Start 2009-06-13T06:19:20 ActivePerl-1003 CPAN-1.94 LIB=C:\PlatSDK\Lib\AMD64;C:\PlatSDK\Lib\AMD64\atlmfc INCLUDE=C:\PlatSDK\Include;C:\PlatSDK\Include\crt;C:\PlatSDK\Include\crt\sys;C:\PlatSDK\Include\mfc;C:\PlatSDK\Include\atl PATH=C:\PlatSDK\Bin\Win64\x86\AMD64;C:\PlatSDK\Bin;C:\PlatSDK\Bin\WinNT;C:\Perl64\site\bin;C:\Perl64\bin;C:\cygwin\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\PROGRA~2\Perforce\;C:\WINDOWS\system32\WINDOW~1\v1.0 Going to read 'C:\cpanfly\var\cpan\Metadata' Database was generated on Fri, 12 Jun 2009 10:27:07 GMT Running make for B/BI/BIRNEY/bioperl-1.4.tar.gz Checksum for C:\cpanfly\var\cpan\sources\authors\id\B\BI\BIRNEY\bioperl-1.4.tar.gz ok bioperl-1.4/ bioperl-1.4/DEPRECATED bioperl-1.4/AUTHORS bioperl-1.4/BUGS bioperl-1.4/Changes bioperl-1.4/INSTALL bioperl-1.4/FAQ bioperl-1.4/Bio/ bioperl-1.4/Bio/Align/ bioperl-1.4/Bio/Align/AlignI.pm bioperl-1.4/Bio/Align/DNAStatistics.pm bioperl-1.4/Bio/Align/PairwiseStatistics.pm bioperl-1.4/Bio/Align/StatisticsI.pm bioperl-1.4/Bio/Align/Utilities.pm bioperl-1.4/Bio/AlignIO.pm bioperl-1.4/Bio/AnalysisI.pm bioperl-1.4/Bio/AnalysisParserI.pm bioperl-1.4/Bio/AnalysisResultI.pm bioperl-1.4/Bio/AnnotatableI.pm bioperl-1.4/Bio/AnnotationCollectionI.pm bioperl-1.4/Bio/AnnotationI.pm bioperl-1.4/Bio/Biblio.pm bioperl-1.4/Bio/ClusterI.pm bioperl-1.4/Bio/ClusterIO.pm bioperl-1.4/Bio/DBLinkContainerI.pm bioperl-1.4/Bio/DasI.pm bioperl-1.4/Bio/DescribableI.pm bioperl-1.4/Bio/FeatureHolderI.pm bioperl-1.4/Bio/Graphics.pm bioperl-1.4/Bio/IdCollectionI.pm bioperl-1.4/Bio/IdentifiableI.pm bioperl-1.4/Bio/LocatableSeq.pm bioperl-1.4/Bio/LocationI.pm bioperl-1.4/Bio/MapIO.pm bioperl-1.4/Bio/OntologyIO.pm bioperl-1.4/Bio/Perl.pm bioperl-1.4/Bio/PrimarySeq.pm bioperl-1.4/Bio/PrimarySeqI.pm bioperl-1.4/Bio/Range.pm bioperl-1.4/Bio/RangeI.pm bioperl-1.4/Bio/SearchDist.pm bioperl-1.4/Bio/SearchIO.pm bioperl-1.4/Bio/Seq.pm bioperl-1.4/Bio/SeqAnalysisParserI.pm bioperl-1.4/Bio/SeqFeatureI.pm bioperl-1.4/Bio/SeqI.pm bioperl-1.4/Bio/SeqIO.pm bioperl-1.4/Bio/SeqUtils.pm bioperl-1.4/Bio/SimpleAlign.pm bioperl-1.4/Bio/SimpleAnalysisI.pm bioperl-1.4/Bio/Species.pm bioperl-1.4/Bio/Taxonomy.pm bioperl-1.4/Bio/TreeIO.pm bioperl-1.4/Bio/UpdateableSeqI.pm bioperl-1.4/Bio/WebAgent.pm bioperl-1.4/Bio/AlignIO/ bioperl-1.4/Bio/AlignIO/bl2seq.pm bioperl-1.4/Bio/AlignIO/clustalw.pm bioperl-1.4/Bio/AlignIO/emboss.pm bioperl-1.4/Bio/AlignIO/fasta.pm bioperl-1.4/Bio/AlignIO/maf.pm bioperl-1.4/Bio/AlignIO/mase.pm bioperl-1.4/Bio/AlignIO/mega.pm bioperl-1.4/Bio/AlignIO/meme.pm bioperl-1.4/Bio/AlignIO/metafasta.pm bioperl-1.4/Bio/AlignIO/msf.pm bioperl-1.4/Bio/AlignIO/nexus.pm bioperl-1.4/Bio/AlignIO/pfam.pm bioperl-1.4/Bio/AlignIO/phylip.pm bioperl-1.4/Bio/AlignIO/prodom.pm bioperl-1.4/Bio/AlignIO/psi.pm bioperl-1.4/Bio/AlignIO/selex.pm bioperl-1.4/Bio/AlignIO/stockholm.pm bioperl-1.4/Bio/Annotation/ bioperl-1.4/Bio/Annotation/AnnotationFactory.pm 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bioperl-1.4/t/data/sim4.for.for bioperl-1.4/t/data/sim4.for.rev bioperl-1.4/t/data/sim4.rev bioperl-1.4/t/data/sofa.ontology bioperl-1.4/t/data/sparsealn.needle bioperl-1.4/t/data/stress_test_medline.xml bioperl-1.4/t/data/stress_test_pubmed.xml bioperl-1.4/t/data/swiss.dat bioperl-1.4/t/data/swisspfam.data bioperl-1.4/t/data/test.ace bioperl-1.4/t/data/test.embl bioperl-1.4/t/data/test.fasta bioperl-1.4/t/data/test.game bioperl-1.4/t/data/test.gcg bioperl-1.4/t/data/test.gcgblast bioperl-1.4/t/data/test.gcgfasta bioperl-1.4/t/data/test.genbank bioperl-1.4/t/data/test.genbank.noseq bioperl-1.4/t/data/test.mase bioperl-1.4/t/data/test.metafasta bioperl-1.4/t/data/test.nh bioperl-1.4/t/data/test.nhx bioperl-1.4/t/data/test.pfam bioperl-1.4/t/data/test.pir bioperl-1.4/t/data/test.raw bioperl-1.4/t/data/test.swiss bioperl-1.4/t/data/test.tab bioperl-1.4/t/data/test.txt bioperl-1.4/t/data/test.waba bioperl-1.4/t/data/test_badlf.gcg bioperl-1.4/t/data/testaln.aln 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bioperl-1.4/t/BioDBGFF.t bioperl-1.4/t/BioFetch_DB.t bioperl-1.4/t/BioGraphics.t bioperl-1.4/t/BlastIndex.t bioperl-1.4/t/Chain.t bioperl-1.4/t/ClusterIO.t bioperl-1.4/t/Coalescent.t bioperl-1.4/t/CodonTable.t bioperl-1.4/t/CoordinateGraph.t bioperl-1.4/t/CoordinateMapper.t bioperl-1.4/t/Correlate.t bioperl-1.4/t/CytoMap.t bioperl-1.4/t/DB.t bioperl-1.4/t/DBCUTG.t bioperl-1.4/t/DBFasta.t bioperl-1.4/t/DNAMutation.t bioperl-1.4/t/Domcut.t bioperl-1.4/t/ECnumber.t bioperl-1.4/t/ELM.t bioperl-1.4/t/EMBL_DB.t bioperl-1.4/t/EMBOSS_Tools.t bioperl-1.4/t/ESEfinder.t bioperl-1.4/t/EncodedSeq.t bioperl-1.4/t/Exception.t bioperl-1.4/t/Exonerate.t bioperl-1.4/t/FootPrinter.t bioperl-1.4/t/GDB.t bioperl-1.4/t/GFF.t bioperl-1.4/t/GOR4.t bioperl-1.4/t/GOterm.t bioperl-1.4/t/GeneCoordinateMapper.t bioperl-1.4/t/Geneid.t bioperl-1.4/t/Genewise.t bioperl-1.4/t/Genomewise.t bioperl-1.4/t/Genpred.t bioperl-1.4/t/GuessSeqFormat.t bioperl-1.4/t/HNN.t bioperl-1.4/t/IUPAC.t bioperl-1.4/t/Index.t bioperl-1.4/t/InstanceSite.t bioperl-1.4/t/InterProParser.t bioperl-1.4/t/LinkageMap.t bioperl-1.4/t/LiveSeq.t bioperl-1.4/t/LocatableSeq.t bioperl-1.4/t/Location.t bioperl-1.4/t/LocationFactory.t bioperl-1.4/t/LocusLink.t bioperl-1.4/t/Map.t bioperl-1.4/t/MapIO.t bioperl-1.4/t/Matrix.t bioperl-1.4/t/MeSH.t bioperl-1.4/t/Measure.t bioperl-1.4/t/MetaSeq.t bioperl-1.4/t/MicrosatelliteMarker.t bioperl-1.4/t/MiniMIMentry.t bioperl-1.4/t/MitoProt.t bioperl-1.4/t/Molphy.t bioperl-1.4/t/Mutation.t bioperl-1.4/t/Mutator.t bioperl-1.4/t/NetPhos.t bioperl-1.4/t/Node.t bioperl-1.4/t/OMIMentry.t bioperl-1.4/t/OMIMentryAllelicVariant.t bioperl-1.4/t/OMIMparser.t bioperl-1.4/t/OddCodes.t bioperl-1.4/t/Ontology.t bioperl-1.4/t/OntologyEngine.t bioperl-1.4/t/PAML.t bioperl-1.4/t/Perl.t bioperl-1.4/t/Phenotype.t bioperl-1.4/t/PhylipDist.t bioperl-1.4/t/Pictogram.t bioperl-1.4/t/PopGen.t bioperl-1.4/t/PopGenSims.t bioperl-1.4/t/PrimarySeq.t bioperl-1.4/t/Primer.t bioperl-1.4/t/Promoterwise.t bioperl-1.4/t/ProtDist.t bioperl-1.4/t/QRNA.t bioperl-1.4/t/RNAChange.t bioperl-1.4/t/RandDistFunctions.t bioperl-1.4/t/RandomTreeFactory.t bioperl-1.4/t/Range.t bioperl-1.4/t/RangeI.t bioperl-1.4/t/RefSeq.t bioperl-1.4/t/Registry.t bioperl-1.4/t/Relationship.t bioperl-1.4/t/RelationshipType.t bioperl-1.4/t/RemoteBlast.t bioperl-1.4/t/RepeatMasker.t bioperl-1.4/t/RestrictionAnalysis.t bioperl-1.4/t/RestrictionEnzyme.t bioperl-1.4/t/RestrictionIO.t bioperl-1.4/t/RootI.t bioperl-1.4/t/RootIO.t bioperl-1.4/t/RootStorable.t bioperl-1.4/t/SNP.t bioperl-1.4/t/Scansite.t bioperl-1.4/t/SearchDist.t bioperl-1.4/t/SearchIO.t bioperl-1.4/t/Seq.t bioperl-1.4/t/SeqAnalysisParser.t bioperl-1.4/t/SeqBuilder.t bioperl-1.4/t/SeqDiff.t bioperl-1.4/t/SeqFeatCollection.t bioperl-1.4/t/SeqFeature.t bioperl-1.4/t/SeqIO.t bioperl-1.4/t/SeqPattern.t bioperl-1.4/t/SeqStats.t bioperl-1.4/t/SeqUtils.t bioperl-1.4/t/SeqWords.t bioperl-1.4/t/SequenceFamily.t bioperl-1.4/t/Sigcleave.t bioperl-1.4/t/Sim4.t bioperl-1.4/t/SimilarityPair.t bioperl-1.4/t/SimpleAlign.t bioperl-1.4/t/SiteMatrix.t bioperl-1.4/t/Sopma.t bioperl-1.4/t/Species.t bioperl-1.4/t/StandAloneBlast.t bioperl-1.4/t/StructIO.t bioperl-1.4/t/Structure.t bioperl-1.4/t/Swiss.t bioperl-1.4/t/Symbol.t bioperl-1.4/t/Taxonomy.t bioperl-1.4/t/Tempfile.t bioperl-1.4/t/Term.t bioperl-1.4/t/Test.pm bioperl-1.4/t/Tools.t bioperl-1.4/t/Tree.t bioperl-1.4/t/TreeIO.t bioperl-1.4/t/UCSCParsers.t bioperl-1.4/t/Unflattener.t bioperl-1.4/t/Unflattener2.t bioperl-1.4/t/UniGene.t bioperl-1.4/t/Variation_IO.t bioperl-1.4/t/WABA.t bioperl-1.4/t/XEMBL_DB.t bioperl-1.4/t/cigarstring.t bioperl-1.4/t/consed.t bioperl-1.4/t/ePCR.t bioperl-1.4/t/est2genome.t bioperl-1.4/t/flat.t bioperl-1.4/t/game.t bioperl-1.4/t/hmmer.t bioperl-1.4/t/largefasta.t bioperl-1.4/t/largepseq.t bioperl-1.4/t/lucy.t bioperl-1.4/t/multiple_fasta.t bioperl-1.4/t/pICalculator.t bioperl-1.4/t/phd.t bioperl-1.4/t/primaryqual.t bioperl-1.4/t/primedseq.t bioperl-1.4/t/primer3.t bioperl-1.4/t/psm.t bioperl-1.4/t/qual.t bioperl-1.4/t/scf.t bioperl-1.4/t/seqfeaturePrimer.t bioperl-1.4/t/sequencetrace.t bioperl-1.4/t/seqwithquality.t bioperl-1.4/t/simpleGOparser.t bioperl-1.4/t/sirna.t bioperl-1.4/t/splicedseq.t bioperl-1.4/t/testformats.pl bioperl-1.4/t/trim.t bioperl-1.4/t/tutorial.t bioperl-1.4/MANIFEST bioperl-1.4/Makefile.old CPAN.pm: Going to build B/BI/BIRNEY/bioperl-1.4.tar.gz >>> C:\Perl64\bin\perl.exe Makefile.PL Generated sub tests. go make show_tests to see available subtests *** Script Install Section **** Bioperl comes with a number of useful scripts which you may wish to install. Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] a * Script Directory biblio * These are scripts to manipulate bibliographic repositories using the Bio::Biblio modules. Activating bp_biblio.pl.... * Script Directory Bio-DB-GFF * These are scripts that go with the Bio::DB::GFF module, a basic seqfeature database. Install these scripts if you wish to use the LDAS distributed annotation server or the Generic Genome Browser. Activating bp_genbank2gff.pl.... Activating bp_bulk_load_gff.pl.... Activating bp_fast_load_gff.pl.... Activating bp_generate_histogram.pl.... Activating bp_load_gff.pl.... Activating bp_pg_bulk_load_gff.pl.... Activating bp_process_gadfly.pl.... Activating bp_process_ncbi_human.pl.... Activating bp_process_sgd.pl.... Activating bp_process_wormbase.pl.... * Script Directory das * This directory is currently empty. For the Lightweight Distributed Annotation System (LDAS) server, see http://www.biodas.org/servers/ * Script Directory DB * These are scripts to fetch sequence data from local and remote sequence repositories using the Open Bio Database Access registry protocol (http://obda.open-bio.org). Activating bp_biofetch_genbank_proxy.pl.... Activating bp_bioflat_index.pl.... Activating bp_biogetseq.pl.... Activating bp_flanks.pl.... * Script Directory graphics * These are scripts to generate graphical images from sequence data. Activating bp_feature_draw.pl.... Activating bp_frend.pl.... Activating bp_search_overview.pl.... * Script Directory index * These are scripts to create and maintain flatfile databases indexed with the Bio::Index modules. Activating bp_fetch.pl.... Activating bp_index.pl.... * Script Directory popgen * Activating bp_composite_LD.pl.... Activating bp_heterogeneity_test.pl.... * Script Directory searchio * Activating bp_filter_search.pl.... * Script Directory seq * These are scripts to interconvert sequence formats and to perform other common sequence manipulations. Activating bp_extract_feature_seq.pl.... Activating bp_seqconvert.pl.... Activating bp_split_seq.pl.... Activating bp_translate_seq.pl.... * Script Directory seqstats * These are scripts to generate common statistics on protein and nucleotide sequences. Activating bp_aacomp.pl.... Activating bp_chaos_plot.pl.... Activating bp_gccalc.pl.... Activating bp_oligo_count.pl.... * Script Directory taxa * These are scripts to create and query taxonomic trees. Activating bp_local_taxonomydb_query.pl.... Activating bp_taxid4species.pl.... * Script Directory tree * These are utilities to generate trees from sequence similarity data. Activating bp_blast2tree.pl.... * Script Directory utilities * These are various sequence-related scripts that were difficult to classify more specifically but are considered general purpose utilities. Activating bp_mrtrans.pl.... Activating bp_nrdb.pl.... Activating bp_sreformat.pl.... Activating bp_dbsplit.pl.... Activating bp_mask_by_search.pl.... Activating bp_mutate.pl.... Activating bp_pairwise_kaks.pl.... Activating bp_remote_blast.pl.... Activating bp_search2alnblocks.pl.... Activating bp_search2BSML.pl.... Activating bp_search2gff.pl.... Activating bp_search2tribe.pl.... Activating bp_seq_length.pl.... ** Bio::DB::GFF Tests section** Do you want to run the BioDBGFF tests (requires a mysql, postgres or oracle database) y/n [n] n Warning: prerequisite DB_File 0 not found. Checking if your kit is complete... Looks good Writing Makefile for Bio ---- Unsatisfied dependencies detected during ---- ---- BIRNEY/bioperl-1.4.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 'C:\cpanfly\etc\distroprefs\DB_File.yml' doc 0 PMQS/DB_File-1.820.tar.gz [disabled] -- NA Disabled via prefs file 'C:\cpanfly\etc\distroprefs\DB_File.yml' doc 0 Running make for B/BI/BIRNEY/bioperl-1.4.tar.gz Has already been unwrapped into directory C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5 CPAN.pm: Going to build B/BI/BIRNEY/bioperl-1.4.tar.gz Warning: Prerequisite 'DB_File => 0' for 'BIRNEY/bioperl-1.4.tar.gz' failed when processing 'PMQS/DB_File-1.820.tar.gz' with 'unwrapped => NO Disabled via prefs file 'C:\cpanfly\etc\distroprefs\DB_File.yml' doc 0'. Continuing, but chances to succeed are limited. >>> nmake Microsoft (R) Program Maintenance Utility Version 7.00.8882 Copyright (C) Microsoft Corp 1988-2000. All rights reserved. cp Bio/Biblio/PubmedBookArticle.pm blib\lib\Bio\Biblio\PubmedBookArticle.pm cp Bio/PopGen/MarkerI.pm blib\lib\Bio\PopGen\MarkerI.pm cp Bio/Matrix/PSM/Psm.pm blib\lib\Bio\Matrix\PSM\Psm.pm cp Bio/Search/HSP/WABAHSP.pm blib\lib\Bio\Search\HSP\WABAHSP.pm cp Bio/Tools/Blast/CHANGES blib\lib\Bio\Tools\Blast\CHANGES cp Bio/WebAgent.pm blib\lib\Bio\WebAgent.pm cp Bio/LiveSeq/ChainI.pm blib\lib\Bio\LiveSeq\ChainI.pm cp Bio/LiveSeq/Mutation.pm blib\lib\Bio\LiveSeq\Mutation.pm cp Bio/AlignIO/mega.pm blib\lib\Bio\AlignIO\mega.pm cp Bio/Tools/HMMER/Set.pm blib\lib\Bio\Tools\HMMER\Set.pm cp Bio/Factory/ObjectFactory.pm blib\lib\Bio\Factory\ObjectFactory.pm cp Bio/SearchIO/megablast.pm blib\lib\Bio\SearchIO\megablast.pm cp Bio/Factory/SeqAnalysisParserFactoryI.pm blib\lib\Bio\Factory\SeqAnalysisParserFactoryI.pm cp Bio/DB/GFF/Aggregator/ucsc_unigene.pm blib\lib\Bio\DB\GFF\Aggregator\ucsc_unigene.pm cp Bio/TreeIO.pm blib\lib\Bio\TreeIO.pm cp Bio/Search/HSP/PSLHSP.pm blib\lib\Bio\Search\HSP\PSLHSP.pm cp Bio/DB/GFF/Aggregator/ucsc_acembly.pm blib\lib\Bio\DB\GFF\Aggregator\ucsc_acembly.pm cp Bio/Cluster/UniGeneI.pm blib\lib\Bio\Cluster\UniGeneI.pm cp Bio/Tools/GuessSeqFormat.pm blib\lib\Bio\Tools\GuessSeqFormat.pm cp Bio/Align/Utilities.pm blib\lib\Bio\Align\Utilities.pm cp Bio/DB/Flat.pm blib\lib\Bio\DB\Flat.pm cp Bio/Tools/Run/README blib\lib\Bio\Tools\Run\README cp Bio/DB/SwissProt.pm blib\lib\Bio\DB\SwissProt.pm cp Bio/SearchIO/fasta.pm blib\lib\Bio\SearchIO\fasta.pm cp Bio/TreeIO/nexus.pm blib\lib\Bio\TreeIO\nexus.pm cp Bio/Biblio/Provider.pm