline_date' ok 112 - get 'medline_date' ok 113 - set 'medline_id' ok 114 - get 'medline_id' ok 115 - set 'medline_page' ok 116 - get 'medline_page' ok 117 - set 'number_of_references' ok 118 - get 'number_of_references' ok 119 - set 'other_languages' ok 120 - get 'other_languages' ok 121 - set 'pmid' ok 122 - get 'pmid' ok 123 - set 'season' ok 124 - get 'season' ok 125 - set 'status' ok 126 - get 'status' ok 127 - set 'vernacular_title' ok 128 - get 'vernacular_title' ok 129 ok 130 - abstract ok 131 - abstract_language ok 132 - abstract_type ok 133 - author_list_complete ok 134 - cross_references_list_complete ok 135 - date ok 136 - date_completed ok 137 - date_created ok 138 - date_revised ok 139 - format ok 140 - identifier ok 141 - language ok 142 - last_modified_date ok 143 - repository_subset ok 144 - rights ok 145 - spatial_location ok 146 - subject_headings_source ok 147 - temporal_period ok 148 - title ok 149 - toc ok 150 - toc_type ok 151 - type ok 152 - first_page ok 153 - last_page ok 154 - issue ok 155 - issue_supplement ok 156 - volume ok 157 - affiliation ok 158 - citation_owner ok 159 - date_of_electronic_publication ok 160 - gene_symbols ok 161 - grant_list_complete ok 162 - medline_date ok 163 - medline_id ok 164 - medline_page ok 165 - number_of_references ok 166 - other_languages ok 167 - pmid ok 168 - season ok 169 - status ok 170 - vernacular_title ok 171 - get 'authors' ok 172 - get 'cross_references' ok 173 - get 'codes' ok 174 - get 'contributors' ok 175 - get 'keywords' ok 176 - get 'publisher' ok 177 - get 'subject_headings' ok 178 - get 'journal' ok 179 - get 'chemicals' ok 180 - get 'comment_ins' ok 181 - get 'comment_ons' ok 182 - get 'erratum_fors' ok 183 - get 'erratum_ins' ok 184 - get 'general_notes' ok 185 - get 'grants' ok 186 - get 'mesh_headings' ok 187 - get 'original_report_ins' ok 188 - get 'other_abstracts' ok 189 - get 'other_ids' ok 190 - get 'republished_froms' ok 191 - get 'republished_ins' ok 192 - get 'retraction_ins' ok 193 - get 'retraction_ofs' ok 194 - get 'summary_for_patients_ins' ok 195 - get 'update_ins' ok 196 - get 'update_ofs' ok 197 - get 'journal' ok 198 - add_author 1 ok 199 - add_author 2 ok 200 - get authors ok 201 - add_contributor 1 ok 202 - add_contributor 2 ok 203 - get contributors ok 204 - add_cross_reference 1 ok 205 - add_cross_reference 2 ok 206 - get cross_references ok 207 - get cross_references ok 208 - set 'abstract' ok 209 - get 'abstract' ok 210 - set 'abstract_language' ok 211 - get 'abstract_language' ok 212 - set 'abstract_type' ok 213 - get 'abstract_type' ok 214 - set 'author_list_complete' ok 215 - get 'author_list_complete' ok 216 - set 'cross_references_list_complete' ok 217 - get 'cross_references_list_complete' ok 218 - set 'date' ok 219 - get 'date' ok 220 - set 'date_completed' ok 221 - get 'date_completed' ok 222 - set 'date_created' ok 223 - get 'date_created' ok 224 - set 'date_revised' ok 225 - get 'date_revised' ok 226 - set 'format' ok 227 - get 'format' ok 228 - set 'identifier' ok 229 - get 'identifier' ok 230 - set 'language' ok 231 - get 'language' ok 232 - set 'last_modified_date' ok 233 - get 'last_modified_date' ok 234 - set 'repository_subset' ok 235 - get 'repository_subset' ok 236 - set 'rights' ok 237 - get 'rights' ok 238 - set 'spatial_location' ok 239 - get 'spatial_location' ok 240 - set 'subject_headings_source' ok 241 - get 'subject_headings_source' ok 242 - set 'temporal_period' ok 243 - get 'temporal_period' ok 244 - set 'title' ok 245 - get 'title' ok 246 - set 'toc' ok 247 - get 'toc' ok 248 - set 'toc_type' ok 249 - get 'toc_type' ok 250 - set 'type' ok 251 - get 'type' ok 252 - set 'first_page' ok 253 - get 'first_page' ok 254 - set 'last_page' ok 255 - get 'last_page' ok 256 - set 'affiliation' ok 257 - get 'affiliation' ok 258 - set 'citation_owner' ok 259 - get 'citation_owner' ok 260 - set 'date_of_electronic_publication' ok 261 - get 'date_of_electronic_publication' ok 262 - set 'gene_symbols' ok 263 - get 'gene_symbols' ok 264 - set 'grant_list_complete' ok 265 - get 'grant_list_complete' ok 266 - set 'medline_date' ok 267 - get 'medline_date' ok 268 - set 'medline_id' ok 269 - get 'medline_id' ok 270 - set 'medline_page' ok 271 - get 'medline_page' ok 272 - set 'number_of_references' ok 273 - get 