Setting PATH to /opt/SUNWspro/bin:/usr/local/bin:/opt/csw/bin:/usr/ccs/bin:/usr/bin:/usr/sbin Start 2009-06-12T22:35:29 ActivePerl-818 CPAN-1.94 Going to read '/export/home/fly818/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 /net/nas/data/cpan/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 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bioperl-1.4/t/data/registry/bdb/seqdatabase.ini bioperl-1.4/t/data/registry/flat/ bioperl-1.4/t/data/registry/flat/seqdatabase.ini bioperl-1.4/t/AAChange.t bioperl-1.4/t/AAReverseMutate.t bioperl-1.4/t/AlignIO.t bioperl-1.4/t/AlignStats.t bioperl-1.4/t/Allele.t bioperl-1.4/t/Alphabet.t bioperl-1.4/t/Annotation.t bioperl-1.4/t/AnnotationAdaptor.t bioperl-1.4/t/Assembly.t bioperl-1.4/t/BPbl2seq.t bioperl-1.4/t/BPlite.t bioperl-1.4/t/BPpsilite.t bioperl-1.4/t/Biblio.t bioperl-1.4/t/BiblioReferences.t bioperl-1.4/t/Biblio_biofetch.t 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 >>> /export/home/fly818/bin/perl 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 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_load_gff.pl.... Activating bp_genbank2gff.pl.... Activating bp_bulk_load_gff.pl.... Activating bp_fast_load_gff.pl.... Activating bp_generate_histogram.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 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 biblio * These are scripts to manipulate bibliographic repositories using the Bio::Biblio modules. Activating bp_biblio.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 graphics * These are scripts to generate graphical images from sequence data. Activating bp_frend.pl.... Activating bp_feature_draw.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_nrdb.pl.... Activating bp_mrtrans.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_search2BSML.pl.... Activating bp_search2alnblocks.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. External Module GD::SVG, Generate optional SVG output, is not installed on this computer. The in Bioperl needs it for Bio::Graphics External Module GD, Graphical Drawing Toolkit, is not installed on this computer. The Bio::Graphics in Bioperl needs it for Rendering Sequences and Features External Module DBD::mysql, Mysql driver, is not installed on this computer. The Bio::DB::GFF in Bioperl needs it for loading and querying of Mysql-based GFF feature databases Information: There are some external packages and perl modules, listed above, which bioperl uses. This only effects the functionality which is listed above: the rest of bioperl will work fine, which includes nearly all of the core packages. The installation of these external packages is very simple. You can read more about bioperl external dependencies in the INSTALL file or at: http://bioperl.org/Core/Latest/INSTALL Enjoy the rest of bioperl, which you can use after going 'make install' 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 '/export/home/fly818/etc/distroprefs/DB_File.yml' doc 0 PMQS/DB_File-1.820.tar.gz [disabled] -- NA Disabled via prefs file '/export/home/fly818/etc/distroprefs/DB_File.yml' doc 0 Running make for B/BI/BIRNEY/bioperl-1.4.tar.gz Has already been unwrapped into directory /export/home/fly818/var/cpan/build/bioperl-1.4-jXjcCH 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 '/export/home/fly818/etc/distroprefs/DB_File.yml' doc 0'. Continuing, but chances to succeed are limited. >>> make 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/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/Biblio/PubmedBookArticle.pm blib/lib/Bio/Biblio/PubmedBookArticle.pm cp Bio/Search/HSP/WABAHSP.pm blib/lib/Bio/Search/HSP/WABAHSP.pm cp Bio/Align/Utilities.pm blib/lib/Bio/Align/Utilities.pm cp Bio/Tools/Run/README blib/lib/Bio/Tools/Run/README cp Bio/DB/Flat.pm blib/lib/Bio/DB/Flat.pm cp Bio/SearchIO/fasta.pm blib/lib/Bio/SearchIO/fasta.pm cp Bio/DB/SwissProt.pm blib/lib/Bio/DB/SwissProt.