blib\lib\Bio\Biblio\Provider.pm cp Bio/Coordinate/Graph.pm blib\lib\Bio\Coordinate\Graph.pm cp Bio/DB/GFF/Aggregator/ucsc_sanger22.pm blib\lib\Bio\DB\GFF\Aggregator\ucsc_sanger22.pm cp Bio/LocationI.pm blib\lib\Bio\LocationI.pm cp Bio/Root/RootI.pm blib\lib\Bio\Root\RootI.pm cp Bio/Taxonomy.pm blib\lib\Bio\Taxonomy.pm cp Bio/Matrix/PSM/PsmI.pm blib\lib\Bio\Matrix\PSM\PsmI.pm cp Bio/TreeIO/TreeEventBuilder.pm blib\lib\Bio\TreeIO\TreeEventBuilder.pm cp Bio/Location/Fuzzy.pm blib\lib\Bio\Location\Fuzzy.pm cp Bio/DBLinkContainerI.pm blib\lib\Bio\DBLinkContainerI.pm cp Bio/SeqIO.pm blib\lib\Bio\SeqIO.pm cp Bio/AnalysisI.pm blib\lib\Bio\AnalysisI.pm cp Bio/LiveSeq/AARange.pm blib\lib\Bio\LiveSeq\AARange.pm cp Bio/DB/Biblio/biofetch.pm blib\lib\Bio\DB\Biblio\biofetch.pm cp Bio/Index/Swissprot.pm blib\lib\Bio\Index\Swissprot.pm cp Bio/Map/MappableI.pm blib\lib\Bio\Map\MappableI.pm cp Bio/Seq/BaseSeqProcessor.pm blib\lib\Bio\Seq\BaseSeqProcessor.pm cp Bio/DB/BiblioI.pm blib\lib\Bio\DB\BiblioI.pm cp Bio/MapIO.pm blib\lib\Bio\MapIO.pm cp Bio/SearchIO/Writer/HSPTableWriter.pm blib\lib\Bio\SearchIO\Writer\HSPTableWriter.pm cp Bio/Graphics/Glyph/segmented_keyglyph.pm blib\lib\Bio\Graphics\Glyph\segmented_keyglyph.pm cp Bio/SearchIO/blasttable.pm blib\lib\Bio\SearchIO\blasttable.pm cp Bio/SeqIO/fastq.pm blib\lib\Bio\SeqIO\fastq.pm cp Bio/LiveSeq/SeqI.pm blib\lib\Bio\LiveSeq\SeqI.pm cp Bio/SeqFeature/Collection.pm blib\lib\Bio\SeqFeature\Collection.pm cp Bio/Annotation/OntologyTerm.pm blib\lib\Bio\Annotation\OntologyTerm.pm cp Bio/Map/SimpleMap.pm blib\lib\Bio\Map\SimpleMap.pm cp Bio/Graphics/Glyph/box.pm blib\lib\Bio\Graphics\Glyph\box.pm cp Bio/Coordinate/Result/Gap.pm blib\lib\Bio\Coordinate\Result\Gap.pm cp Bio/Graphics/Glyph/cds.pm blib\lib\Bio\Graphics\Glyph\cds.pm cp Bio/Tree/TreeI.pm blib\lib\Bio\Tree\TreeI.pm cp Bio/Tools/Run/RemoteBlast.pm blib\lib\Bio\Tools\Run\RemoteBlast.pm cp Bio/Seq/Meta/Array.pm blib\lib\Bio\Seq\Meta\Array.pm cp Bio/Graphics/Glyph/extending_arrow.pm blib\lib\Bio\Graphics\Glyph\extending_arrow.pm cp Bio/Search/Hit/PsiBlastHit.pm blib\lib\Bio\Search\Hit\PsiBlastHit.pm cp Bio/LiveSeq/Repeat_Unit.pm blib\lib\Bio\LiveSeq\Repeat_Unit.pm cp Bio/Restriction/Enzyme/MultiCut.pm blib\lib\Bio\Restriction\Enzyme\MultiCut.pm cp Bio/DB/GFF/Adaptor/memory.pm blib\lib\Bio\DB\GFF\Adaptor\memory.pm cp Bio/DB/UpdateableSeqI.pm blib\lib\Bio\DB\UpdateableSeqI.pm cp Bio/Restriction/IO/base.pm blib\lib\Bio\Restriction\IO\base.pm cp Bio/DB/RefSeq.pm blib\lib\Bio\DB\RefSeq.pm cp Bio/Tools/RepeatMasker.pm blib\lib\Bio\Tools\RepeatMasker.pm cp Bio/Coordinate/Result/Match.pm blib\lib\Bio\Coordinate\Result\Match.pm cp Bio/Search/Result/HMMERResult.pm blib\lib\Bio\Search\Result\HMMERResult.pm cp Bio/SearchIO/wise.pm blib\lib\Bio\SearchIO\wise.pm cp Bio/Tools/Analysis/Protein/ELM.pm blib\lib\Bio\Tools\Analysis\Protein\ELM.pm cp Bio/Phenotype/Phenotype.pm blib\lib\Bio\Phenotype\Phenotype.pm cp Bio/Seq/TraceI.pm blib\lib\Bio\Seq\TraceI.pm cp Bio/Seq/PrimaryQual.pm blib\lib\Bio\Seq\PrimaryQual.pm cp Bio/DB/Failover.pm blib\lib\Bio\DB\Failover.pm cp Bio/Map/CytoMap.pm blib\lib\Bio\Map\CytoMap.pm cp Bio/Variation/Allele.pm blib\lib\Bio\Variation\Allele.pm cp Bio/LiveSeq/IO/Loader.pm blib\lib\Bio\LiveSeq\IO\Loader.pm cp Bio/Biblio/IO.pm blib\lib\Bio\Biblio\IO.pm cp Bio/Biblio/BiblioBase.pm blib\lib\Bio\Biblio\BiblioBase.pm cp Bio/DB/NCBIHelper.pm blib\lib\Bio\DB\NCBIHelper.pm cp Bio/DB/GFF/Feature.pm blib\lib\Bio\DB\GFF\Feature.pm cp Bio/Phenotype/OMIM/MiniMIMentry.pm blib\lib\Bio\Phenotype\OMIM\MiniMIMentry.pm cp Bio/UpdateableSeqI.pm blib\lib\Bio\UpdateableSeqI.pm cp Bio/Tools/Phylo/PAML/ModelResult.pm blib\lib\Bio\Tools\Phylo\PAML\ModelResult.pm cp Bio/Biblio/Thesis.pm blib\lib\Bio\Biblio\Thesis.pm cp Bio/Event/EventHandlerI.pm blib\lib\Bio\Event\EventHandlerI.pm cp Bio/Seq/PrimedSeq.pm blib\lib\Bio\Seq\PrimedSeq.pm cp Bio/Structure/Chain.pm blib\lib\Bio\Structure\Chain.pm cp Bio/AlignIO/prodom.pm blib\lib\Bio\AlignIO\prodom.pm cp Bio/Assembly/ContigAnalysis.pm blib\lib\Bio\Assembly\ContigAnalysis.pm cp Bio/Coordinate/ExtrapolatingPair.pm blib\lib\Bio\Coordinate\ExtrapolatingPair.pm cp Bio/SimpleAnalysisI.pm blib\lib\Bio\SimpleAnalysisI.pm cp Bio/Graphics/Glyph/group.pm blib\lib\Bio\Graphics\Glyph\group.pm cp Bio/IdCollectionI.pm blib\lib\Bio\IdCollectionI.pm cp Bio/Tree/AlleleNode.pm blib\lib\Bio\Tree\AlleleNode.pm cp Bio/Tools/Gel.pm blib\lib\Bio\Tools\Gel.pm cp Bio/SeqIO/largefasta.pm blib\lib\Bio\SeqIO\largefasta.pm cp Bio/Annotation/SimpleValue.pm blib\lib\Bio\Annotation\SimpleValue.pm cp Bio/AlignIO/emboss.pm blib\lib\Bio\AlignIO\emboss.pm cp Bio/Align/AlignI.pm blib\lib\Bio\Align\AlignI.pm cp Bio/Graphics/Glyph/generic.pm blib\lib\Bio\Graphics\Glyph\generic.pm cp Bio/Graphics/Glyph/processed_transcript.pm blib\lib\Bio\Graphics\Glyph\processed_transcript.pm cp Bio/Graphics/ConfiguratorI.pm blib\lib\Bio\Graphics\ConfiguratorI.pm cp Bio/DB/Fasta.pm blib\lib\Bio\DB\Fasta.pm cp Bio/Graphics/Glyph/minmax.pm blib\lib\Bio\Graphics\Glyph\minmax.pm cp Bio/TreeIO/lintree.pm blib\lib\Bio\TreeIO\lintree.pm cp Bio/Biblio.pm blib\lib\Bio\Biblio.pm cp Bio/DB/GFF/Adaptor/memory_iterator.pm blib\lib\Bio\DB\GFF\Adaptor\memory_iterator.pm cp Bio/Phenotype/OMIM/OMIMparser.pm blib\lib\Bio\Phenotype\OMIM\OMIMparser.pm cp Bio/Restriction/Enzyme.pm blib\lib\Bio\Restriction\Enzyme.pm cp Bio/SeqIO/game/seqHandler.pm blib\lib\Bio\SeqIO\game\seqHandler.pm cp Bio/Matrix/PSM/InstanceSite.pm blib\lib\Bio\Matrix\PSM\InstanceSite.pm cp Bio/Tree/TreeFunctionsI.pm blib\lib\Bio\Tree\TreeFunctionsI.pm cp Bio/Matrix/MatrixI.pm blib\lib\Bio\Matrix\MatrixI.pm cp Bio/Matrix/PSM/IO.pm blib\lib\Bio\Matrix\PSM\IO.pm cp Bio/TreeIO/svggraph.pm blib\lib\Bio\TreeIO\svggraph.pm cp Bio/Taxonomy/Tree.pm blib\lib\Bio\Taxonomy\Tree.pm cp Bio/Ontology/RelationshipType.pm blib\lib\Bio\Ontology\RelationshipType.pm cp Bio/Cluster/UniGene.pm blib\lib\Bio\Cluster\UniGene.pm cp Bio/CodonUsage/Table.pm blib\lib\Bio\CodonUsage\Table.pm cp Bio/DB/Query/WebQuery.pm blib\lib\Bio\DB\Query\WebQuery.pm cp Bio/Ontology/OntologyI.pm blib\lib\Bio\Ontology\OntologyI.pm cp Bio/SeqFeature/Generic.pm blib\lib\Bio\SeqFeature\Generic.pm cp Bio/SearchIO/hmmer.pm blib\lib\Bio\SearchIO\hmmer.pm cp Bio/PopGen/PopulationI.pm blib\lib\Bio\PopGen\PopulationI.pm cp Bio/SeqIO/ctf.pm blib\lib\Bio\SeqIO\ctf.pm cp Bio/LiveSeq/IO/SRS.pm blib\lib\Bio\LiveSeq\IO\SRS.pm cp Bio/Tools/SeqPattern.pm blib\lib\Bio\Tools\SeqPattern.pm cp Bio/SearchIO/psl.pm blib\lib\Bio\SearchIO\psl.pm cp Bio/LiveSeq/DNA.pm blib\lib\Bio\LiveSeq\DNA.pm cp Bio/Index/AbstractSeq.pm blib\lib\Bio\Index\AbstractSeq.pm cp Bio/AlignIO.pm blib\lib\Bio\AlignIO.pm cp Bio/Tree/NodeI.pm blib\lib\Bio\Tree\NodeI.pm cp Bio/Tools/Prints.pm blib\lib\Bio\Tools\Prints.pm cp Bio/SeqFeature/Gene/Exon.pm blib\lib\Bio\SeqFeature\Gene\Exon.pm cp Bio/DescribableI.pm blib\lib\Bio\DescribableI.pm cp Bio/Structure/StructureI.pm blib\lib\Bio\Structure\StructureI.pm cp Bio/Search/Result/ResultI.pm blib\lib\Bio\Search\Result\ResultI.pm cp Bio/Symbol/AlphabetI.pm blib\lib\Bio\Symbol\AlphabetI.pm cp Bio/Graphics/Glyph/rndrect.pm blib\lib\Bio\Graphics\Glyph\rndrect.pm cp Bio/RangeI.pm blib\lib\Bio\RangeI.pm cp Bio/Matrix/PSM/InstanceSiteI.pm blib\lib\Bio\Matrix\PSM\InstanceSiteI.pm cp Bio/Root/Global.pm blib\lib\Bio\Root\Global.pm cp Bio/SeqFeature/SimilarityPair.pm blib\lib\Bio\SeqFeature\SimilarityPair.pm cp Bio/SeqIO/raw.pm blib\lib\Bio\SeqIO\raw.pm cp Bio/Tools/Analysis/Protein/GOR4.pm blib\lib\Bio\Tools\Analysis\Protein\GOR4.pm cp Bio/Search/Processor.pm blib\lib\Bio\Search\Processor.pm cp Bio/Seq.pm blib\lib\Bio\Seq.pm cp Bio/Biblio/Article.pm blib\lib\Bio\Biblio\Article.pm cp Bio/Tools/HMMER/Results.pm blib\lib\Bio\Tools\HMMER\Results.pm cp Bio/Search/BlastUtils.pm blib\lib\Bio\Search\BlastUtils.pm cp Bio/Biblio/Organisation.pm blib\lib\Bio\Biblio\Organisation.pm cp Bio/Tree/RandomFactory.pm blib\lib\Bio\Tree\RandomFactory.pm cp Bio/Tools/Phylo/PAML/Result.pm blib\lib\Bio\Tools\Phylo\PAML\Result.pm cp Bio/Structure/IO/pdb.pm blib\lib\Bio\Structure\IO\pdb.pm cp Bio/Graphics/Feature.pm blib\lib\Bio\Graphics\Feature.pm cp Bio/Search/HSP/PsiBlastHSP.pm blib\lib\Bio\Search\HSP\PsiBlastHSP.pm cp Bio/Index/GenBank.pm blib\lib\Bio\Index\GenBank.pm cp Bio/Biblio/MedlineJournalArticle.pm blib\lib\Bio\Biblio\MedlineJournalArticle.pm cp Bio/Restriction/IO/itype2.pm blib\lib\Bio\Restriction\IO\itype2.pm cp Bio/CodonUsage/IO.pm blib\lib\Bio\CodonUsage\IO.pm cp Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm blib\lib\Bio\DB\GFF\Aggregator\ucsc_sanger22pseudo.pm cp Bio/Location/SplitLocationI.pm blib\lib\Bio\Location\SplitLocationI.pm cp Bio/Taxonomy/Node.pm blib\lib\Bio\Taxonomy\Node.pm cp Bio/Variation/IO/xml.pm blib\lib\Bio\Variation\IO\xml.pm cp Bio/DB/GFF/Aggregator/alignment.pm blib\lib\Bio\DB\GFF\Aggregator\alignment.pm cp Bio/SeqIO/metafasta.pm blib\lib\Bio\SeqIO\metafasta.pm cp Bio/SeqFeature/Gene/NC_Feature.pm blib\lib\Bio\SeqFeature\Gene\NC_Feature.pm cp Bio/Matrix/Generic.pm blib\lib\Bio\Matrix\Generic.pm cp Bio/FeatureHolderI.pm blib\lib\Bio\FeatureHolderI.pm cp Bio/Tools/dpAlign.pm blib\lib\Bio\Tools\dpAlign.pm cp Bio/OntologyIO.pm blib\lib\Bio\OntologyIO.pm cp Bio/Ontology/RelationshipI.pm blib\lib\Bio\Ontology\RelationshipI.pm cp Bio/Restriction/IO.pm blib\lib\Bio\Restriction\IO.pm cp Bio/SeqFeature/Gene/TranscriptI.pm blib\lib\Bio\SeqFeature\Gene\TranscriptI.pm cp Bio/DB/RandomAccessI.pm blib\lib\Bio\DB\RandomAccessI.pm cp Bio/Cluster/FamilyI.pm blib\lib\Bio\Cluster\FamilyI.pm cp Bio/SeqIO/kegg.pm blib\lib\Bio\SeqIO\kegg.pm cp Bio/SeqIO/qual.pm blib\lib\Bio\SeqIO\qual.pm cp Bio/SearchIO/axt.pm blib\lib\Bio\SearchIO\axt.pm cp Bio/Ontology/TermI.pm blib\lib\Bio\Ontology\TermI.pm cp Bio/SeqIO/pln.pm blib\lib\Bio\SeqIO\pln.pm cp Bio/AnalysisResultI.pm blib\lib\Bio\AnalysisResultI.pm cp Bio/Search/Result/BlastResult.pm blib\lib\Bio\Search\Result\BlastResult.pm cp Bio/PopGen/Simulation/Coalescent.pm blib\lib\Bio\PopGen\Simulation\Coalescent.pm cp Bio/Assembly/ScaffoldI.pm blib\lib\Bio\Assembly\ScaffoldI.pm cp Bio/Annotation/AnnotationFactory.pm blib\lib\Bio\Annotation\AnnotationFactory.pm cp Bio/SeqIO/locuslink.pm blib\lib\Bio\SeqIO\locuslink.pm cp Bio/Phenotype/MeSH/Twig.pm blib\lib\Bio\Phenotype\MeSH\Twig.pm cp Bio/Structure/Atom.pm blib\lib\Bio\Structure\Atom.pm cp Bio/Tools/Sim4/Exon.pm blib\lib\Bio\Tools\Sim4\Exon.pm cp Bio/PopGen/Genotype.pm blib\lib\Bio\PopGen\Genotype.pm cp Bio/Tools/pICalculator.pm blib\lib\Bio\Tools\pICalculator.pm cp Bio/DB/GFF/Aggregator/match.pm blib\lib\Bio\DB\GFF\Aggregator\match.pm cp Bio/DB/GFF/Aggregator/ucsc_softberry.pm blib\lib\Bio\DB\GFF\Aggregator\ucsc_softberry.pm cp Bio/Map/PositionI.pm blib\lib\Bio\Map\PositionI.pm cp Bio/Biblio/BookArticle.pm blib\lib\Bio\Biblio\BookArticle.pm cp Bio/Restriction/IO/withrefm.pm blib\lib\Bio\Restriction\IO\withrefm.pm cp Bio/DB/Flat/BDB/swiss.pm blib\lib\Bio\DB\Flat\BDB\swiss.pm cp Bio/Tools/SeqStats.pm blib\lib\Bio\Tools\SeqStats.pm cp Bio/LiveSeq/Transcript.pm blib\lib\Bio\LiveSeq\Transcript.pm cp Bio/Ontology/OntologyEngineI.pm blib\lib\Bio\Ontology\OntologyEngineI.pm cp Bio/Search/HSP/FastaHSP.pm blib\lib\Bio\Search\HSP\FastaHSP.pm cp Bio/Ontology/Term.pm blib\lib\Bio\Ontology\Term.pm cp Bio/Tools/Primer/Assessor/Base.pm blib\lib\Bio\Tools\Primer\Assessor\Base.pm cp Bio/Graphics/Util.pm blib\lib\Bio\Graphics\Util.pm cp Bio/DB/Flat/BDB.pm blib\lib\Bio\DB\Flat\BDB.pm cp Bio/AlignIO/mase.pm blib\lib\Bio\AlignIO\mase.pm cp Bio/Graphics/Glyph/ex.pm blib\lib\Bio\Graphics\Glyph\ex.pm cp Bio/Tools/Phylo/Molphy/Result.pm blib\lib\Bio\Tools\Phylo\Molphy\Result.pm cp Bio/Graphics/Glyph/diamond.pm blib\lib\Bio\Graphics\Glyph\diamond.pm cp Bio/Graphics/Glyph/ellipse.pm blib\lib\Bio\Graphics\Glyph\ellipse.pm cp Bio/SeqFeature/Tools/TypeMapper.pm blib\lib\Bio\SeqFeature\Tools\TypeMapper.pm cp Bio/SeqIO/scf.pm blib\lib\Bio\SeqIO\scf.pm cp Bio/MapIO/mapmaker.pm blib\lib\Bio\MapIO\mapmaker.pm cp Bio/Ontology/OntologyStore.pm blib\lib\Bio\Ontology\OntologyStore.pm cp Bio/OntologyIO/InterProParser.pm blib\lib\Bio\OntologyIO\InterProParser.pm cp Bio/Taxonomy/FactoryI.pm blib\lib\Bio\Taxonomy\FactoryI.pm cp Bio/DB/GFF/Adaptor/dbi/caching_handle.pm blib\lib\Bio\DB\GFF\Adaptor\dbi\caching_handle.pm cp Bio/Tools/Analysis/Protein/HNN.pm blib\lib\Bio\Tools\Analysis\Protein\HNN.pm cp Bio/Location/Atomic.pm blib\lib\Bio\Location\Atomic.pm cp Bio/Ontology/Ontology.pm blib\lib\Bio\Ontology\Ontology.pm cp Bio/PopGen/IO/prettybase.pm blib\lib\Bio\PopGen\IO\prettybase.pm cp Bio/Tools/QRNA.pm blib\lib\Bio\Tools\QRNA.pm cp Bio/SeqIO/fasta.pm blib\lib\Bio\SeqIO\fasta.pm cp Bio/Root/Root.pm blib\lib\Bio\Root\Root.pm cp Bio/Graphics/Glyph/oval.pm blib\lib\Bio\Graphics\Glyph\oval.pm cp Bio/DB/GFF/Aggregator/ucsc_twinscan.pm blib\lib\Bio\DB\GFF\Aggregator\ucsc_twinscan.pm cp Bio/SeqFeature/Gene/Transcript.pm blib\lib\Bio\SeqFeature\Gene\Transcript.pm cp Bio/DB/BioFetch.pm blib\lib\Bio\DB\BioFetch.pm cp Bio/SeqIO/phd.pm blib\lib\Bio\SeqIO\phd.pm cp Bio/Factory/LocationFactoryI.pm blib\lib\Bio\Factory\LocationFactoryI.pm cp Bio/SeqFeature/AnnotationAdaptor.pm blib\lib\Bio\SeqFeature\AnnotationAdaptor.pm cp Bio/Graphics/Glyph/anchored_arrow.pm blib\lib\Bio\Graphics\Glyph\anchored_arrow.pm cp Bio/SeqFeature/Similarity.pm blib\lib\Bio\SeqFeature\Similarity.pm cp Bio/Tools/Sigcleave.pm blib\lib\Bio\Tools\Sigcleave.pm cp Bio/Tools/Alignment/Trim.pm blib\lib\Bio\Tools\Alignment\Trim.pm cp Bio/Tools/Alignment/Consed.pm blib\lib\Bio\Tools\Alignment\Consed.pm cp Bio/Restriction/EnzymeI.pm blib\lib\Bio\Restriction\EnzymeI.pm cp Bio/SearchIO/sim4.pm blib\lib\Bio\SearchIO\sim4.pm cp Bio/Phenotype/OMIM/OMIMentry.pm blib\lib\Bio\Phenotype\OMIM\OMIMentry.pm cp Bio/Map/MarkerI.pm blib\lib\Bio\Map\MarkerI.pm cp Bio/SearchIO/waba.pm blib\lib\Bio\SearchIO\waba.pm cp Bio/DB/Flat/BDB/genbank.pm blib\lib\Bio\DB\Flat\BDB\genbank.pm cp Bio/DB/Taxonomy/entrez.pm blib\lib\Bio\DB\Taxonomy\entrez.pm cp Bio/Tools/ESTScan.pm blib\lib\Bio\Tools\ESTScan.pm cp Bio/AlignIO/phylip.pm blib\lib\Bio\AlignIO\phylip.pm cp Bio/Variation/SeqDiff.pm blib\lib\Bio\Variation\SeqDiff.pm cp Bio/Factory/DriverFactory.pm blib\lib\Bio\Factory\DriverFactory.pm cp Bio/Coordinate/Result.pm blib\lib\Bio\Coordinate\Result.pm cp Bio/Biblio/PubmedJournalArticle.pm blib\lib\Bio\Biblio\PubmedJournalArticle.pm cp Bio/PopGen/IO.pm blib\lib\Bio\PopGen\IO.pm cp Bio/SeqAnalysisParserI.pm blib\lib\Bio\SeqAnalysisParserI.pm cp Bio/Variation/RNAChange.pm blib\lib\Bio\Variation\RNAChange.pm