'number_of_references' ok 274 - set 'other_languages' ok 275 - get 'other_languages' ok 276 - set 'pmid' ok 277 - get 'pmid' ok 278 - set 'season' ok 279 - get 'season' ok 280 - set 'status' ok 281 - get 'status' ok 282 - set 'vernacular_title' ok 283 - get 'vernacular_title' ok 284 ok 285 - abstract ok 286 - abstract_language ok 287 - abstract_type ok 288 - author_list_complete ok 289 - cross_references_list_complete ok 290 - date ok 291 - date_completed ok 292 - date_created ok 293 - date_revised ok 294 - format ok 295 - identifier ok 296 - language ok 297 - last_modified_date ok 298 - repository_subset ok 299 - rights ok 300 - spatial_location ok 301 - subject_headings_source ok 302 - temporal_period ok 303 - title ok 304 - toc ok 305 - toc_type ok 306 - type ok 307 - first_page ok 308 - last_page ok 309 - affiliation ok 310 - citation_owner ok 311 - date_of_electronic_publication ok 312 - gene_symbols ok 313 - grant_list_complete ok 314 - medline_date ok 315 - medline_id ok 316 - medline_page ok 317 - number_of_references ok 318 - other_languages ok 319 - pmid ok 320 - season ok 321 - status ok 322 - vernacular_title ok 323 - get 'authors' ok 324 - get 'cross_references' ok 325 - get 'codes' ok 326 - get 'contributors' ok 327 - get 'keywords' ok 328 - get 'publisher' ok 329 - get 'subject_headings' ok 330 - get 'book' ok 331 - get 'chemicals' ok 332 - get 'comment_ins' ok 333 - get 'comment_ons' ok 334 - get 'erratum_fors' ok 335 - get 'erratum_ins' ok 336 - get 'general_notes' ok 337 - get 'grants' ok 338 - get 'mesh_headings' ok 339 - get 'original_report_ins' ok 340 - get 'other_abstracts' ok 341 - get 'other_ids' ok 342 - get 'republished_froms' ok 343 - get 'republished_ins' ok 344 - get 'retraction_ins' ok 345 - get 'retraction_ofs' ok 346 - get 'summary_for_patients_ins' ok 347 - get 'update_ins' ok 348 - get 'update_ofs' ok 349 - get 'book' ok 350 - set 'abstract' ok 351 - get 'abstract' ok 352 - set 'abstract_language' ok 353 - get 'abstract_language' ok 354 - set 'abstract_type' ok 355 - get 'abstract_type' ok 356 - set 'author_list_complete' ok 357 - get 'author_list_complete' ok 358 - set 'cross_references_list_complete' ok 359 - get 'cross_references_list_complete' ok 360 - set 'date' ok 361 - get 'date' ok 362 - set 'date_completed' ok 363 - get 'date_completed' ok 364 - set 'date_created' ok 365 - get 'date_created' ok 366 - set 'date_revised' ok 367 - get 'date_revised' ok 368 - set 'format' ok 369 - get 'format' ok 370 - set 'identifier' ok 371 - get 'identifier' ok 372 - set 'language' ok 373 - get 'language' ok 374 - set 'last_modified_date' ok 375 - get 'last_modified_date' ok 376 - set 'repository_subset' ok 377 - get 'repository_subset' ok 378 - set 'rights' ok 379 - get 'rights' ok 380 - set 'spatial_location' ok 381 - get 'spatial_location' ok 382 - set 'subject_headings_source' ok 383 - get 'subject_headings_source' ok 384 - set 'temporal_period' ok 385 - get 'temporal_period' ok 386 - set 'title' ok 387 - get 'title' ok 388 - set 'toc' ok 389 - get 'toc' ok 390 - set 'toc_type' ok 391 - get 'toc_type' ok 392 - set 'type' ok 393 - get 'type' ok 394 - set 'edition' ok 395 - get 'edition' ok 396 - set 'isbn' ok 397 - get 'isbn' ok 398 - set 'series' ok 399 - get 'series' ok 400 - set 'volume' ok 401 - get 'volume' ok 402 ok 403 - abstract ok 404 - abstract_language ok 405 - abstract_type ok 406 - author_list_complete ok 407 - cross_references_list_complete ok 408 - date ok 409 - date_completed ok 410 - date_created ok 411 - date_revised ok 412 - format ok 413 - identifier ok 414 - language ok 415 - last_modified_date ok 416 - repository_subset ok 417 - rights ok 418 - spatial_location ok 419 - subject_headings_source ok 420 - temporal_period ok 421 - title ok 422 - toc ok 423 - toc_type ok 424 - type ok 425 - edition ok 426 - isbn ok 427 - series ok 428 - volume ok 429 - get 'authors' ok 430 - get 'cross_references' ok 431 - get 'codes' ok 432 - get 'contributors' ok 433 - get 'keywords' ok 434 - get 'publisher' ok 435 - get 'subject_headings' ok 436 - get 'editor' ok 437 - set 'abbreviation' ok 438 - get 'abbreviation' ok 439 - set 'issn' ok 440 - get 'issn' ok 441 - set 'name' ok 442 - get 'name' ok 443 - set 'coden' ok 444 - get 'coden' ok 445 - set 'country' ok 446 - get 'country' ok 447 - set 'medline_code' ok 