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/Root/RootI.pm blib/lib/Bio/Root/RootI.pm cp Bio/LocationI.pm blib/lib/Bio/LocationI.pm cp Bio/Taxonomy.pm blib/lib/Bio/Taxonomy.pm cp Bio/TreeIO/TreeEventBuilder.pm blib/lib/Bio/TreeIO/TreeEventBuilder.pm cp Bio/Matrix/PSM/PsmI.pm blib/lib/Bio/Matrix/PSM/PsmI.pm cp Bio/DBLinkContainerI.pm blib/lib/Bio/DBLinkContainerI.pm cp Bio/Location/Fuzzy.pm blib/lib/Bio/Location/Fuzzy.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/Annotation/OntologyTerm.pm blib/lib/Bio/Annotation/OntologyTerm.pm cp Bio/Map/SimpleMap.pm blib/lib/Bio/Map/SimpleMap.pm cp Bio/Coordinate/Result/Gap.pm blib/lib/Bio/Coordinate/Result/Gap.pm cp Bio/Seq/Meta/Array.pm blib/lib/Bio/Seq/Meta/Array.pm cp Bio/Tools/Run/RemoteBlast.pm blib/lib/Bio/Tools/Run/RemoteBlast.pm cp Bio/DB/BiblioI.pm blib/lib/Bio/DB/BiblioI.pm cp Bio/SearchIO/Writer/HSPTableWriter.pm blib/lib/Bio/SearchIO/Writer/HSPTableWriter.pm cp Bio/MapIO.pm blib/lib/Bio/MapIO.pm cp Bio/SearchIO/blasttable.pm blib/lib/Bio/SearchIO/blasttable.pm cp Bio/Graphics/Glyph/segmented_keyglyph.pm blib/lib/Bio/Graphics/Glyph/segmented_keyglyph.pm cp Bio/SeqFeature/Collection.pm blib/lib/Bio/SeqFeature/Collection.pm cp Bio/Graphics/Glyph/box.pm blib/lib/Bio/Graphics/Glyph/box.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/Graphics/Glyph/extending_arrow.pm blib/lib/Bio/Graphics/Glyph/extending_arrow.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/SeqIO/fastq.pm blib/lib/Bio/SeqIO/fastq.pm cp Bio/LiveSeq/SeqI.pm blib/lib/Bio/LiveSeq/SeqI.pm cp Bio/Tools/Analysis/Protein/ELM.pm blib/lib/Bio/Tools/Analysis/Protein/ELM.pm cp Bio/Seq/TraceI.pm blib/lib/Bio/Seq/TraceI.pm cp Bio/Phenotype/Phenotype.pm blib/lib/Bio/Phenotype/Phenotype.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/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/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/Tools/Gel.pm blib/lib/Bio/Tools/Gel.pm cp Bio/Tree/AlleleNode.pm blib/lib/Bio/Tree/AlleleNode.pm cp Bio/DB/NCBIHelper.pm blib/lib/Bio/DB/NCBIHelper.pm cp Bio/Biblio/BiblioBase.pm blib/lib/Bio/Biblio/BiblioBase.pm cp Bio/Biblio/IO.pm blib/lib/Bio/Biblio/IO.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/Event/EventHandlerI.pm blib/lib/Bio/Event/EventHandlerI.pm cp Bio/Biblio/Thesis.pm blib/lib/Bio/Biblio/Thesis.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/Phenotype/OMIM/OMIMparser.pm blib/lib/Bio/Phenotype/OMIM/OMIMparser.pm cp Bio/DB/GFF/Adaptor/memory_iterator.pm blib/lib/Bio/DB/GFF/Adaptor/memory_iterator.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/SeqIO/largefasta.pm blib/lib/Bio/SeqIO/largefasta.pm cp Bio/AlignIO/emboss.pm blib/lib/Bio/AlignIO/emboss.pm cp Bio/Annotation/SimpleValue.pm blib/lib/Bio/Annotation/SimpleValue.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/DB/Query/WebQuery.pm blib/lib/Bio/DB/Query/WebQuery.pm cp Bio/Ontology/OntologyI.pm blib/lib/Bio/Ontology/OntologyI.pm cp Bio/SearchIO/hmmer.pm blib/lib/Bio/SearchIO/hmmer.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/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/SeqFeature/Generic.pm blib/lib/Bio/SeqFeature/Generic.pm cp Bio/PopGen/PopulationI.pm blib/lib/Bio/PopGen/PopulationI.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/Search/Processor.pm blib/lib/Bio/Search/Processor.pm cp Bio/Tools/Analysis/Protein/GOR4.pm blib/lib/Bio/Tools/Analysis/Protein/GOR4.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/Biblio/Organisation.pm blib/lib/Bio/Biblio/Organisation.pm cp Bio/Search/BlastUtils.pm blib/lib/Bio/Search/BlastUtils.pm cp Bio/Tree/RandomFactory.pm blib/lib/Bio/Tree/RandomFactory.pm cp Bio/Structure/IO/pdb.pm blib/lib/Bio/Structure/IO/pdb.pm cp Bio/Tools/Phylo/PAML/Result.pm blib/lib/Bio/Tools/Phylo/PAML/Result.