cp Bio/SearchIO.pm blib\lib\Bio\SearchIO.pm cp Bio/Search/Result/WABAResult.pm blib\lib\Bio\Search\Result\WABAResult.pm cp Bio/DB/MANIFEST blib\lib\Bio\DB\MANIFEST cp Bio/SeqIO/embl.pm blib\lib\Bio\SeqIO\embl.pm cp Bio/SeqIO/tigr.pm blib\lib\Bio\SeqIO\tigr.pm cp Bio/Biblio/IO/medline2ref.pm blib\lib\Bio\Biblio\IO\medline2ref.pm cp Bio/SeqIO/asciitree.pm blib\lib\Bio\SeqIO\asciitree.pm cp Bio/Graphics/Glyph/pinsertion.pm blib\lib\Bio\Graphics\Glyph\pinsertion.pm cp Bio/Tools/AnalysisResult.pm blib\lib\Bio\Tools\AnalysisResult.pm cp Bio/Graphics/Glyph/toomany.pm blib\lib\Bio\Graphics\Glyph\toomany.pm cp Bio/Biblio/Journal.pm blib\lib\Bio\Biblio\Journal.pm cp Bio/DB/GFF/Aggregator/transcript.pm blib\lib\Bio\DB\GFF\Aggregator\transcript.pm cp Bio/Search/HSP/GenericHSP.pm blib\lib\Bio\Search\HSP\GenericHSP.pm cp Bio/DB/GFF/Util/Rearrange.pm blib\lib\Bio\DB\GFF\Util\Rearrange.pm cp Bio/AnnotationCollectionI.pm blib\lib\Bio\AnnotationCollectionI.pm cp Bio/SeqFeatureI.pm blib\lib\Bio\SeqFeatureI.pm cp Bio/Factory/ObjectFactoryI.pm blib\lib\Bio\Factory\ObjectFactoryI.pm cp Bio/AnalysisParserI.pm blib\lib\Bio\AnalysisParserI.pm cp Bio/Matrix/PSM/IO/transfac.pm blib\lib\Bio\Matrix\PSM\IO\transfac.pm cp Bio/Tools/Analysis/Protein/Sopma.pm blib\lib\Bio\Tools\Analysis\Protein\Sopma.pm cp Bio/Matrix/PSM/PsmHeader.pm blib\lib\Bio\Matrix\PSM\PsmHeader.pm cp Bio/SearchDist.pm blib\lib\Bio\SearchDist.pm cp Bio/Expression/FeatureGroup/FeatureGroupMas50.pm blib\lib\Bio\Expression\FeatureGroup\FeatureGroupMas50.pm cp Bio/Tools/ECnumber.pm blib\lib\Bio\Tools\ECnumber.pm cp Bio/LiveSeq/Range.pm blib\lib\Bio\LiveSeq\Range.pm cp Bio/Restriction/EnzymeCollection.pm blib\lib\Bio\Restriction\EnzymeCollection.pm cp Bio/Tools/Pseudowise.pm blib\lib\Bio\Tools\Pseudowise.pm cp Bio/Matrix/IO/phylip.pm blib\lib\Bio\Matrix\IO\phylip.pm cp Bio/Tools/Genscan.pm blib\lib\Bio\Tools\Genscan.pm cp Bio/OntologyIO/soflat.pm blib\lib\Bio\OntologyIO\soflat.pm cp Bio/Tools/GFF.pm blib\lib\Bio\Tools\GFF.pm cp Bio/Tools/Blast.pm blib\lib\Bio\Tools\Blast.pm cp Bio/Das/SegmentI.pm blib\lib\Bio\Das\SegmentI.pm cp Bio/Das/FeatureTypeI.pm blib\lib\Bio\Das\FeatureTypeI.pm cp Bio/Graphics/Glyph/graded_segments.pm blib\lib\Bio\Graphics\Glyph\graded_segments.pm cp bptutorial.pl blib\lib\bptutorial.pl cp Bio/Structure/Model.pm blib\lib\Bio\Structure\Model.pm cp Bio/Graphics/Glyph/dna.pm blib\lib\Bio\Graphics\Glyph\dna.pm cp Bio/Restriction/Analysis.pm blib\lib\Bio\Restriction\Analysis.pm cp Bio/Tree/Node.pm blib\lib\Bio\Tree\Node.pm cp Bio/Seq/SeqFastaSpeedFactory.pm blib\lib\Bio\Seq\SeqFastaSpeedFactory.pm cp Bio/LiveSeq/Repeat_Region.pm blib\lib\Bio\LiveSeq\Repeat_Region.pm cp Bio/Tools/RandomDistFunctions.pm blib\lib\Bio\Tools\RandomDistFunctions.pm cp Bio/Annotation/Reference.pm blib\lib\Bio\Annotation\Reference.pm cp Bio/Phenotype/MeSH/Term.pm blib\lib\Bio\Phenotype\MeSH\Term.pm cp Bio/Coordinate/MapperI.pm blib\lib\Bio\Coordinate\MapperI.pm cp Bio/DB/WebDBSeqI.pm blib\lib\Bio\DB\WebDBSeqI.pm cp Bio/TreeIO/tabtree.pm blib\lib\Bio\TreeIO\tabtree.pm cp Bio/Tools/Primer3.pm blib\lib\Bio\Tools\Primer3.pm cp Bio/DB/GFF/Adaptor/dbi/pg.pm blib\lib\Bio\DB\GFF\Adaptor\dbi\pg.pm cp Bio/Seq/SeqFactory.pm blib\lib\Bio\Seq\SeqFactory.pm cp Bio/Tools/Seg.pm blib\lib\Bio\Tools\Seg.pm cp Bio/SeqIO/genbank.pm blib\lib\Bio\SeqIO\genbank.pm cp Bio/PrimarySeq.pm blib\lib\Bio\PrimarySeq.pm cp Bio/AlignIO/pfam.pm blib\lib\Bio\AlignIO\pfam.pm cp Bio/AlignIO/nexus.pm blib\lib\Bio\AlignIO\nexus.pm cp Bio/DB/GFF/Aggregator/none.pm blib\lib\Bio\DB\GFF\Aggregator\none.pm cp Bio/DB/GFF/Adaptor/dbi.pm blib\lib\Bio\DB\GFF\Adaptor\dbi.pm cp Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm blib\lib\Bio\OntologyIO\Handlers\InterPro_BioSQL_Handler.pm cp Bio/Tools/Signalp.pm blib\lib\Bio\Tools\Signalp.pm cp Bio/Location/CoordinatePolicyI.pm blib\lib\Bio\Location\CoordinatePolicyI.pm cp biodesign.pod blib\lib\biodesign.pod cp Bio/SearchIO/Writer/GbrowseGFF.pm blib\lib\Bio\SearchIO\Writer\GbrowseGFF.pm cp Bio/PopGen/Population.pm blib\lib\Bio\PopGen\Population.pm cp Bio/Root/HTTPget.pm blib\lib\Bio\Root\HTTPget.pm cp Bio/AlignIO/maf.pm blib\lib\Bio\AlignIO\maf.pm cp Bio/Graphics/Pictogram.pm blib\lib\Bio\Graphics\Pictogram.pm cp Bio/Search/Result/ResultFactory.pm blib\lib\Bio\Search\Result\ResultFactory.pm cp Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm blib\lib\Bio\Phenotype\OMIM\OMIMentryAllelicVariant.pm cp Bio/Tools/Phylo/Phylip/ProtDist.pm blib\lib\Bio\Tools\Phylo\Phylip\ProtDist.pm cp Bio/Annotation/Collection.pm blib\lib\Bio\Annotation\Collection.pm cp Bio/Tools/IUPAC.pm blib\lib\Bio\Tools\IUPAC.pm cp Bio/DB/Taxonomy/flatfile.pm blib\lib\Bio\DB\Taxonomy\flatfile.pm cp Bio/Graphics/Glyph/triangle.pm blib\lib\Bio\Graphics\Glyph\triangle.pm cp Bio/Graphics.pm blib\lib\Bio\Graphics.pm cp Bio/DB/GFF/Aggregator/ucsc_refgene.pm blib\lib\Bio\DB\GFF\Aggregator\ucsc_refgene.pm cp Bio/SeqIO/abi.pm blib\lib\Bio\SeqIO\abi.pm cp Bio/AlignIO/msf.pm blib\lib\Bio\AlignIO\msf.pm cp Bio/AlignIO/bl2seq.pm blib\lib\Bio\AlignIO\bl2seq.pm cp Bio/Tools/BPbl2seq.pm blib\lib\Bio\Tools\BPbl2seq.pm cp Bio/Ontology/SimpleOntologyEngine.pm blib\lib\Bio\Ontology\SimpleOntologyEngine.pm cp Bio/Variation/IO.pm blib\lib\Bio\Variation\IO.pm cp Bio/Root/Storable.pm blib\lib\Bio\Root\Storable.pm cp Bio/Ontology/PathI.pm blib\lib\Bio\Ontology\PathI.pm cp Bio/AnnotationI.pm blib\lib\Bio\AnnotationI.pm cp Bio/Restriction/IO/bairoch.pm blib\lib\Bio\Restriction\IO\bairoch.pm cp Bio/Tools/WWW.pm blib\lib\Bio\Tools\WWW.pm cp Bio/SeqIO/game/gameSubs.pm blib\lib\Bio\SeqIO\game\gameSubs.pm cp Bio/Seq/LargePrimarySeq.pm blib\lib\Bio\Seq\LargePrimarySeq.pm cp Bio/SearchIO/Writer/BSMLResultWriter.pm blib\lib\Bio\SearchIO\Writer\BSMLResultWriter.pm cp Bio/SearchIO/exonerate.pm blib\lib\Bio\SearchIO\exonerate.pm cp Bio/Factory/HitFactoryI.pm blib\lib\Bio\Factory\HitFactoryI.pm cp Bio/SimpleAlign.pm blib\lib\Bio\SimpleAlign.pm cp Bio/Matrix/PSM/SiteMatrix.pm blib\lib\Bio\Matrix\PSM\SiteMatrix.pm cp Bio/Graphics/RendererI.pm blib\lib\Bio\Graphics\RendererI.pm cp Bio/Expression/FeatureSet/FeatureSetMas50.pm blib\lib\Bio\Expression\FeatureSet\FeatureSetMas50.pm cp Bio/Tools/Blast/Sbjct.pm blib\lib\Bio\Tools\Blast\Sbjct.pm cp Bio/Tools/Phylo/PAML.pm blib\lib\Bio\Tools\Phylo\PAML.pm cp Bio/Graphics/FeatureFile/Iterator.pm blib\lib\Bio\Graphics\FeatureFile\Iterator.pm cp Bio/LiveSeq/Intron.pm blib\lib\Bio\LiveSeq\Intron.pm cp Bio/DB/GFF/Aggregator/clone.pm blib\lib\Bio\DB\GFF\Aggregator\clone.pm cp Bio/Map/Position.pm blib\lib\Bio\Map\Position.pm cp Bio/PrimarySeqI.pm blib\lib\Bio\PrimarySeqI.pm cp Bio/Graphics/Glyph/alignment.pm blib\lib\Bio\Graphics\Glyph\alignment.pm cp Bio/Root/IOManager.pm blib\lib\Bio\Root\IOManager.pm cp Bio/LiveSeq/Gene.pm blib\lib\Bio\LiveSeq\Gene.pm cp Bio/Ontology/Relationship.pm blib\lib\Bio\Ontology\Relationship.pm cp Bio/Search/Hit/HitFactory.pm blib\lib\Bio\Search\Hit\HitFactory.pm cp Bio/DB/Flat/BDB/fasta.pm blib\lib\Bio\DB\Flat\BDB\fasta.pm cp Bio/Seq/SequenceTrace.pm blib\lib\Bio\Seq\SequenceTrace.pm cp Bio/Factory/ApplicationFactoryI.pm blib\lib\Bio\Factory\ApplicationFactoryI.pm cp Bio/DB/GFF/Typename.pm blib\lib\Bio\DB\GFF\Typename.pm cp Bio/Search/HSP/HSPFactory.pm blib\lib\Bio\Search\HSP\HSPFactory.pm cp Bio/DB/GFF/Homol.pm blib\lib\Bio\DB\GFF\Homol.pm cp Bio/Event/EventGeneratorI.pm blib\lib\Bio\Event\EventGeneratorI.pm cp Bio/AlignIO/psi.pm blib\lib\Bio\AlignIO\psi.pm cp Bio/Graphics/Glyph/redgreen_box.pm blib\lib\Bio\Graphics\Glyph\redgreen_box.pm cp Bio/Tools/BPlite/Sbjct.pm blib\lib\Bio\Tools\BPlite\Sbjct.pm cp biodatabases.pod blib\lib\biodatabases.pod cp Bio/Graphics/FeatureFile.pm blib\lib\Bio\Graphics\FeatureFile.pm cp Bio/Map/Microsatellite.pm blib\lib\Bio\Map\Microsatellite.pm cp Bio/LiveSeq/Translation.pm blib\lib\Bio\LiveSeq\Translation.pm cp Bio/Search/Hit/HitI.pm blib\lib\Bio\Search\Hit\HitI.pm cp Bio/DB/SeqI.pm blib\lib\Bio\DB\SeqI.pm cp Bio/Search/Iteration/GenericIteration.pm blib\lib\Bio\Search\Iteration\GenericIteration.pm cp Bio/Index/SwissPfam.pm blib\lib\Bio\Index\SwissPfam.pm cp Bio/DB/GenBank.pm blib\lib\Bio\DB\GenBank.pm cp Bio/Graphics/Glyph/Factory.pm blib\lib\Bio\Graphics\Glyph\Factory.pm cp Bio/Tools/BPlite/HSP.pm blib\lib\Bio\Tools\BPlite\HSP.pm cp Bio/SeqFeature/SiRNA/Oligo.pm blib\lib\Bio\SeqFeature\SiRNA\Oligo.pm cp Bio/Ontology/Path.pm blib\lib\Bio\Ontology\Path.pm cp Bio/Assembly/IO/phrap.pm blib\lib\Bio\Assembly\IO\phrap.pm cp Bio/PopGen/IndividualI.pm blib\lib\Bio\PopGen\IndividualI.pm cp Bio/DB/MeSH.pm blib\lib\Bio\DB\MeSH.pm cp Bio/DB/GFF/Aggregator/coding.pm blib\lib\Bio\DB\GFF\Aggregator\coding.pm cp Bio/Index/EMBL.pm blib\lib\Bio\Index\EMBL.pm cp Bio/SeqFeature/Gene/GeneStructureI.pm blib\lib\Bio\SeqFeature\Gene\GeneStructureI.pm cp Bio/ClusterIO.pm blib\lib\Bio\ClusterIO.pm cp Bio/DB/EMBL.pm blib\lib\Bio\DB\EMBL.pm cp Bio/DB/DBFetch.pm blib\lib\Bio\DB\DBFetch.pm cp Bio/DB/Taxonomy.pm blib\lib\Bio\DB\Taxonomy.pm cp Bio/Tools/Blast/README blib\lib\Bio\Tools\Blast\README cp Bio/Matrix/Scoring.pm blib\lib\Bio\Matrix\Scoring.pm cp Bio/Map/CytoPosition.pm blib\lib\Bio\Map\CytoPosition.pm cp Bio/Seq/Meta.pm blib\lib\Bio\Seq\Meta.pm cp Bio/Tools/SiRNA.pm blib\lib\Bio\Tools\SiRNA.pm cp Bio/Phenotype/Correlate.pm blib\lib\Bio\Phenotype\Correlate.pm cp Bio/Biblio/Ref.pm blib\lib\Bio\Biblio\Ref.pm cp Bio/DB/Query/GenBank.pm blib\lib\Bio\DB\Query\GenBank.pm cp Bio/Search/GenericDatabase.pm blib\lib\Bio\Search\GenericDatabase.pm cp Bio/SeqFeature/Tools/Unflattener.pm blib\lib\Bio\SeqFeature\Tools\Unflattener.pm cp Bio/LiveSeq/Prim_Transcript.pm blib\lib\Bio\LiveSeq\Prim_Transcript.pm cp Bio/Tools/Promoterwise.pm blib\lib\Bio\Tools\Promoterwise.pm cp Bio/Tools/Geneid.pm blib\lib\Bio\Tools\Geneid.pm cp Bio/Root/Version.pm blib\lib\Bio\Root\Version.pm cp Bio/Tree/NodeNHX.pm blib\lib\Bio\Tree\NodeNHX.pm cp Bio/AlignIO/clustalw.pm blib\lib\Bio\AlignIO\clustalw.pm cp Bio/Factory/FTLocationFactory.pm blib\lib\Bio\Factory\FTLocationFactory.pm cp Bio/DB/GFF/Adaptor/dbi/mysql.pm blib\lib\Bio\DB\GFF\Adaptor\dbi\mysql.pm cp Bio/DB/Ace.pm blib\lib\Bio\DB\Ace.pm cp Bio/Align/DNAStatistics.pm blib\lib\Bio\Align\DNAStatistics.pm cp Bio/Coordinate/Utils.pm blib\lib\Bio\Coordinate\Utils.pm cp Bio/Root/Vector.pm blib\lib\Bio\Root\Vector.pm cp Bio/LiveSeq/IO/BioPerl.pm blib\lib\Bio\LiveSeq\IO\BioPerl.pm cp Bio/Variation/IO/flat.pm blib\lib\Bio\Variation\IO\flat.pm cp Bio/SeqIO/chadoxml.pm blib\lib\Bio\SeqIO\chadoxml.pm cp Bio/PopGen/PopStats.pm blib\lib\Bio\PopGen\PopStats.pm cp Bio/Factory/SequenceProcessorI.pm blib\lib\Bio\Factory\SequenceProcessorI.pm cp Bio/Location/AvWithinCoordPolicy.pm blib\lib\Bio\Location\AvWithinCoordPolicy.pm cp Bio/Structure/SecStr/DSSP/Res.pm blib\lib\Bio\Structure\SecStr\DSSP\Res.pm cp Bio/Biblio/TechReport.pm blib\lib\Bio\Biblio\TechReport.pm cp Bio/Graphics/Glyph/translation.pm blib\lib\Bio\Graphics\Glyph\translation.pm cp Bio/SearchIO/SearchResultEventBuilder.pm blib\lib\Bio\SearchIO\SearchResultEventBuilder.pm cp Bio/Location/Simple.pm blib\lib\Bio\Location\Simple.pm cp Bio/SeqIO/gcg.pm blib\lib\Bio\SeqIO\gcg.pm cp Bio/SeqIO/alf.pm blib\lib\Bio\SeqIO\alf.pm cp Bio/SeqI.pm blib\lib\Bio\SeqI.pm cp Bio/Seq/QualI.pm blib\lib\Bio\Seq\QualI.pm cp Bio/Map/LinkagePosition.pm blib\lib\Bio\Map\LinkagePosition.pm cp Bio/Ontology/SimpleGOEngine.pm blib\lib\Bio\Ontology\SimpleGOEngine.pm cp Bio/Cluster/ClusterFactory.pm blib\lib\Bio\Cluster\ClusterFactory.pm cp Bio/PopGen/IO/csv.pm blib\lib\Bio\PopGen\IO\csv.pm cp Bio/SeqFeature/Gene/Poly_A_site.pm blib\lib\Bio\SeqFeature\Gene\Poly_A_site.pm cp Bio/Matrix/PSM/SiteMatrixI.pm blib\lib\Bio\Matrix\PSM\SiteMatrixI.pm cp Bio/SeqFeature/Gene/ExonI.pm blib\lib\Bio\SeqFeature\Gene\ExonI.pm cp Bio/Tools/Hmmpfam.pm blib\lib\Bio\Tools\Hmmpfam.pm cp Bio/Graphics/Glyph/primers.pm blib\lib\Bio\Graphics\Glyph\primers.pm cp Bio/Expression/FeatureGroup.pm blib\lib\Bio\Expression\FeatureGroup.pm cp Bio/DB/GFF/Aggregator/ucsc_genscan.pm blib\lib\Bio\DB\GFF\Aggregator\ucsc_genscan.pm cp Bio/Ontology/InterProTerm.pm blib\lib\Bio\Ontology\InterProTerm.pm cp Bio/Graphics/Glyph/heterogeneous_segments.pm blib\lib\Bio\Graphics\Glyph\heterogeneous_segments.pm cp Bio/IdentifiableI.pm blib\lib\Bio\IdentifiableI.pm cp Bio/Graphics/Glyph/crossbox.pm blib\lib\Bio\Graphics\Glyph\crossbox.pm cp Bio/Coordinate/Chain.pm blib\lib\Bio\Coordinate\Chain.pm cp Bio/Tools/Grail.pm blib\lib\Bio\Tools\Grail.pm cp Bio/Tools/Blast/HTML.pm blib\lib\Bio\Tools\Blast\HTML.pm cp Bio/DB/InMemoryCache.pm blib\lib\Bio\DB\InMemoryCache.pm cp Bio/PopGen/GenotypeI.pm blib\lib\Bio\PopGen\GenotypeI.pm cp Bio/DB/GFF/Segment.pm blib\lib\Bio\DB\GFF\Segment.pm cp Bio/Symbol/DNAAlphabet.pm blib\lib\Bio\Symbol\DNAAlphabet.pm cp Bio/OntologyIO/goflat.pm blib\lib\Bio\OntologyIO\goflat.pm cp Bio/DB/FileCache.pm blib\lib\Bio\DB\FileCache.pm cp Bio/Tools/Blast/HSP.pm blib\lib\Bio\Tools\Blast\HSP.pm cp Bio/DB/GFF/Util/Binning.pm blib\lib\Bio\DB\GFF\Util\Binning.pm cp Bio/Biblio/Person.pm blib\lib\Bio\Biblio\Person.pm cp Bio/Map/Marker.pm blib\lib\Bio\Map\Marker.pm cp Bio/Matrix/PSM/PsmHeaderI.pm blib\lib\Bio\Matrix\PSM\PsmHeaderI.pm cp Bio/Tools/CodonTable.pm blib\lib\Bio\Tools\CodonTable.pm cp Bio/SeqIO/bsml.pm blib\lib\Bio\SeqIO\bsml.pm cp Bio/DB/QueryI.pm blib\lib\Bio\DB\QueryI.pm cp Bio/Tools/AlignFactory.pm blib\lib\Bio\Tools\AlignFactory.pm cp Bio/Graphics/Glyph/segments.pm blib\lib\Bio\Graphics\Glyph\segments.pm cp Bio/Seq/SeqWithQuality.pm blib\lib\Bio\Seq\SeqWithQuality.pm cp Bio/Annotation/DBLink.pm blib\lib\Bio\Annotation\DBLink.pm cp Bio/SearchIO/FastHitEventBuilder.pm blib\lib\Bio\SearchIO\FastHitEventBuilder.pm cp Bio/Search/Hit/BlastHit.pm blib\lib\Bio\Search\Hit\BlastHit.pm cp Bio/DB/XEMBL.pm blib\lib\Bio\DB\XEMBL.pm cp Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm blib\lib\Bio\DB\GFF\Adaptor\dbi\mysqlopt.pm cp Bio/Graphics/Glyph/redgreen_segment.pm blib\lib\Bio\Graphics\Glyph\redgreen_segment.pm cp Bio/SearchIO/blast.pm blib\lib\Bio\SearchIO\blast.pm cp Bio/DB/GFF/Adaptor/biofetch_oracle.pm blib\lib\Bio\DB\GFF\Adaptor\biofetch_oracle.pm cp Bio/Species.pm blib\lib\Bio\Species.pm cp Bio/Tools/Primer/AssessorI.pm blib\lib\Bio\Tools\Primer\AssessorI.pm cp Bio/Seq/RichSeqI.pm blib\lib\Bio\Seq\RichSeqI.pm cp Bio/Tools/Prediction/Exon.pm blib\lib\Bio\Tools\Prediction\Exon.pm cp Bio/SearchIO/Writer/HitTableWriter.pm blib\lib\Bio\SearchIO\Writer\HitTableWriter.pm cp Bio/SearchIO/EventHandlerI.pm blib\lib\Bio\SearchIO\EventHandlerI.pm cp