448 - get 'medline_code' ok 449 - set 'medline_ta' ok 450 - get 'medline_ta' ok 451 - set 'nlm_unique_id' ok 452 - get 'nlm_unique_id' ok 453 ok 454 - abbreviation ok 455 - issn ok 456 - name ok 457 - coden ok 458 - country ok 459 - medline_code ok 460 - medline_ta ok 461 - nlm_unique_id ok 462 - set 'doc_number' ok 463 - get 'doc_number' ok 464 - set 'doc_office' ok 465 - get 'doc_office' ok 466 - set 'doc_type' ok 467 - get 'doc_type' ok 468 ok 469 - doc_number ok 470 - doc_office ok 471 - doc_type ok 472 - get 'applicants' ok 473 - set 'url' ok 474 - get 'url' ok 475 - set 'estimated_size' ok 476 - get 'estimated_size' ok 477 - set 'cost' ok 478 - get 'cost' ok 479 ok 480 - url ok 481 - estimated_size ok 482 - cost ok 483 - set 'type' ok 484 - get 'type' ok 485 - set 'affiliation' ok 486 - get 'affiliation' ok 487 - set 'email' ok 488 - get 'email' ok 489 - set 'firstname' ok 490 - get 'firstname' ok 491 - set 'forename' ok 492 - get 'forename' ok 493 - set 'initials' ok 494 - get 'initials' ok 495 - set 'lastname' ok 496 - get 'lastname' ok 497 - set 'middlename' ok 498 - get 'middlename' ok 499 - set 'postal_address' ok 500 - get 'postal_address' ok 501 - set 'suffix' ok 502 - get 'suffix' ok 503 ok 504 - type ok 505 - affiliation ok 506 - email ok 507 - firstname ok 508 - forename ok 509 - initials ok 510 - lastname ok 511 - middlename ok 512 - postal_address ok 513 - suffix ok 514 - set 'type' ok 515 - get 'type' ok 516 - set 'name' ok 517 - get 'name' ok 518 ok 519 - type ok 520 - name ok 521 - set 'type' ok 522 - get 'type' ok 523 - set 'name' ok 524 - get 'name' ok 525 ok 526 - type ok 527 - name ok 528 - set 'pubmed_status' ok 529 - get 'pubmed_status' ok 530 - set 'pubmed_provider_id' ok 531 - get 'pubmed_provider_id' ok 532 ok 533 - pubmed_status ok 534 - pubmed_provider_id ok 535 - get 'pubmed_history_list' ok 536 - get 'pubmed_article_id_list' ok 537 - get 'pubmed_url_list' 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 ...................... 1..12 ok 1 - use Bio::ClusterIO; ok 2 - use Bio::Cluster::ClusterFactory; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 - The object isa Bio::Cluster::UniGeneI ok 12 - The object isa Bio::Cluster::UniGeneI ok t/ClusterIO/SequenceFamily.t ................. 1..19 ok 1 - use Bio::SeqIO; ok 2 - use Bio::Cluster::SequenceFamily; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok t/ClusterIO/unigene.t ........................ 1..73 ok 1 - use Bio::ClusterIO; ok 2 - new Bio::ClusterIO object defined ok 3 ok 4 - The object isa Bio::Cluster::UniGeneI ok 5 - The object isa Bio::ClusterI ok 6 - The object isa Bio::IdentifiableI ok 7 - The object isa Bio::DescribableI ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 - The object isa Bio::PrimarySeqI ok 49 ok 50 ok 51 - annotation object defined ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 - The object isa Bio::PrimarySeqI ok 67 ok 68 - next cluster ok 69 ok 70 ok 71 ok 72 ok 73 ok t/Coordinate/CoordinateGraph.t ............... 1..7 ok 1 - use Bio::Coordinate::Graph; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok t/Coordinate/CoordinateMapper.t .............. 1..175 ok 1 - use Bio::Location::Simple; ok 2 - use Bio::Coordinate::Pair; ok 3 - use Bio::Coordinate::Result::Match; ok 4 - use Bio::Coordinate::Result::Gap; ok 5 - use Bio::Coordinate::Chain; ok 6 - use Bio::Coordinate::Collection; ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - The object isa Bio::Coordinate::Result ok 15 - The object isa Bio::Location::SplitLocationI ok 16 ok 17 ok 18 ok 19 - The object isa Bio::LocationI ok 20 - The object isa Bio::Coordinate::Result::Match ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 - The object isa Bio::Coordinate::Result::Gap ok 38 - The object isa Bio::LocationI ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 - The object isa Bio::Coordinate::Result::Match ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 - Match: |314696| Test: 314696| ok 139 ok 140 ok 141 ok 142 - Match: |341| Test: 341| ok 143 ok 144 ok 145 ok 146 - Match: |315843| Test: 315843| ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 - Match: |627011| Test: 627011| ok 153 ok 154 ok 155 ok 156 - Match: |chr1| Test: chr1| ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok t/Coordinate/GeneCoordinateMapper.t .......... 