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/Location/SplitLocationI.pm blib/lib/Bio/Location/SplitLocationI.pm cp Bio/SeqFeature/Gene/NC_Feature.pm blib/lib/Bio/SeqFeature/Gene/NC_Feature.pm cp Bio/SeqIO/metafasta.pm blib/lib/Bio/SeqIO/metafasta.pm cp Bio/OntologyIO.pm blib/lib/Bio/OntologyIO.pm cp Bio/Ontology/RelationshipI.pm blib/lib/Bio/Ontology/RelationshipI.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/Restriction/IO/itype2.pm blib/lib/Bio/Restriction/IO/itype2.pm cp Bio/Biblio/MedlineJournalArticle.pm blib/lib/Bio/Biblio/MedlineJournalArticle.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/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/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/SeqFeature/Gene/TranscriptI.pm blib/lib/Bio/SeqFeature/Gene/TranscriptI.pm cp Bio/Restriction/IO.pm blib/lib/Bio/Restriction/IO.pm cp Bio/Cluster/FamilyI.pm blib/lib/Bio/Cluster/FamilyI.pm cp Bio/DB/RandomAccessI.pm blib/lib/Bio/DB/RandomAccessI.pm cp Bio/SeqIO/qual.pm blib/lib/Bio/SeqIO/qual.pm cp Bio/SeqIO/kegg.pm blib/lib/Bio/SeqIO/kegg.pm cp Bio/SearchIO/axt.pm blib/lib/Bio/SearchIO/axt.pm cp Bio/SeqIO/pln.pm blib/lib/Bio/SeqIO/pln.pm cp Bio/Ontology/TermI.pm blib/lib/Bio/Ontology/TermI.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/Tools/Sim4/Exon.pm blib/lib/Bio/Tools/Sim4/Exon.pm cp Bio/Structure/Atom.pm blib/lib/Bio/Structure/Atom.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/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/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/diamond.pm blib/lib/Bio/Graphics/Glyph/diamond.pm cp Bio/SeqFeature/Gene/Transcript.pm blib/lib/Bio/SeqFeature/Gene/Transcript.pm cp Bio/SeqFeature/Tools/TypeMapper.pm blib/lib/Bio/SeqFeature/Tools/TypeMapper.pm cp Bio/Graphics/Glyph/ellipse.pm blib/lib/Bio/Graphics/Glyph/ellipse.pm cp Bio/SeqIO/scf.pm blib/lib/Bio/SeqIO/scf.pm cp Bio/Taxonomy/FactoryI.pm blib/lib/Bio/Taxonomy/FactoryI.pm cp Bio/OntologyIO/InterProParser.pm blib/lib/Bio/OntologyIO/InterProParser.pm cp Bio/Ontology/OntologyStore.pm blib/lib/Bio/Ontology/OntologyStore.pm cp Bio/MapIO/mapmaker.pm blib/lib/Bio/MapIO/mapmaker.pm cp Bio/Tools/Analysis/Protein/HNN.pm blib/lib/Bio/Tools/Analysis/Protein/HNN.pm cp Bio/DB/GFF/Adaptor/dbi/caching_handle.pm blib/lib/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm cp Bio/Location/Atomic.pm blib/lib/Bio/Location/Atomic.pm cp Bio/Tools/QRNA.pm blib/lib/Bio/Tools/QRNA.pm cp Bio/PopGen/IO/prettybase.pm blib/lib/Bio/PopGen/IO/prettybase.pm cp Bio/Ontology/Ontology.pm blib/lib/Bio/Ontology/Ontology.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/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/SeqIO/phd.pm blib/lib/Bio/SeqIO/phd.pm cp Bio/DB/BioFetch.pm blib/lib/Bio/DB/BioFetch.pm cp Bio/SeqFeature/AnnotationAdaptor.pm blib/lib/Bio/SeqFeature/AnnotationAdaptor.pm cp Bio/Factory/LocationFactoryI.pm blib/lib/Bio/Factory/LocationFactoryI.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/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/Factory/ObjectFactoryI.pm blib/lib/Bio/Factory/ObjectFactoryI.pm cp Bio/AnalysisParserI.pm blib/lib/Bio/AnalysisParserI.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/Matrix/PSM/IO/transfac.pm blib/lib/Bio/Matrix/PSM/IO/transfac.pm cp Bio/Matrix/PSM/PsmHeader.pm blib/lib/Bio/Matrix/PSM/PsmHeader.pm cp Bio/Tools/Analysis/Protein/Sopma.pm blib/lib/Bio/Tools/Analysis/Protein/Sopma.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/Matrix/IO/phylip.pm blib/lib/Bio/Matrix/IO/phylip.pm cp Bio/Tools/Pseudowise.pm blib/lib/Bio/Tools/Pseudowise.