Bio/Variation/AAReverseMutate.pm blib\lib\Bio\Variation\AAReverseMutate.pm cp Bio/Tools/Prediction/Gene.pm blib\lib\Bio\Tools\Prediction\Gene.pm cp Bio/SeqFeature/Primer.pm blib\lib\Bio\SeqFeature\Primer.pm cp Bio/Search/SearchUtils.pm blib\lib\Bio\Search\SearchUtils.pm cp Bio/Biblio/WebResource.pm blib\lib\Bio\Biblio\WebResource.pm cp Bio/AlignIO/fasta.pm blib\lib\Bio\AlignIO\fasta.pm cp Bio/Tools/Phylo/Molphy.pm blib\lib\Bio\Tools\Phylo\Molphy.pm cp Bio/Search/Hit/HMMERHit.pm blib\lib\Bio\Search\Hit\HMMERHit.pm cp Bio/Tools/Run/StandAloneBlast.pm blib\lib\Bio\Tools\Run\StandAloneBlast.pm cp Bio/Tools/MZEF.pm blib\lib\Bio\Tools\MZEF.pm cp Bio/Root/Err.pm blib\lib\Bio\Root\Err.pm cp Bio/SearchIO/Writer/ResultTableWriter.pm blib\lib\Bio\SearchIO\Writer\ResultTableWriter.pm cp Bio/Tools/Primer/Feature.pm blib\lib\Bio\Tools\Primer\Feature.pm cp Bio/Ontology/RelationshipFactory.pm blib\lib\Bio\Ontology\RelationshipFactory.pm cp Bio/DB/GFF/Adaptor/biofetch.pm blib\lib\Bio\DB\GFF\Adaptor\biofetch.pm cp Bio/Tools/Est2Genome.pm blib\lib\Bio\Tools\Est2Genome.pm cp Bio/Search/HSP/HMMERHSP.pm blib\lib\Bio\Search\HSP\HMMERHSP.pm cp Bio/Variation/DNAMutation.pm blib\lib\Bio\Variation\DNAMutation.pm cp Bio/Factory/MapFactoryI.pm blib\lib\Bio\Factory\MapFactoryI.pm cp Bio/Symbol/README.Symbol blib\lib\Bio\Symbol\README.Symbol cp Bio/Tree/Tree.pm blib\lib\Bio\Tree\Tree.pm cp Bio/Tools/EMBOSS/Palindrome.pm blib\lib\Bio\Tools\EMBOSS\Palindrome.pm cp Bio/Structure/IO.pm blib\lib\Bio\Structure\IO.pm cp Bio/SeqIO/game/gameWriter.pm blib\lib\Bio\SeqIO\game\gameWriter.pm cp bioperl.pod blib\lib\bioperl.pod cp Bio/Variation/SNP.pm blib\lib\Bio\Variation\SNP.pm cp Bio/Factory/AnalysisI.pm blib\lib\Bio\Factory\AnalysisI.pm cp Bio/SearchIO/SearchWriterI.pm blib\lib\Bio\SearchIO\SearchWriterI.pm cp Bio/SeqFeature/Gene/Promoter.pm blib\lib\Bio\SeqFeature\Gene\Promoter.pm cp Bio/SeqFeature/FeaturePair.pm blib\lib\Bio\SeqFeature\FeaturePair.pm cp Bio/Graphics/Glyph/transcript2.pm blib\lib\Bio\Graphics\Glyph\transcript2.pm cp Bio/Location/Split.pm blib\lib\Bio\Location\Split.pm cp Bio/SeqIO/exp.pm blib\lib\Bio\SeqIO\exp.pm cp Bio/Cluster/SequenceFamily.pm blib\lib\Bio\Cluster\SequenceFamily.pm cp Bio/SeqIO/swiss.pm blib\lib\Bio\SeqIO\swiss.pm cp Bio/Tools/Analysis/DNA/ESEfinder.pm blib\lib\Bio\Tools\Analysis\DNA\ESEfinder.pm cp Bio/DB/Makefile.PL blib\lib\Bio\DB\Makefile.PL cp Bio/ClusterIO/unigene.pm blib\lib\Bio\ClusterIO\unigene.pm cp Bio/DB/XEMBLService.pm blib\lib\Bio\DB\XEMBLService.pm cp Bio/Tools/PrositeScan.pm blib\lib\Bio\Tools\PrositeScan.pm cp Bio/Annotation/StructuredValue.pm blib\lib\Bio\Annotation\StructuredValue.pm cp Bio/DB/Flat/BinarySearch.pm blib\lib\Bio\DB\Flat\BinarySearch.pm cp Bio/Tools/FootPrinter.pm blib\lib\Bio\Tools\FootPrinter.pm cp Bio/SeqIO/FTHelper.pm blib\lib\Bio\SeqIO\FTHelper.pm cp Bio/Graphics/Glyph/dot.pm blib\lib\Bio\Graphics\Glyph\dot.pm cp Bio/Tools/Coil.pm blib\lib\Bio\Tools\Coil.pm cp Bio/Restriction/Enzyme/MultiSite.pm blib\lib\Bio\Restriction\Enzyme\MultiSite.pm cp Bio/Root/IO.pm blib\lib\Bio\Root\IO.pm cp Bio/Coordinate/Collection.pm blib\lib\Bio\Coordinate\Collection.pm cp Bio/Graphics/Glyph/transcript.pm blib\lib\Bio\Graphics\Glyph\transcript.pm cp Bio/Biblio/IO/pubmedxml.pm blib\lib\Bio\Biblio\IO\pubmedxml.pm cp Bio/Search/Result/GenericResult.pm blib\lib\Bio\Search\Result\GenericResult.pm cp Bio/Matrix/PSM/IO/mast.pm blib\lib\Bio\Matrix\PSM\IO\mast.pm cp Bio/Biblio/MedlineBook.pm blib\lib\Bio\Biblio\MedlineBook.pm cp Bio/Ontology/GOterm.pm blib\lib\Bio\Ontology\GOterm.pm cp Bio/Symbol/Symbol.pm blib\lib\Bio\Symbol\Symbol.pm cp Bio/DB/GFF/Featname.pm blib\lib\Bio\DB\GFF\Featname.pm cp Bio/Symbol/Alphabet.pm blib\lib\Bio\Symbol\Alphabet.pm cp Bio/Graphics/Glyph/xyplot.pm blib\lib\Bio\Graphics\Glyph\xyplot.pm cp Bio/LocatableSeq.pm blib\lib\Bio\LocatableSeq.pm cp Bio/DB/CUTG.pm blib\lib\Bio\DB\CUTG.pm cp Bio/Matrix/IO/scoring.pm blib\lib\Bio\Matrix\IO\scoring.pm cp Bio/Factory/ObjectBuilderI.pm blib\lib\Bio\Factory\ObjectBuilderI.pm cp Bio/DB/Universal.pm blib\lib\Bio\DB\Universal.pm cp Bio/SeqIO/ztr.pm blib\lib\Bio\SeqIO\ztr.pm cp Bio/Structure/Entry.pm blib\lib\Bio\Structure\Entry.pm cp Bio/Tools/OddCodes.pm blib\lib\Bio\Tools\OddCodes.pm cp Bio/Matrix/PSM/IO/meme.pm blib\lib\Bio\Matrix\PSM\IO\meme.pm cp Bio/Biblio/JournalArticle.pm blib\lib\Bio\Biblio\JournalArticle.pm cp Bio/Coordinate/Pair.pm blib\lib\Bio\Coordinate\Pair.pm cp Bio/DB/GFF/Aggregator/processed_transcript.pm blib\lib\Bio\DB\GFF\Aggregator\processed_transcript.pm cp Bio/Tools/Lucy.pm blib\lib\Bio\Tools\Lucy.pm cp Bio/Index/Fasta.pm blib\lib\Bio\Index\Fasta.pm cp Bio/Align/StatisticsI.pm blib\lib\Bio\Align\StatisticsI.pm cp Bio/SeqFeature/PositionProxy.pm blib\lib\Bio\SeqFeature\PositionProxy.pm cp Bio/Tools/SeqAnal.pm blib\lib\Bio\Tools\SeqAnal.pm cp Bio/LiveSeq/IO/README blib\lib\Bio\LiveSeq\IO\README cp Bio/DB/GFF/Adaptor/ace.pm blib\lib\Bio\DB\GFF\Adaptor\ace.pm cp Bio/Structure/SecStr/STRIDE/Res.pm blib\lib\Bio\Structure\SecStr\STRIDE\Res.pm cp Bio/Biblio/MedlineBookArticle.pm blib\lib\Bio\Biblio\MedlineBookArticle.pm cp Bio/Coordinate/ResultI.pm blib\lib\Bio\Coordinate\ResultI.pm cp Bio/Tools/Primer/Pair.pm blib\lib\Bio\Tools\Primer\Pair.pm cp Bio/PopGen/Statistics.pm blib\lib\Bio\PopGen\Statistics.pm cp Bio/Tools/Analysis/SimpleAnalysisBase.pm blib\lib\Bio\Tools\Analysis\SimpleAnalysisBase.pm cp Bio/Tools/Analysis/Protein/NetPhos.pm blib\lib\Bio\Tools\Analysis\Protein\NetPhos.pm cp Bio/Tools/Analysis/Protein/Scansite.pm blib\lib\Bio\Tools\Analysis\Protein\Scansite.pm cp Bio/Graphics/Glyph/arrow.pm blib\lib\Bio\Graphics\Glyph\arrow.pm cp Bio/DB/Flat/BDB/swissprot.pm blib\lib\Bio\DB\Flat\BDB\swissprot.pm cp Bio/Graphics/Panel.pm blib\lib\Bio\Graphics\Panel.pm cp Bio/ClusterI.pm blib\lib\Bio\ClusterI.pm cp Bio/SeqFeature/CollectionI.pm blib\lib\Bio\SeqFeature\CollectionI.pm cp Bio/Biblio/MedlineArticle.pm blib\lib\Bio\Biblio\MedlineArticle.pm cp Bio/Phenotype/PhenotypeI.pm blib\lib\Bio\Phenotype\PhenotypeI.pm cp Bio/AlignIO/metafasta.pm blib\lib\Bio\AlignIO\metafasta.pm cp Bio/Taxonomy/Taxon.pm blib\lib\Bio\Taxonomy\Taxon.pm cp Bio/Seq/LargeSeq.pm blib\lib\Bio\Seq\LargeSeq.pm cp Bio/DB/GDB.pm blib\lib\Bio\DB\GDB.pm cp Bio/Tools/Profile.pm blib\lib\Bio\Tools\Profile.pm cp Bio/Graphics/Glyph/ruler_arrow.pm blib\lib\Bio\Graphics\Glyph\ruler_arrow.pm cp Bio/Tools/Genemark.pm blib\lib\Bio\Tools\Genemark.pm cp Bio/Biblio/Patent.pm blib\lib\Bio\Biblio\Patent.pm cp Bio/Matrix/IO.pm blib\lib\Bio\Matrix\IO.pm cp Bio/DB/GFF/Aggregator.pm blib\lib\Bio\DB\GFF\Aggregator.pm cp Bio/Seq/RichSeq.pm blib\lib\Bio\Seq\RichSeq.pm cp Bio/SeqFeature/SiRNA/Pair.pm blib\lib\Bio\SeqFeature\SiRNA\Pair.pm cp Bio/DB/GFF.pm blib\lib\Bio\DB\GFF.pm cp Bio/Tools/BPpsilite.pm blib\lib\Bio\Tools\BPpsilite.pm cp Bio/Graphics/Glyph/track.pm blib\lib\Bio\Graphics\Glyph\track.pm cp Bio/PopGen/Simulation/GeneticDrift.pm blib\lib\Bio\PopGen\Simulation\GeneticDrift.pm cp Bio/Factory/ResultFactoryI.pm blib\lib\Bio\Factory\ResultFactoryI.pm cp Bio/Seq/MetaI.pm blib\lib\Bio\Seq\MetaI.pm cp Bio/SeqFeature/Computation.pm blib\lib\Bio\SeqFeature\Computation.pm cp Bio/Seq/EncodedSeq.pm blib\lib\Bio\Seq\EncodedSeq.pm cp Bio/Tools/Analysis/Protein/Domcut.pm blib\lib\Bio\Tools\Analysis\Protein\Domcut.pm cp Bio/Variation/README blib\lib\Bio\Variation\README cp Bio/DB/Registry.pm blib\lib\Bio\DB\Registry.pm cp bioscripts.pod blib\lib\bioscripts.pod cp Bio/Variation/VariantI.pm blib\lib\Bio\Variation\VariantI.pm cp Bio/Tools/Glimmer.pm blib\lib\Bio\Tools\Glimmer.pm cp Bio/Factory/SequenceFactoryI.pm blib\lib\Bio\Factory\SequenceFactoryI.pm cp Bio/Graphics/Glyph/line.pm blib\lib\Bio\Graphics\Glyph\line.pm cp Bio/Root/Utilities.pm blib\lib\Bio\Root\Utilities.pm cp Bio/Search/Hit/GenericHit.pm blib\lib\Bio\Search\Hit\GenericHit.pm cp Bio/Tools/RestrictionEnzyme.pm blib\lib\Bio\Tools\RestrictionEnzyme.pm cp Bio/Map/LinkageMap.pm blib\lib\Bio\Map\LinkageMap.pm cp Bio/AlignIO/stockholm.pm blib\lib\Bio\AlignIO\stockholm.pm cp Bio/OntologyIO/Handlers/InterProHandler.pm blib\lib\Bio\OntologyIO\Handlers\InterProHandler.pm cp Bio/DB/GFF/Adaptor/dbi/mysqlace.pm blib\lib\Bio\DB\GFF\Adaptor\dbi\mysqlace.pm cp Bio/PopGen/Individual.pm blib\lib\Bio\PopGen\Individual.pm cp Bio/Graphics/Glyph/splice_site.pm blib\lib\Bio\Graphics\Glyph\splice_site.pm cp Bio/DasI.pm blib\lib\Bio\DasI.pm cp Bio/Tools/Analysis/Protein/Mitoprot.pm blib\lib\Bio\Tools\Analysis\Protein\Mitoprot.pm cp Bio/OntologyIO/simplehierarchy.pm blib\lib\Bio\OntologyIO\simplehierarchy.pm cp Bio/Assembly/Scaffold.pm blib\lib\Bio\Assembly\Scaffold.pm cp Bio/Assembly/Contig.pm blib\lib\Bio\Assembly\Contig.pm cp Bio/SeqUtils.pm blib\lib\Bio\SeqUtils.pm cp Bio/TreeIO/nhx.pm blib\lib\Bio\TreeIO\nhx.pm cp Bio/Structure/Residue.pm blib\lib\Bio\Structure\Residue.pm cp Bio/DB/GFF/Adaptor/dbi/iterator.pm blib\lib\Bio\DB\GFF\Adaptor\dbi\iterator.pm cp Bio/Tools/Sim4/Results.pm blib\lib\Bio\Tools\Sim4\Results.pm cp Bio/OntologyIO/Handlers/BaseSAXHandler.pm blib\lib\Bio\OntologyIO\Handlers\BaseSAXHandler.pm cp Bio/Variation/AAChange.pm blib\lib\Bio\Variation\AAChange.pm cp Bio/Index/Fastq.pm blib\lib\Bio\Index\Fastq.pm cp Bio/SearchIO/Writer/TextResultWriter.pm blib\lib\Bio\SearchIO\Writer\TextResultWriter.pm cp Bio/Range.pm blib\lib\Bio\Range.pm cp Bio/OntologyIO/dagflat.pm blib\lib\Bio\OntologyIO\dagflat.pm cp Bio/SeqIO/pir.pm blib\lib\Bio\SeqIO\pir.pm cp Bio/Factory/SequenceStreamI.pm blib\lib\Bio\Factory\SequenceStreamI.pm cp Bio/ClusterIO/dbsnp.pm blib\lib\Bio\ClusterIO\dbsnp.pm cp Bio/SearchIO/IteratedSearchResultEventBuilder.pm blib\lib\Bio\SearchIO\IteratedSearchResultEventBuilder.pm cp Bio/Root/Xref.pm blib\lib\Bio\Root\Xref.pm cp Bio/AlignIO/meme.pm blib\lib\Bio\AlignIO\meme.pm cp Bio/Tools/Run/WrapperBase.pm blib\lib\Bio\Tools\Run\WrapperBase.pm cp Bio/Map/MapI.pm blib\lib\Bio\Map\MapI.pm cp Bio/PopGen/Marker.pm blib\lib\Bio\PopGen\Marker.pm cp Bio/Location/WidestCoordPolicy.pm blib\lib\Bio\Location\WidestCoordPolicy.pm cp Bio/Tools/Genomewise.pm blib\lib\Bio\Tools\Genomewise.pm cp Bio/Annotation/Comment.pm blib\lib\Bio\Annotation\Comment.pm cp Bio/Matrix/PhylipDist.pm blib\lib\Bio\Matrix\PhylipDist.pm cp Bio/Tools/BPlite.pm blib\lib\Bio\Tools\BPlite.pm cp Bio/Biblio/PubmedArticle.pm blib\lib\Bio\Biblio\PubmedArticle.pm cp Bio/Symbol/ProteinAlphabet.pm blib\lib\Bio\Symbol\ProteinAlphabet.pm cp Bio/Tools/Genewise.pm blib\lib\Bio\Tools\Genewise.pm cp Bio/Search/HSP/HSPI.pm blib\lib\Bio\Search\HSP\HSPI.pm cp Bio/Perl.pm blib\lib\Bio\Perl.pm cp Bio/LiveSeq/Exon.pm blib\lib\Bio\LiveSeq\Exon.pm cp Bio/SeqIO/game/gameHandler.pm blib\lib\Bio\SeqIO\game\gameHandler.pm cp Bio/LiveSeq/Chain.pm blib\lib\Bio\LiveSeq\Chain.pm cp Bio/Map/CytoMarker.pm blib\lib\Bio\Map\CytoMarker.pm cp Bio/AlignIO/selex.pm blib\lib\Bio\AlignIO\selex.pm cp Bio/SeqFeature/Gene/UTR.pm blib\lib\Bio\SeqFeature\Gene\UTR.pm cp Bio/Seq/SeqBuilder.pm blib\lib\Bio\Seq\SeqBuilder.pm cp Bio/Biblio/Service.pm blib\lib\Bio\Biblio\Service.pm cp Bio/Biblio/MedlineJournal.pm blib\lib\Bio\Biblio\MedlineJournal.pm cp Bio/DB/Flat/BDB/embl.pm blib\lib\Bio\DB\Flat\BDB\embl.pm cp Bio/Search/HSP/BlastHSP.pm blib\lib\Bio\Search\HSP\BlastHSP.pm cp Bio/LiveSeq/Mutator.pm blib\lib\Bio\LiveSeq\Mutator.pm cp Bio/Tools/Eponine.pm blib\lib\Bio\Tools\Eponine.pm cp Bio/SeqFeature/Gene/Intron.pm blib\lib\Bio\SeqFeature\Gene\Intron.pm cp Bio/DB/GFF/RelSegment.pm blib\lib\Bio\DB\GFF\RelSegment.pm cp Bio/Phenotype/Measure.pm blib\lib\Bio\Phenotype\Measure.pm cp Bio/DB/GFF/Aggregator/ucsc_ensgene.pm blib\lib\Bio\DB\GFF\Aggregator\ucsc_ensgene.pm cp Bio/Annotation/TypeManager.pm blib\lib\Bio\Annotation\TypeManager.pm cp Bio/Map/OrderedPosition.pm blib\lib\Bio\Map\OrderedPosition.pm cp Bio/SeqIO/MultiFile.pm blib\lib\Bio\SeqIO\MultiFile.pm cp Bio/Tools/Tmhmm.pm blib\lib\Bio\Tools\Tmhmm.pm cp Bio/Factory/SeqAnalysisParserFactory.pm blib\lib\Bio\Factory\SeqAnalysisParserFactory.pm cp Bio/DB/GenPept.pm blib\lib\Bio\DB\GenPept.pm cp Bio/SeqIO/game/featHandler.pm blib\lib\Bio\SeqIO\game\featHandler.pm cp Bio/Index/Blast.pm blib\lib\Bio\Index\Blast.pm cp Bio/Search/DatabaseI.pm blib\lib\Bio\Search\DatabaseI.pm cp Bio/Tools/Blat.pm blib\lib\Bio\Tools\Blat.pm cp Bio/Graphics/Glyph.pm blib\lib\Bio\Graphics\Glyph.pm cp Bio/Symbol/SymbolI.pm blib\lib\Bio\Symbol\SymbolI.pm cp Bio/Tools/EPCR.pm blib\lib\Bio\Tools\EPCR.pm cp Bio/Tools/pSW.pm blib\lib\Bio\Tools\pSW.pm cp Bio/Location/NarrowestCoordPolicy.pm blib\lib\Bio\Location\NarrowestCoordPolicy.pm cp Bio/AnnotatableI.pm blib\lib\Bio\AnnotatableI.pm cp Bio/Biblio/Proceeding.pm blib\lib\Bio\Biblio\Proceeding.pm cp Bio/TreeIO/newick.pm blib\lib\Bio\TreeIO\newick.pm cp Bio/SeqFeature/Gene/GeneStructure.pm blib\lib\Bio\SeqFeature\Gene\GeneStructure.pm cp Bio/Biblio/Book.pm blib\lib\Bio\Biblio\Book.pm cp Bio/SearchIO/Writer/HTMLResultWriter.pm blib\lib\Bio\SearchIO\Writer\HTMLResultWriter.pm cp Bio/Tree/Statistics.pm blib\lib\Bio\Tree\Statistics.pm cp Bio/Tools/BPlite/Iteration.pm blib\lib\Bio\Tools\BPlite\Iteration.pm cp Bio/Align/PairwiseStatistics.pm blib\lib\Bio\Align\PairwiseStatistics.pm cp Bio/Assembly/IO.pm blib\lib\Bio\Assembly\IO.pm cp Bio/Ontology/TermFactory.pm blib\lib\Bio\Ontology\TermFactory.pm cp Bio/Tools/SeqWords.pm blib\lib\Bio\Tools\SeqWords.pm cp Bio/DB/GFF/Adaptor/dbi/oracleace.pm blib\lib\Bio\DB\GFF\Adaptor\dbi\oracleace.pm cp Bio/Expression/FeatureI.pm blib\lib\Bio\Expression\FeatureI.pm cp Bio/Map/OrderedPositionWithDistance.pm blib\lib\Bio\Map\OrderedPositionWithDistance.pm cp Bio/Biblio/IO/pubmed2ref.pm blib\lib\Bio\Biblio\IO\pubmed2ref.pm cp Bio/SeqIO/game.pm blib\lib\Bio\SeqIO\game.pm cp Bio/Index/Abstract.pm blib\lib\Bio\Index\Abstract.pm cp Bio/SearchIO/blastxml.pm blib\lib\Bio\SearchIO\blastxml.pm cp Bio/Search/Iteration/IterationI.pm blib\lib\Bio\Search\Iteration\IterationI.pm cp Bio/Tools/HMMER/Domain.pm blib\lib\Bio\Tools\HMMER\Domain.pm cp Bio/DB/GFF/Adaptor/dbi/oracle.pm blib\lib\Bio\DB\GFF\Adaptor\dbi\oracle.pm cp Bio/Coordinate/GeneMapper.pm blib\lib\Bio\Coordinate\GeneMapper.pm cp Bio/Biblio/IO/medlinexml.pm blib\lib\Bio\Biblio\IO\medlinexml.pm cp Bio/Location/FuzzyLocationI.pm blib\lib\Bio\Location\FuzzyLocationI.pm cp Bio/SeqIO/ace.pm blib\lib\Bio\SeqIO\ace.pm cp Bio/Search/Hit/Fasta.pm blib\lib\Bio\Search\Hit\Fasta.pm cp Bio/Graphics/Glyph/span.pm blib\lib\Bio\Graphics\Glyph\span.pm cp Bio/Root/Exception.pm blib\lib\Bio\Root\Exception.pm cp Bio/DB/Biblio/soap.pm blib\lib\Bio\DB\Biblio\soap.pm cp Bio/Factory/TreeFactoryI.pm blib\lib\Bio\Factory\TreeFactoryI.pm cp Bio/Root/Object.pm blib\lib\Bio\Root\Object.pm cp Bio/SeqIO/tab.pm blib\lib\Bio\SeqIO\tab.pm cp Bio/Assembly/IO/ace.pm blib\lib\Bio\Assembly\IO\ace.pm C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_heterogeneity_test.pl blib\script\bp_heterogeneity_test.pl pl2bat.bat blib\script\bp_heterogeneity_test.