1..116 ok 1 - use Bio::Location::Simple; ok 2 - use Bio::Coordinate::Pair; ok 3 - use Bio::Coordinate::ExtrapolatingPair; ok 4 - use Bio::Coordinate::GeneMapper; ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - The object isa Bio::Location::Simple ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 - The object isa Bio::Location::Simple ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok t/LiveSeq/Chain.t ............................ 1..45 ok 1 - use Bio::LiveSeq::Chain; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok t/LiveSeq/LiveSeq.t .......................... 1..48 ok 1 - use Bio::LiveSeq::IO::BioPerl; ok 2 ok 3 ok 4 - Bio::LiveSeq::Gene ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok t/LiveSeq/Mutation.t ......................... 1..19 ok 1 - use Bio::LiveSeq::Mutation; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok t/LiveSeq/Mutator.t .......................... 1..24 ok 1 - use Bio::LiveSeq::Mutator; ok 2 - use Bio::LiveSeq::IO::BioPerl; ok 3 - use Bio::Variation::IO; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok t/LocalDB/BioDBGFF.t ......................... 1..279 ok 1 - use Bio::DB::GFF; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 # skip fetch_feature_by_gid() not implemented by this adaptor ok 104 # skip fetch_feature_by_gid() not implemented by this adaptor ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 # skip delete_groups() not implemented by this adaptor ok 135 # skip delete_groups() not implemented by this adaptor ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 ok 156 ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok 176 ok 177 ok 178 ok 179 ok 180 ok 181 ok 182 ok 183 ok 184 ok 185 ok 186 ok 187 ok 188 ok 189 ok 190 ok 191 ok 192 ok 193 ok 194 ok 195 ok 196 ok 197 ok 198 ok 199 ok 200 ok 201 ok 202 ok 203 ok 204 ok 205 ok 206 ok 207 ok 208 ok 209 ok 210 ok 211 ok 212 ok 213 ok 214 ok 215 ok 216 ok 217 ok 218 ok 219 ok 220 ok 221 ok 222 ok 223 ok 224 ok 225 ok 226 ok 227 ok 228 ok 229 ok 230 ok 231 ok 232 ok 233 ok 234 ok 235 ok 236 ok 237 ok 238 ok 239 ok 240 ok 241 ok 242 # skip fetch_feature_by_gid() not implemented by this adaptor ok 243 # skip fetch_feature_by_gid() not implemented by this adaptor ok 244 ok 245 ok 246 ok 247 ok 248 ok 249 ok 250 # skip preferred groups are not supported by gff3 ok 251 # skip preferred groups are not supported by gff3 ok 252 # skip preferred groups are not supported by gff3 ok 253 ok 254 ok 255 ok 256 ok 257 ok 258 ok 259 ok 260 ok 261 ok 262 ok 263 ok 264 ok 265 ok 266 ok 267 ok 268 ok 269 ok 270 ok 271 ok 272 ok 273 # skip delete_groups() not implemented by this adaptor ok 274 # skip delete_groups() not implemented by this adaptor ok 275 ok 276 ok 277 ok 278 ok 279 ok t/LocalDB/BlastIndex.t ....................... 1..26 ok 1 - use Cwd; ok 2 - use Bio::SearchIO; ok 3 - use Bio::Index::Blast; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok AnyDBM_File doesn't define an EXISTS method at Bio/DB/Fasta.pm line 617 # Looks like you planned 15 tests but ran 6. # Looks like your test exited with 9 just after 6. t/LocalDB/DBFasta.t .......................... 1..15 ok 1 - use Bio::Root::IO; ok 2 - use File::Copy; ok 3 ok 4 ok 5 ok 6 Dubious, test returned 9 (wstat 2304, 0x900) Failed 9/15 subtests AnyDBM_File doesn't define an EXISTS method at Bio/DB/Qual.pm line 585 # Looks like you planned 38 tests but ran 11. # Looks like your test exited with 9 just after 11. t/LocalDB/DBQual.t ........................... 1..38 ok 1 - use Bio::Root::IO; ok 2 - use File::Copy; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 Dubious, test returned 9 (wstat 2304, 0x900) Failed 27/38 subtests t/LocalDB/Flat.t ............................. skipped: The optional module DB_File (or dependencies thereof) was not installed t/LocalDB/Index.t ............................ skipped: The optional module DB_File (or dependencies thereof) was not installed t/LocalDB/Registry.t ......................... 