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_biogetseq.pl blib\script\bp_biogetseq.pl pl2bat.bat blib\script\bp_biogetseq.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_biblio.pl blib\script\bp_biblio.pl pl2bat.bat blib\script\bp_biblio.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_extract_feature_seq.pl blib\script\bp_extract_feature_seq.pl pl2bat.bat blib\script\bp_extract_feature_seq.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_process_gadfly.pl blib\script\bp_process_gadfly.pl pl2bat.bat blib\script\bp_process_gadfly.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_aacomp.pl blib\script\bp_aacomp.pl pl2bat.bat blib\script\bp_aacomp.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_nrdb.pl blib\script\bp_nrdb.pl pl2bat.bat blib\script\bp_nrdb.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_mrtrans.pl blib\script\bp_mrtrans.pl pl2bat.bat blib\script\bp_mrtrans.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_load_gff.pl blib\script\bp_load_gff.pl pl2bat.bat blib\script\bp_load_gff.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_process_sgd.pl blib\script\bp_process_sgd.pl pl2bat.bat blib\script\bp_process_sgd.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_gccalc.pl blib\script\bp_gccalc.pl pl2bat.bat blib\script\bp_gccalc.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_feature_draw.pl blib\script\bp_feature_draw.pl pl2bat.bat blib\script\bp_feature_draw.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_sreformat.pl blib\script\bp_sreformat.pl pl2bat.bat blib\script\bp_sreformat.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_oligo_count.pl blib\script\bp_oligo_count.pl pl2bat.bat blib\script\bp_oligo_count.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_translate_seq.pl blib\script\bp_translate_seq.pl pl2bat.bat blib\script\bp_translate_seq.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_flanks.pl blib\script\bp_flanks.pl pl2bat.bat blib\script\bp_flanks.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_index.pl blib\script\bp_index.pl pl2bat.bat blib\script\bp_index.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_seq_length.pl blib\script\bp_seq_length.pl pl2bat.bat blib\script\bp_seq_length.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_search2alnblocks.pl blib\script\bp_search2alnblocks.pl pl2bat.bat blib\script\bp_search2alnblocks.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_search2tribe.pl blib\script\bp_search2tribe.pl pl2bat.bat blib\script\bp_search2tribe.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_generate_histogram.pl blib\script\bp_generate_histogram.pl pl2bat.bat blib\script\bp_generate_histogram.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_dbsplit.pl blib\script\bp_dbsplit.pl pl2bat.bat blib\script\bp_dbsplit.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_composite_LD.pl blib\script\bp_composite_LD.pl pl2bat.bat blib\script\bp_composite_LD.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_filter_search.pl blib\script\bp_filter_search.pl pl2bat.bat blib\script\bp_filter_search.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_mutate.pl blib\script\bp_mutate.pl pl2bat.bat blib\script\bp_mutate.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_bioflat_index.pl blib\script\bp_bioflat_index.pl pl2bat.bat blib\script\bp_bioflat_index.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_seqconvert.pl blib\script\bp_seqconvert.pl pl2bat.bat blib\script\bp_seqconvert.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_local_taxonomydb_query.pl blib\script\bp_local_taxonomydb_query.pl pl2bat.bat blib\script\bp_local_taxonomydb_query.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_process_ncbi_human.pl blib\script\bp_process_ncbi_human.pl pl2bat.bat blib\script\bp_process_ncbi_human.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_fetch.pl blib\script\bp_fetch.pl pl2bat.bat blib\script\bp_fetch.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_search2gff.pl blib\script\bp_search2gff.pl pl2bat.bat blib\script\bp_search2gff.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_process_wormbase.pl blib\script\bp_process_wormbase.pl pl2bat.bat blib\script\bp_process_wormbase.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_fast_load_gff.pl blib\script\bp_fast_load_gff.pl pl2bat.bat blib\script\bp_fast_load_gff.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_split_seq.pl blib\script\bp_split_seq.pl pl2bat.bat blib\script\bp_split_seq.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_bulk_load_gff.pl blib\script\bp_bulk_load_gff.pl pl2bat.bat blib\script\bp_bulk_load_gff.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_pg_bulk_load_gff.pl blib\script\bp_pg_bulk_load_gff.pl pl2bat.bat blib\script\bp_pg_bulk_load_gff.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_blast2tree.pl blib\script\bp_blast2tree.pl pl2bat.bat blib\script\bp_blast2tree.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_chaos_plot.pl blib\script\bp_chaos_plot.pl pl2bat.bat blib\script\bp_chaos_plot.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_search2BSML.pl blib\script\bp_search2BSML.pl pl2bat.bat blib\script\bp_search2BSML.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_remote_blast.pl blib\script\bp_remote_blast.pl pl2bat.bat blib\script\bp_remote_blast.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_frend.pl blib\script\bp_frend.pl pl2bat.bat blib\script\bp_frend.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_mask_by_search.pl blib\script\bp_mask_by_search.pl pl2bat.bat blib\script\bp_mask_by_search.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_search_overview.pl blib\script\bp_search_overview.pl pl2bat.bat blib\script\bp_search_overview.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_genbank2gff.pl blib\script\bp_genbank2gff.pl pl2bat.bat blib\script\bp_genbank2gff.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_pairwise_kaks.pl blib\script\bp_pairwise_kaks.pl pl2bat.bat blib\script\bp_pairwise_kaks.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_biofetch_genbank_proxy.pl blib\script\bp_biofetch_genbank_proxy.pl pl2bat.bat blib\script\bp_biofetch_genbank_proxy.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_taxid4species.pl blib\script\bp_taxid4species.pl pl2bat.bat blib\script\bp_taxid4species.pl BIRNEY/bioperl-1.4.tar.gz nmake -- OK Running make test >>> nmake test TEST_VERBOSE=1 Microsoft (R) Program Maintenance Utility Version 7.00.8882 Copyright (C) Microsoft Corp 1988-2000. All rights reserved. C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_heterogeneity_test.pl blib\script\bp_heterogeneity_test.pl pl2bat.bat blib\script\bp_heterogeneity_test.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_biogetseq.pl blib\script\bp_biogetseq.pl pl2bat.bat blib\script\bp_biogetseq.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_biblio.pl blib\script\bp_biblio.pl pl2bat.bat blib\script\bp_biblio.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_extract_feature_seq.pl blib\script\bp_extract_feature_seq.pl pl2bat.bat blib\script\bp_extract_feature_seq.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_process_gadfly.pl blib\script\bp_process_gadfly.pl pl2bat.bat blib\script\bp_process_gadfly.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_aacomp.pl blib\script\bp_aacomp.pl pl2bat.bat blib\script\bp_aacomp.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_nrdb.pl blib\script\bp_nrdb.pl pl2bat.bat blib\script\bp_nrdb.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_mrtrans.pl blib\script\bp_mrtrans.pl pl2bat.bat blib\script\bp_mrtrans.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_load_gff.pl blib\script\bp_load_gff.pl pl2bat.bat blib\script\bp_load_gff.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_process_sgd.pl blib\script\bp_process_sgd.pl pl2bat.bat blib\script\bp_process_sgd.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_gccalc.pl blib\script\bp_gccalc.pl pl2bat.bat blib\script\bp_gccalc.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_feature_draw.pl blib\script\bp_feature_draw.pl pl2bat.bat blib\script\bp_feature_draw.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_sreformat.pl blib\script\bp_sreformat.pl pl2bat.bat blib\script\bp_sreformat.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_oligo_count.pl blib\script\bp_oligo_count.pl pl2bat.bat blib\script\bp_oligo_count.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_translate_seq.pl blib\script\bp_translate_seq.pl pl2bat.bat blib\script\bp_translate_seq.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_flanks.pl blib\script\bp_flanks.pl pl2bat.bat blib\script\bp_flanks.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_index.pl blib\script\bp_index.pl pl2bat.bat blib\script\bp_index.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_seq_length.pl blib\script\bp_seq_length.pl pl2bat.bat blib\script\bp_seq_length.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_search2alnblocks.pl blib\script\bp_search2alnblocks.pl pl2bat.bat blib\script\bp_search2alnblocks.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_search2tribe.pl blib\script\bp_search2tribe.pl pl2bat.bat blib\script\bp_search2tribe.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_generate_histogram.pl blib\script\bp_generate_histogram.pl pl2bat.bat blib\script\bp_generate_histogram.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_dbsplit.pl blib\script\bp_dbsplit.pl pl2bat.bat blib\script\bp_dbsplit.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_composite_LD.pl blib\script\bp_composite_LD.pl pl2bat.bat blib\script\bp_composite_LD.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_filter_search.pl blib\script\bp_filter_search.pl pl2bat.bat blib\script\bp_filter_search.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_mutate.pl blib\script\bp_mutate.pl pl2bat.bat blib\script\bp_mutate.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_bioflat_index.pl blib\script\bp_bioflat_index.pl pl2bat.bat blib\script\bp_bioflat_index.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_seqconvert.pl blib\script\bp_seqconvert.pl pl2bat.bat blib\script\bp_seqconvert.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_local_taxonomydb_query.pl blib\script\bp_local_taxonomydb_query.pl pl2bat.bat blib\script\bp_local_taxonomydb_query.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_process_ncbi_human.pl blib\script\bp_process_ncbi_human.pl pl2bat.bat blib\script\bp_process_ncbi_human.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_fetch.pl blib\script\bp_fetch.pl pl2bat.bat blib\script\bp_fetch.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_search2gff.pl blib\script\bp_search2gff.pl pl2bat.bat blib\script\bp_search2gff.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_process_wormbase.pl blib\script\bp_process_wormbase.pl pl2bat.bat blib\script\bp_process_wormbase.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_fast_load_gff.pl blib\script\bp_fast_load_gff.pl pl2bat.bat blib\script\bp_fast_load_gff.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_split_seq.pl blib\script\bp_split_seq.pl pl2bat.bat blib\script\bp_split_seq.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_bulk_load_gff.pl blib\script\bp_bulk_load_gff.pl pl2bat.bat blib\script\bp_bulk_load_gff.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_pg_bulk_load_gff.pl blib\script\bp_pg_bulk_load_gff.pl pl2bat.bat blib\script\bp_pg_bulk_load_gff.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_blast2tree.pl blib\script\bp_blast2tree.pl pl2bat.bat blib\script\bp_blast2tree.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_chaos_plot.pl blib\script\bp_chaos_plot.pl pl2bat.bat blib\script\bp_chaos_plot.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_search2BSML.pl blib\script\bp_search2BSML.pl pl2bat.bat blib\script\bp_search2BSML.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_remote_blast.pl blib\script\bp_remote_blast.pl pl2bat.bat blib\script\bp_remote_blast.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_frend.pl blib\script\bp_frend.pl pl2bat.bat blib\script\bp_frend.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_mask_by_search.pl blib\script\bp_mask_by_search.pl pl2bat.bat blib\script\bp_mask_by_search.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_search_overview.pl blib\script\bp_search_overview.pl pl2bat.bat blib\script\bp_search_overview.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_genbank2gff.pl blib\script\bp_genbank2gff.pl pl2bat.bat blib\script\bp_genbank2gff.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_pairwise_kaks.pl blib\script\bp_pairwise_kaks.pl pl2bat.bat blib\script\bp_pairwise_kaks.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_biofetch_genbank_proxy.pl blib\script\bp_biofetch_genbank_proxy.pl pl2bat.bat blib\script\bp_biofetch_genbank_proxy.pl C:\Perl64\bin\perl.exe -MExtUtils::Command -e "cp" -- ./scripts_temp/bp_taxid4species.pl blib\script\bp_taxid4species.pl pl2bat.bat blib\script\bp_taxid4species.pl C:\Perl64\bin\perl.exe "-MExtUtils::Command::MM" "-e" "test_harness(1, 'blib\lib', 'blib\arch')" t/*.t Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 89. Subroutine start redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 111. Subroutine end redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 137. Subroutine length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 174. Subroutine location_type redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 265. Subroutine to_FTstring redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 312. Subroutine trunc redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 343. t/AAChange.t ................. 1..25 ok 1 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 t/AAReverseMutate.t .......... 1..16 ok 1 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 Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 160, line 88. Subroutine algorithm redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 239, line 88. Subroutine algorithm_version redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 259, line 88. Subroutine next_hit redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 286, line 88. Subroutine query_name redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 304, line 88. Subroutine query_accession redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 324, line 88. Subroutine query_length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 345, line 88. Subroutine query_description redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 366, line 88. Subroutine database_name redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 388, line 88. Subroutine database_letters redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 411, line 88. Subroutine database_entries redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 433, line 88. Subroutine get_parameter redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 454, line 88. Subroutine available_parameters redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 469, line 88. Subroutine get_statistic redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 486, line 88. Subroutine available_statistics redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 501, line 88. Subroutine add_hit redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 520, line 88. Subroutine rewind redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 543, line 88. Subroutine _nexthitindex redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 556, line 88. Subroutine add_parameter redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 573, line 88. Subroutine add_statistic redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 590, line 88. Subroutine num_hits redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 608, line 88. Subroutine hits redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 628, line 88. Subroutine algorithm_reference redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 649, line 88. Subroutine program_reference redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 658, line 88. Subroutine no_hits_found redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 667, line 88. Subroutine set_no_hits_found redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 684, line 88. Subroutine to_string redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 705, line 88. Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 116, line 88. Subroutine add_hsp redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 175, line 88. Subroutine name redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 202, line 88. Subroutine accession redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 222, line 88. Subroutine description redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 242, line 88. Subroutine length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 262, line 88. Subroutine algorithm redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 287, line 88. Subroutine raw_score redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 309, line 88. Subroutine score redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 325, line 88. Subroutine significance redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 340, line 88. Subroutine bits redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 371, line 88. Subroutine next_hsp redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 399, line 88. Subroutine hsps redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 425, line 88. Subroutine num_hsps redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 454, line 88. Subroutine rewind redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 475, line 88. Subroutine ambiguous_aln redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 502, line 88. Subroutine overlap redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 516, line 88. Subroutine n redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 547, line 88. Subroutine p redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 596, line 88. Subroutine hsp redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 640, line 88. Subroutine logical_length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 680, line 88. Subroutine length_aln redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 733, line 88. Subroutine gaps redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 791, line 88. Subroutine matches redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 825, line 88. Subroutine start redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 883, line 88. Subroutine end redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 941, line 88. Subroutine range redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 985, line 88. Subroutine frac_identical redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1032, line 88. Subroutine frac_conserved redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1092, line 88. Subroutine frac_aligned_query redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1141, line 88. Subroutine frac_aligned_hit redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1177, line 88. Subroutine num_unaligned_hit redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1226, line 88. Subroutine num_unaligned_query redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1258, line 88. Subroutine seq_inds redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1296, line 88. Subroutine strand redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1329, line 88. Subroutine frame redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1387, line 88. Subroutine rank redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1421, line 88. Subroutine locus redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1437, line 88. Subroutine each_accession_number redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1465, line 88. Subroutine tiled_hsps redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1513, line 88. Subroutine query_length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1530, line 88. Subroutine Bio::Search::Hit::GenericHit::num_unaligned_sbjct redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1202, line 88. Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 77, line 32. Subroutine significance redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 114, line 32. Subroutine bits redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 130, line 32. Subroutine frac_identical redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 146, line 32. Subroutine seqlength redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 162, line 32. Subroutine seqdesc redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 182, line 32. Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 89, line 32. Subroutine start redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 111, line 32. Subroutine end redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 137, line 32. Subroutine length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 174, line 32. Subroutine location_type redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 265, line 32. Subroutine to_FTstring redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 312, line 32. Subroutine trunc redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 343, line 32. t/AlignIO.t .................. 1..75 ok 1 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 t/AlignStats.t ............... 1..21 ok 1 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 t/Allele.t ................... 1..15 ok 1 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 t/Alphabet.t ................. 1..90 ok 1 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 Useless localization of scalar assignment at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Root/Object.pm line 699. t/Annotation.t ............... 1..63 ok 1 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 t/AnnotationAdaptor.t ........ 1..21 ok 1 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 DB_File not installed. This means the Assembly modules are not available. Skipping tests. t/Assembly.t ................. 1..13 ok 1 # DB_File not installed ok 2 # DB_File not installed ok 3 # DB_File not installed ok 4 # DB_File not installed ok 5 # DB_File not installed ok 6 # DB_File not installed ok 7 # DB_File not installed ok 8 # DB_File not installed ok 9 # DB_File not installed ok 10 # DB_File not installed ok 11 # DB_File not installed ok 12 # DB_File not installed ok 13 # DB_File not installed ok t/Biblio.t ................... 1..24 ok 1 ok 2 ok 3 ok 4 Reading and parsing MEDLINE XML file... ok 5 ok 6 ok 7 Getting citations using callback... ok 8 ok 9 ok 10 ok 11 Reading and parsing XML string... ok 12 ok 13 Reading and parsing XML string handle... ok 14 ok 15 ok 16 Reading and parsing PUBMED XML file... ok 17 ok 18 ok 19 ok 20 Testing FH ok 21 ok 22 ok 23 ok 24 ok t/Biblio_biofetch.t .......... 1..11 ok 1 ok 2 # No network access - could not connect to Medline ok 3 # No network access - could not connect to Medline ok 4 # No network access - could not connect to Medline ok 5 # No network access - could not connect to Medline ok 6 # No network access - could not connect to Medline ok 7 # No network access - could not connect to Medline ok 8 # No network access - could not connect to Medline ok 9 # No network access - could not connect to Medline ok 10 # No network access - could not connect to Medline ok 11 # No network access - could not connect to Medline ok t/BiblioReferences.t ......... 1..537 Testing 'use Bio::Biblio:: ...' ok 1 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 Testing 'new Bio::Biblio:: ...' 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 Testing Bio::Biblio::MedlineJournalArticle ... 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 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 Testing Bio::Biblio::MedlineBookArticle ... 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 ok 250 ok 251 ok 252 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 ok 274 ok 275 ok 276 ok 277 ok 278 ok 279 ok 280 ok 281 ok 282 ok 283 ok 284 ok 285 ok 286 ok 287 ok 288 ok 289 ok 290 ok 291 ok 292 ok 293 ok 294 ok 295 ok 296 ok 297 ok 298 ok 299 ok 300 ok 301 ok 302 ok 303 ok 304 ok 305 ok 306 ok 307 ok 308 ok 309 ok 310 ok 311 ok 312 ok 313 ok 314 ok 315 ok 316 ok 317 ok 318 ok 319 ok 320 ok 321 ok 322 ok 323 ok 324 ok 325 ok 326 ok 327 ok 328 ok 329 ok 330 ok 331 ok 332 ok 333 ok 334 ok 335 ok 336 ok 337 ok 338 ok 339 ok 340 ok 341 ok 342 ok 343 ok 344 ok 345 ok 346 ok 347 ok 348 ok 349 Testing Bio::Biblio::MedlineBook ... ok 350 ok 351 ok 352 ok 353 ok 354 ok 355 ok 356 ok 357 ok 358 ok 359 ok 360 ok 361 ok 362 ok 363 ok 364 ok 365 ok 366 ok 367 ok 368 ok 369 ok 370 ok 371 ok 372 ok 373 ok 374 ok 375 ok 376 ok 377 ok 378 ok 379 ok 380 ok 381 ok 382 ok 383 ok 384 ok 385 ok 386 ok 387 ok 388 ok 389 ok 390 ok 391 ok 392 ok 393 ok 394 ok 395 ok 396 ok 397 ok 398 ok 399 ok 400 ok 401 ok 402 ok 403 ok 404 ok 405 ok 406 ok 407 ok 408 ok 409 ok 410 ok 411 ok 412 ok 413 ok 414 ok 415 ok 416 ok 417 ok 418 ok 419 ok 420 ok 421 ok 422 ok 423 ok 424 ok 425 ok 426 ok 427 ok 428 ok 429 ok 430 ok 431 ok 432 ok 433 ok 434 ok 435 ok 436 Testing Bio::Biblio::MedlineJournal ... ok 437 ok 438 ok 439 ok 440 ok 441 ok 442 ok 443 ok 444 ok 445 ok 446 ok 447 ok 448 ok 449 ok 450 ok 451 ok 452 ok 453 ok 454 ok 455 ok 456 ok 457 ok 458 ok 459 ok 460 ok 461 Testing Bio::Biblio::Patent ... ok 462 ok 463 ok 464 ok 465 ok 466 ok 467 ok 468 ok 469 ok 470 ok 471 ok 472 Testing Bio::Biblio::WebResource ... ok 473 ok 474 ok 475 ok 476 ok 477 ok 478 ok 479 ok 480 ok 481 ok 482 Testing Bio::Biblio::Person ... ok 483 ok 484 ok 485 ok 486 ok 487 ok 488 ok 489 ok 490 ok 491 ok 492 ok 493 ok 494 ok 495 ok 496 ok 497 ok 498 ok 499 ok 500 ok 501 ok 502 ok 503 ok 504 ok 505 ok 506 ok 507 ok 508 ok 509 ok 510 ok 511 ok 512 ok 513 Testing Bio::Biblio::Organisation ... ok 514 ok 515 ok 516 ok 517 ok 518 ok 519 ok 520 Testing Bio::Biblio::Service ... ok 521 ok 522 ok 523 ok 524 ok 525 ok 526 ok 527 Testing Bio::Biblio::PubmedJournalArticle ... ok 528 ok 529 ok 530 ok 531 ok 532 ok 533 ok 534 ok 535 ok 536 ok 537 ok t/BioDBGFF.t ................. 1..133 ok 1 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 # fetch_feature_by_gid() not implemented by this adaptor ok 101 # fetch_feature_by_gid() not implemented by this adaptor 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 # delete_groups() not implemented by this adaptor ok 129 # delete_groups() not implemented by this adaptor ok 130 ok 131 ok 132 ok 133 ok Subroutine new redefined at Bio\Location\Simple.pm line 89, line 129. Subroutine start redefined at Bio\Location\Simple.pm line 111, line 129. Subroutine end redefined at Bio\Location\Simple.pm line 137, line 129. Subroutine length redefined at Bio\Location\Simple.pm line 174, line 129. Subroutine location_type redefined at Bio\Location\Simple.pm line 265, line 129. Subroutine to_FTstring redefined at Bio\Location\Simple.pm line 312, line 129. Subroutine trunc redefined at Bio\Location\Simple.pm line 343, line 129. Subroutine new redefined at Bio\Location\Fuzzy.pm line 137, line 43. Subroutine location_type redefined at Bio\Location\Fuzzy.pm line 164, line 43. Subroutine start redefined at Bio\Location\Fuzzy.pm line 226, line 43. Subroutine end redefined at Bio\Location\Fuzzy.pm line 251, line 43. Subroutine min_start redefined at Bio\Location\Fuzzy.pm line 276, line 43. Subroutine max_start redefined at Bio\Location\Fuzzy.pm line 295, line 43. Subroutine start_pos_type redefined at Bio\Location\Fuzzy.pm line 315, line 43. Subroutine min_end redefined at Bio\Location\Fuzzy.pm line 344, line 43. Subroutine max_end redefined at Bio\Location\Fuzzy.pm line 363, line 43. Subroutine end_pos_type redefined at Bio\Location\Fuzzy.pm line 383, line 43. Subroutine to_FTstring redefined at Bio\Location\Fuzzy.pm line 450, line 43. Subroutine _fuzzypointdecode redefined at Bio\Location\Fuzzy.pm line 537, line 43. t/BioFetch_DB.t .............. 1..27 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 not ok 8 # Test 8 got: 'unknown id' (t/BioFetch_DB.t at line 79) # Expected: 'BUM' ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 not ok 20 # Test 20 got: '1611' (t/BioFetch_DB.t at line 116) # Expected: '408' not ok 21 # Test 21 got: '408' (t/BioFetch_DB.t at line 117) # Expected: '1611' ok 22 ok 23 ok 24 ok 25 ok 26 not ok 27 # Test 27 got: '3776' (t/BioFetch_DB.t at line 138) # Expected: '3775' Failed 4/27 subtests t/BioGraphics.t .............. 