1..14 ok 1 - use Bio::DB::Registry; ok 2 - use Bio::DB::Flat; ok 3 ok 4 # skip The optional module DB_File (or dependencies thereof) was not installed ok 5 # skip The optional module DB_File (or dependencies thereof) was not installed ok 6 # skip Network tests have not been requested ok 7 # skip Network tests have not been requested ok 8 # skip Network tests have not been requested ok 9 # skip Network tests have not been requested ok 10 # skip Network tests have not been requested ok 11 # skip Network tests have not been requested ok 12 # skip Network tests have not been requested ok 13 # skip Network tests have not been requested ok 14 # skip Network tests have not been requested ok # Failed test 'use Bio::DB::SeqFeature::Store::GFF3Loader;' # at t/LocalDB/SeqFeature.t line 17. # Tried to use 'Bio::DB::SeqFeature::Store::GFF3Loader'. # Error: Can't locate DB_File.pm in @INC (@INC contains: . /home/lstein/projects/bioperl-live /export/home/fly1003/var/cpan/build/BioPerl-1.6.1-RKMIUZ/blib/lib /export/home/fly1003/var/cpan/build/BioPerl-1.6.1-RKMIUZ/blib/arch /export/home/fly1003/var/cpan/build/BioPerl-1.6.1-RKMIUZ /export/home/fly1003/var/megalib /export/home/fly1003/ap1003/site/lib /export/home/fly1003/ap1003/lib) at Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. # Compilation failed in require at Bio/DB/SeqFeature/Store/GFF3Loader.pm line 73. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/GFF3Loader.pm line 73. # Compilation failed in require at (eval 48) line 2. # BEGIN failed--compilation aborted at (eval 48) line 2. # Looks like you failed 1 test of 69. t/LocalDB/SeqFeature.t ....................... 1..69 ok 1 - use Bio::DB::SeqFeature::Store; not ok 2 - use Bio::DB::SeqFeature::Store::GFF3Loader; ok 3 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 4 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 5 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 6 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 7 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 8 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 9 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 10 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 11 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 12 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 13 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 14 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 15 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 16 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 17 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 18 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 19 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 20 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 21 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 22 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 23 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 24 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 25 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 26 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 27 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 28 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 29 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 30 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 31 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 32 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 33 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 34 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 35 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 36 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 37 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 38 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 39 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 40 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 41 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 42 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 43 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 44 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 45 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 46 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 47 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 48 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 49 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 50 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 51 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 52 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 53 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 