1..14 ok 1 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 Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 160, line 533. Subroutine algorithm redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 239, line 533. Subroutine algorithm_version redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 259, line 533. Subroutine next_hit redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 286, line 533. Subroutine query_name redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 304, line 533. Subroutine query_accession redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 324, line 533. Subroutine query_length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 345, line 533. Subroutine query_description redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 366, line 533. Subroutine database_name redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 388, line 533. Subroutine database_letters redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 411, line 533. Subroutine database_entries redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 433, line 533. Subroutine get_parameter redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 454, line 533. Subroutine available_parameters redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 469, line 533. Subroutine get_statistic redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 486, line 533. Subroutine available_statistics redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 501, line 533. Subroutine add_hit redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 520, line 533. Subroutine rewind redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 543, line 533. Subroutine _nexthitindex redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 556, line 533. Subroutine add_parameter redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 573, line 533. Subroutine add_statistic redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 590, line 533. Subroutine num_hits redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 608, line 533. Subroutine hits redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 628, line 533. Subroutine algorithm_reference redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 649, line 533. Subroutine program_reference redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 658, line 533. Subroutine no_hits_found redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 667, line 533. Subroutine set_no_hits_found redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 684, line 533. Subroutine to_string redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 705, line 533. Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 116, line 533. Subroutine add_hsp redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 175, line 533. Subroutine name redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 202, line 533. Subroutine accession redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 222, line 533. Subroutine description redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 242, line 533. Subroutine length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 262, line 533. Subroutine algorithm redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 287, line 533. Subroutine raw_score redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 309, line 533. Subroutine score redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 325, line 533. Subroutine significance redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 340, line 533. Subroutine bits redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 371, line 533. Subroutine next_hsp redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 399, line 533. Subroutine hsps redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 425, line 533. Subroutine num_hsps redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 454, line 533. Subroutine rewind redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 475, line 533. Subroutine ambiguous_aln redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 502, line 533. Subroutine overlap redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 516, line 533. Subroutine n redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 547, line 533. Subroutine p redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 596, line 533. Subroutine hsp redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 640, line 533. Subroutine logical_length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 680, line 533. Subroutine length_aln redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 733, line 533. Subroutine gaps redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 791, line 533. Subroutine matches redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 825, line 533. Subroutine start redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 883, line 533. Subroutine end redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 941, line 533. Subroutine range redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 985, line 533. Subroutine frac_identical redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1032, line 533. Subroutine frac_conserved redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1092, line 533. Subroutine frac_aligned_query redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1141, line 533. Subroutine frac_aligned_hit redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1177, line 533. Subroutine num_unaligned_hit redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1226, line 533. Subroutine num_unaligned_query redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1258, line 533. Subroutine seq_inds redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1296, line 533. Subroutine strand redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1329, line 533. Subroutine frame redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1387, line 533. Subroutine rank redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1421, line 533. Subroutine locus redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1437, line 533. Subroutine each_accession_number redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1465, line 533. Subroutine tiled_hsps redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1513, line 533. Subroutine query_length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1530, line 533. Subroutine Bio::Search::Hit::GenericHit::num_unaligned_sbjct redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1202, line 533. Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 77, line 58. Subroutine significance redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 114, line 58. Subroutine bits redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 130, line 58. Subroutine frac_identical redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 146, line 58. Subroutine seqlength redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 162, line 58. Subroutine seqdesc redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 182, line 58. Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 89, line 58. Subroutine start redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 111, line 58. Subroutine end redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 137, line 58. Subroutine length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 174, line 58. Subroutine location_type redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 265, line 58. Subroutine to_FTstring redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 312, line 58. Subroutine trunc redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 343, line 58. t/BlastIndex.t ............... 1..13 ok 1 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 Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 77, line 32. Subroutine significance redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 114, line 32. Subroutine bits redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 130, line 32. Subroutine frac_identical redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 146, line 32. Subroutine seqlength redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 162, line 32. Subroutine seqdesc redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 182, line 32. Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 89, line 32. Subroutine start redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 111, line 32. Subroutine end redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 137, line 32. Subroutine length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 174, line 32. Subroutine location_type redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 265, line 32. Subroutine to_FTstring redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 312, line 32. Subroutine trunc redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 343, line 32. t/BPbl2seq.t ................. 1..108 ok 1 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 ok 104 ok 105 ok 106 ok 107 ok 108 ok Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 77, line 165. Subroutine significance redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 114, line 165. Subroutine bits redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 130, line 165. Subroutine frac_identical redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 146, line 165. Subroutine seqlength redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 162, line 165. Subroutine seqdesc redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 182, line 165. Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 89, line 165. Subroutine start redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 111, line 165. Subroutine end redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 137, line 165. Subroutine length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 174, line 165. Subroutine location_type redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 265, line 165. Subroutine to_FTstring redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 312, line 165. Subroutine trunc redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 343, line 165. t/BPlite.t ................... 1..97 ok 1 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 Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 77, line 263. Subroutine significance redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 114, line 263. Subroutine bits redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 130, line 263. Subroutine frac_identical redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 146, line 263. Subroutine seqlength redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 162, line 263. Subroutine seqdesc redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 182, line 263. Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 89, line 263. Subroutine start redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 111, line 263. Subroutine end redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 137, line 263. Subroutine length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 174, line 263. Subroutine location_type redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 265, line 263. Subroutine to_FTstring redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 312, line 263. Subroutine trunc redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 343, line 263. t/BPpsilite.t ................ 1..11 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok t/Chain.t .................... 1..45 ok 1 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 Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 160. Subroutine algorithm redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 239. Subroutine algorithm_version redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 259. Subroutine next_hit redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 286. Subroutine query_name redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 304. Subroutine query_accession redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 324. Subroutine query_length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 345. Subroutine query_description redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 366. Subroutine database_name redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 388. Subroutine database_letters redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 411. Subroutine database_entries redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 433. Subroutine get_parameter redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 454. Subroutine available_parameters redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 469. Subroutine get_statistic redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 486. Subroutine available_statistics redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 501. Subroutine add_hit redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 520. Subroutine rewind redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 543. Subroutine _nexthitindex redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 556. Subroutine add_parameter redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 573. Subroutine add_statistic redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 590. Subroutine num_hits redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 608. Subroutine hits redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 628. Subroutine algorithm_reference redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 649. Subroutine program_reference redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 658. Subroutine no_hits_found redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 667. Subroutine set_no_hits_found redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 684. Subroutine to_string redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Result/GenericResult.pm line 705. Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 116. Subroutine add_hsp redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 175. Subroutine name redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 202. Subroutine accession redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 222. Subroutine description redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 242. Subroutine length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 262. Subroutine algorithm redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 287. Subroutine raw_score redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 309. Subroutine score redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 325. Subroutine significance redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 340. Subroutine bits redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 371. Subroutine next_hsp redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 399. Subroutine hsps redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 425. Subroutine num_hsps redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 454. Subroutine rewind redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 475. Subroutine ambiguous_aln redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 502. Subroutine overlap redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 516. Subroutine n redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 547. Subroutine p redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 596. Subroutine hsp redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 640. Subroutine logical_length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 680. Subroutine length_aln redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 733. Subroutine gaps redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 791. Subroutine matches redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 825. Subroutine start redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 883. Subroutine end redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 941. Subroutine range redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 985. Subroutine frac_identical redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1032. Subroutine frac_conserved redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1092. Subroutine frac_aligned_query redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1141. Subroutine frac_aligned_hit redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1177. Subroutine num_unaligned_hit redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1226. Subroutine num_unaligned_query redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1258. Subroutine seq_inds redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1296. Subroutine strand redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1329. Subroutine frame redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1387. Subroutine rank redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1421. Subroutine locus redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1437. Subroutine each_accession_number redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1465. Subroutine tiled_hsps redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1513. Subroutine query_length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1530. Subroutine Bio::Search::Hit::GenericHit::num_unaligned_sbjct redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Search/Hit/GenericHit.pm line 1202. Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 77, line 165. Subroutine significance redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 114, line 165. Subroutine bits redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 130, line 165. Subroutine frac_identical redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 146, line 165. Subroutine seqlength redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 162, line 165. Subroutine seqdesc redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\SeqFeature\Similarity.pm line 182, line 165. Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 89, line 165. Subroutine start redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 111, line 165. Subroutine end redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 137, line 165. Subroutine length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 174, line 165. Subroutine location_type redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 265, line 165. Subroutine to_FTstring redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 312, line 165. Subroutine trunc redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 343, line 165. t/cigarstring.t .............. 1..3 ok 1 ok 2 ok 3 ok t/ClusterIO.t ................ 1..12 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Tree.pm line 93. Subroutine nodelete redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Tree.pm line 120. Subroutine get_nodes redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Tree.pm line 137. Subroutine get_root_node redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Tree.pm line 173. Subroutine set_root_node redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Tree.pm line 188. Subroutine total_branch_length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Tree.pm line 212. Subroutine id redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Tree.pm line 234. Subroutine score redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Tree.pm line 255. Subroutine cleanup_tree redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Tree.pm line 292. Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 101. Subroutine add_Descendent redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 153. Subroutine each_Descendent redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 189. Subroutine remove_Descendent redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 225. Subroutine remove_all_Descendents redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 272. Subroutine ancestor redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 306. Subroutine branch_length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 323. Subroutine bootstrap redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 348. Subroutine description redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 370. Subroutine id redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 395. Subroutine internal_id redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 419. Subroutine _creation_id redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 435. Subroutine is_Leaf redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 456. Subroutine height redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 482. Subroutine invalidate_height redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 515. Subroutine add_tag_value redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 536. Subroutine remove_tag redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 556. Subroutine remove_all_tags redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 577. Subroutine get_all_tags redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 594. Subroutine get_tag_values redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 610. Subroutine has_tag redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 626. Subroutine node_cleanup redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Tree\Node.pm line 631. t/Coalescent.t ............... 1..11 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok t/CodonTable.t ............... 1..38 ok 1 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 t/consed.t ................... 1..16 ok 1 # Cannot run consed module on windows ok 2 # Cannot run consed module on windows ok 3 # Cannot run consed module on windows ok 4 # Cannot run consed module on windows ok 5 # Cannot run consed module on windows ok 6 # Cannot run consed module on windows ok 7 # Cannot run consed module on windows ok 8 # Cannot run consed module on windows ok 9 # Cannot run consed module on windows ok 10 # Cannot run consed module on windows ok 11 # Cannot run consed module on windows ok 12 # Cannot run consed module on windows ok 13 # Cannot run consed module on windows ok 14 # Cannot run consed module on windows ok 15 # Cannot run consed module on windows ok 16 # Cannot run consed module on windows ok t/CoordinateGraph.t .......... 1..7 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 89. Subroutine start redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 111. Subroutine end redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 137. Subroutine length redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 174. Subroutine location_type redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 265. Subroutine to_FTstring redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 312. Subroutine trunc redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Simple.pm line 343. Subroutine add_sub_Location redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Coordinate\Result.pm line 101. Subroutine add_result redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Coordinate\Result.pm line 127. Subroutine seq_id redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Coordinate\Result.pm line 151. Subroutine each_gap redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Coordinate\Result.pm line 182. Subroutine each_match redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Coordinate\Result.pm line 207. Subroutine match redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Coordinate\Result.pm line 228. Subroutine gap redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Coordinate\Result.pm line 251. Subroutine purge_gaps redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Coordinate\Result.pm line 274. Subroutine new redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Split.pm line 90. Subroutine each_Location redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Split.pm line 122. Subroutine sub_Location redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Split.pm line 151. Subroutine add_sub_Location redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Split.pm line 214. Subroutine splittype redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Split.pm line 238. Subroutine is_single_sequence redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Split.pm line 266. Subroutine strand redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Split.pm line 301. Subroutine start redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Split.pm line 341. Subroutine end redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Split.pm line 359. Subroutine min_start redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Split.pm line 377. Subroutine max_start redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Split.pm line 398. Subroutine start_pos_type redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Split.pm line 420. Subroutine min_end redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Split.pm line 440. Subroutine max_end redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Split.pm line 462. Subroutine end_pos_type redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Split.pm line 485. Subroutine seq_id redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Split.pm line 510. Subroutine to_FTstring redefined at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio\Location\Split.pm line 556. t/CoordinateMapper.t ......... 1..170 ok 1 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 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 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 Useless localization of scalar assignment at C:\cpanfly\var\cpan\build\bioperl-1.4-62cSW5\blib\lib/Bio/Root/Object.pm line 699. t/Correlate.t ................ 1..15 ok 1 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 t/CytoMap.t .................. 1..109 ok 1 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 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok Subroutine new redefined at Bio\Location\Simple.pm line 89, line 30. Subroutine start redefined at Bio\Location\Simple.pm line 111, line 30. Subroutine end redefined at Bio\Location\Simple.pm line 137, line 30. Subroutine length redefined at Bio\Location\Simple.pm line 174, line 30. Subroutine location_type redefined at Bio\Location\Simple.pm line 265, line 30. Subroutine to_FTstring redefined at Bio\Location\Simple.pm line 312, line 30. Subroutine trunc redefined at Bio\Location\Simple.pm line 343, line 30. Subroutine new redefined at Bio\Location\Fuzzy.pm line 137, line 38. Subroutine location_type redefined at Bio\Location\Fuzzy.pm line 164, line 38. Subroutine start redefined at Bio\Location\Fuzzy.pm line 226, line 38. Subroutine end redefined at Bio\Location\Fuzzy.pm line 251, line 38. Subroutine min_start redefined at Bio\Location\Fuzzy.pm line 276, line 38. Subroutine max_start redefined at Bio\Location\Fuzzy.pm line 295, line 38. Subroutine start_pos_type redefined at Bio\Location\Fuzzy.pm line 315, line 38. Subroutine min_end redefined at Bio\Location\Fuzzy.pm line 344, line 38. Subroutine max_end redefined at Bio\Location\Fuzzy.pm line 363, line 38. Subroutine end_pos_type redefined at Bio\Location\Fuzzy.pm line 383, line 38. Subroutine to_FTstring redefined at Bio\Location\Fuzzy.pm line 450, line 38. Subroutine _fuzzypointdecode redefined at Bio\Location\Fuzzy.pm line 537, line 38. Subroutine new redefined at Bio\Location\Split.pm line 90, line 44. Subroutine each_Location redefined at Bio\Location\Split.pm line 122, line 44. Subroutine sub_Location redefined at Bio\Location\Split.pm line 151, line 44. Subroutine add_sub_Location redefined at Bio\Location\Split.pm line 214, line 44. Subroutine splittype redefined at Bio\Location\Split.pm line 238, line 44. Subroutine is_single_sequence redefined at Bio\Location\Split.pm line 266, line 44. Subroutine strand redefined at Bio\Location\Split.pm line 301, line 44. Subroutine start redefined at Bio\Location\Split.pm line 341, line 44. Subroutine end redefined at Bio\Location\Split.pm line 359, line 44. Subroutine min_start redefined at Bio\Location\Split.pm line 377, line 44. Subroutine max_start redefined at Bio\Location\Split.pm line 398, line 44. Subroutine start_pos_type redefined at Bio\Location\Split.pm line 420, line 44. Subroutine min_end redefined at Bio\Location\Split.pm line 440, line 44. Subroutine max_end redefined at Bio\Location\Split.pm line 462, line 44. Subroutine end_pos_type redefined at Bio\Location\Split.pm line 485, line 44. Subroutine seq_id redefined at Bio\Location\Split.pm line 510, line 44. Subroutine to_FTstring redefined at Bio\Location\Split.pm line 556, line 44. Timeout (max run time is 300s) C:\Perl64\bin\perl.exe exits with 37