54 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 55 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 56 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 57 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 58 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 59 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 60 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 61 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 62 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 63 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 64 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 65 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 66 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 67 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 68 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # ok 69 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126. # Compilation failed in require at (eval 49) line 3. # at t/LocalDB/SeqFeature.t line 28 # Dubious, test returned 1 (wstat 256, 0x100) Failed 1/69 subtests (less 67 skipped subtests: 1 okay) ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't locate DB_File.pm in @INC (@INC contains: . /export/home/fly1003/var/cpan/build/BioPerl-1.6.1-RKMIUZ/blib/lib /export/home/fly1003/var/cpan/build/BioPerl-1.6.1-RKMIUZ/blib/arch /export/home/fly1003/var/cpan/build/BioPerl-1.6.1-RKMIUZ /export/home/fly1003/var/megalib /export/home/fly1003/ap1003/site/lib /export/home/fly1003/ap1003/lib) at Bio/DB/Taxonomy/flatfile.pm line 90. BEGIN failed--compilation aborted at Bio/DB/Taxonomy/flatfile.pm line 90. Compilation failed in require at Bio/Root/Root.pm line 439. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441 STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:264 STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:115 STACK: t/LocalDB/transfac_pro.t:18 ----------------------------------------------------------- Bio::DB::Taxonomy: flatfile cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't locate DB_File.pm in @INC (@INC contains: . /export/home/fly1003/var/cpan/build/BioPerl-1.6.1-RKMIUZ/blib/lib /export/home/fly1003/var/cpan/build/BioPerl-1.6.1-RKMIUZ/blib/arch /export/home/fly1003/var/cpan/build/BioPerl-1.6.1-RKMIUZ /export/home/fly1003/var/megalib /export/home/fly1003/ap1003/site/lib /export/home/fly1003/ap1003/lib) at Bio/DB/Taxonomy/flatfile.pm line 90. BEGIN failed--compilation aborted at Bio/DB/Taxonomy/flatfile.pm line 90. Compilation failed in require at Bio/Root/Root.pm line 439. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441 STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:264 STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:115 STACK: t/LocalDB/transfac_pro.t:18 ----------------------------------------------------------- For more information about the Bio::DB::Taxonomy system please see the Bio::DB::Taxonomy docs. This includes ways of checking for formats at compile time, not run time. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::DB::TFBS::transfac_pro. Can't locate DB_File.pm in @INC (@INC contains: . /export/home/fly1003/var/cpan/build/BioPerl-1.6.1-RKMIUZ/blib/lib /export/home/fly1003/var/cpan/build/BioPerl-1.6.1-RKMIUZ/blib/arch /export/home/fly1003/var/cpan/build/BioPerl-1.6.1-RKMIUZ /export/home/fly1003/var/megalib /export/home/fly1003/ap1003/site/lib /export/home/fly1003/ap1003/lib) at Bio/DB/TFBS/transfac_pro.pm line 118. BEGIN failed--compilation aborted at Bio/DB/TFBS/transfac_pro.pm line 118. Compilation failed in require at Bio/Root/Root.pm line 439. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441 STACK: Bio::DB::TFBS::_load_tax_module Bio/DB/TFBS.pm:151 STACK: Bio::DB::TFBS::new Bio/DB/TFBS.pm:130 STACK: t/LocalDB/transfac_pro.t:25 ----------------------------------------------------------- Bio::DB::TFBS: transfac_pro cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::DB::TFBS::transfac_pro. Can't locate DB_File.pm in @INC (@INC contains: . /export/home/fly1003/var/cpan/build/BioPerl-1.6.1-RKMIUZ/blib/lib /export/home/fly1003/var/cpan/build/BioPerl-1.6.1-RKMIUZ/blib/arch /export/home/fly1003/var/cpan/build/BioPerl-1.6.1-RKMIUZ /export/home/fly1003/var/megalib /export/home/fly1003/ap1003/site/lib /export/home/fly1003/ap1003/lib) at Bio/DB/TFBS/transfac_pro.pm line 118. BEGIN failed--compilation aborted at Bio/DB/TFBS/transfac_pro.pm line 118. Compilation failed in require at Bio/Root/Root.pm line 439. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441 STACK: Bio::DB::TFBS::_load_tax_module Bio/DB/TFBS.pm:151 STACK: Bio::DB::TFBS::new Bio/DB/TFBS.pm:130 STACK: t/LocalDB/transfac_pro.t:25 ----------------------------------------------------------- For more information about the Bio::DB::TFBS system please see the Bio::DB::TFBS docs. This includes ways of checking for formats at compile time, not run time. # Failed test at t/LocalDB/transfac_pro.t line 25. Can't call method "get_reference_ids" on an undefined value at t/LocalDB/transfac_pro.t line 33. # Looks like you planned 115 tests but ran 4. # Looks like you failed 1 test of 4 run. # Looks like your test exited with 2 just after 4. t/LocalDB/transfac_pro.t ..................... 1..115 ok 1 - use Bio::Matrix::PSM::IO; ok 2 - use Bio::DB::TFBS; ok 3 - use Bio::DB::Taxonomy; not ok 4 Dubious, test returned 2 (wstat 512, 0x200) Failed 112/115 subtests t/Map/Cyto.t ................................. 1..110 ok 1 - use Bio::Map::CytoMap; ok 2 - use Bio::Map::CytoPosition; ok 3 - use Bio::Map::CytoMarker; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - The object isa Bio::Map::CytoPosition ok 15 ok 16 ok 17 ok 18 - The object isa Bio::Range ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok t/Map/Linkage.t .............................. 1..18 ok 1 - use Bio::Map::LinkagePosition; ok 2 - use Bio::Map::Microsatellite; ok 3 - use Bio::Map::LinkageMap; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok t/Map/Map.t .................................. 1..267 ok 1 - use Bio::Map::SimpleMap; ok 2 - use Bio::Map::Marker; ok 3 - use Bio::Map::Position; ok 4 - use Bio::Map::Relative; ok 5 - use Bio::Map::Mappable; ok 6 ok 7 ok 8 ok 9 ok 10 - Length is 0 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 - use Bio::Map::Gene; ok 152 - use Bio::Map::GeneMap; ok 153 - use Bio::Map::TranscriptionFactor; ok 154 - use Bio::Map::GeneRelative; ok 155 - use Bio::Map::GenePosition; ok 156 - use Bio::Map::Prediction; ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok 176 ok 177 ok 178 ok 179 ok 180 ok 181 ok 182 ok 183 ok 184 ok 185 ok 186 ok 187 ok 188 ok 189 ok 190 ok 191 ok 192 ok 193 ok 194 ok 195 ok 196 ok 197 ok 198 ok 199 ok 200 ok 201 ok 202 ok 203 ok 204 ok 205 ok 206 ok 207 ok 208 ok 209 ok 210 ok 211 ok 212 ok 213 ok 214 ok 215 ok 216 ok 217 ok 218 ok 219 ok 220 ok 221 ok 222 ok 223 ok 224 ok 225 ok 226 ok 227 ok 228 ok 229 ok 230 ok 231 ok 232 ok 233 ok 234 ok 235 ok 236 ok 237 ok 238 ok 239 ok 240 ok 241 ok 242 ok 243 ok 244 ok 245 ok 246 ok 247 ok 248 ok 249 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 250 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 251 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 252 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 253 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 254 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 255 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 256 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 257 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 258 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 259 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 260 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 261 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 262 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 263 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 264 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 265 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 266 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 267 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok t/Map/MapIO.t ................................ 1..51 ok 1 - use Bio::MapIO; ok 2 ok 3 - The object isa Bio::Map::MapI ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok t/Map/MicrosatelliteMarker.t ................. 1..8 ok 1 - use Bio::Map::SimpleMap; ok 2 - use Bio::Map::Position; ok 3 - use Bio::Map::Microsatellite; ok 4 ok 5 ok 6 ok 7 ok 8 ok make: *** [test] Terminated Timeout (max run time is 300s) /export/home/fly1003/bin/perl killed by signal 15