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/Blast.pm blib/lib/Bio/Tools/Blast.pm cp Bio/Tools/GFF.pm blib/lib/Bio/Tools/GFF.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/Das/SegmentI.pm blib/lib/Bio/Das/SegmentI.pm cp Bio/SeqFeatureI.pm blib/lib/Bio/SeqFeatureI.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/Graphics/Glyph/dna.pm blib/lib/Bio/Graphics/Glyph/dna.pm cp Bio/Structure/Model.pm blib/lib/Bio/Structure/Model.pm cp Bio/Restriction/Analysis.pm blib/lib/Bio/Restriction/Analysis.pm cp Bio/Seq/SeqFastaSpeedFactory.pm blib/lib/Bio/Seq/SeqFastaSpeedFactory.pm cp Bio/Tree/Node.pm blib/lib/Bio/Tree/Node.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/Coordinate/MapperI.pm blib/lib/Bio/Coordinate/MapperI.pm cp Bio/Phenotype/MeSH/Term.pm blib/lib/Bio/Phenotype/MeSH/Term.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/AlignIO/maf.pm blib/lib/Bio/AlignIO/maf.pm cp Bio/Tools/Seg.pm blib/lib/Bio/Tools/Seg.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/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/PopGen/Population.pm blib/lib/Bio/PopGen/Population.pm cp Bio/SearchIO/Writer/GbrowseGFF.pm blib/lib/Bio/SearchIO/Writer/GbrowseGFF.pm cp Bio/AlignIO/bl2seq.pm blib/lib/Bio/AlignIO/bl2seq.pm cp Bio/Root/HTTPget.pm blib/lib/Bio/Root/HTTPget.pm cp Bio/Ontology/SimpleOntologyEngine.pm blib/lib/Bio/Ontology/SimpleOntologyEngine.pm cp Bio/Tools/BPbl2seq.pm blib/lib/Bio/Tools/BPbl2seq.pm cp Bio/Ontology/PathI.pm blib/lib/Bio/Ontology/PathI.pm cp Bio/Root/Storable.pm blib/lib/Bio/Root/Storable.pm cp Bio/Variation/IO.pm blib/lib/Bio/Variation/IO.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/Seq/LargePrimarySeq.pm blib/lib/Bio/Seq/LargePrimarySeq.pm cp Bio/SeqIO/game/gameSubs.pm blib/lib/Bio/SeqIO/game/gameSubs.pm cp Bio/SearchIO/Writer/BSMLResultWriter.pm blib/lib/Bio/SearchIO/Writer/BSMLResultWriter.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/SeqIO/abi.pm blib/lib/Bio/SeqIO/abi.pm cp Bio/DB/GFF/Aggregator/ucsc_refgene.pm blib/lib/Bio/DB/GFF/Aggregator/ucsc_refgene.pm cp Bio/AlignIO/msf.pm blib/lib/Bio/AlignIO/msf.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/Factory/HitFactoryI.pm blib/lib/Bio/Factory/HitFactoryI.pm cp Bio/SearchIO/exonerate.pm blib/lib/Bio/SearchIO/exonerate.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/Expression/FeatureSet/FeatureSetMas50.pm blib/lib/Bio/Expression/FeatureSet/FeatureSetMas50.pm cp Bio/Graphics/RendererI.pm blib/lib/Bio/Graphics/RendererI.pm cp Bio/Tools/Phylo/PAML.pm blib/lib/Bio/Tools/Phylo/PAML.pm cp Bio/Tools/Blast/Sbjct.pm blib/lib/Bio/Tools/Blast/Sbjct.pm cp Bio/Graphics/FeatureFile/Iterator.pm blib/lib/Bio/Graphics/FeatureFile/Iterator.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/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/Tools/BPlite/HSP.pm blib/lib/Bio/Tools/BPlite/HSP.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/Graphics/Glyph/Factory.pm blib/lib/Bio/Graphics/Glyph/Factory.pm cp Bio/SeqFeature/SiRNA/Oligo.pm blib/lib/Bio/SeqFeature/SiRNA/Oligo.pm cp Bio/Assembly/IO/phrap.pm blib/lib/Bio/Assembly/IO/phrap.pm cp Bio/Ontology/Path.pm blib/lib/Bio/Ontology/Path.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/DB/Ace.pm blib/lib/Bio/DB/Ace.pm cp Bio/DB/GFF/Adaptor/dbi/mysql.pm blib/lib/Bio/DB/GFF/Adaptor/dbi/mysql.pm cp Bio/Factory/FTLocationFactory.pm blib/lib/Bio/Factory/FTLocationFactory.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/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/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/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/Location/Simple.pm blib/lib/Bio/Location/Simple.pm cp Bio/SearchIO/SearchResultEventBuilder.pm blib/lib/Bio/SearchIO/SearchResultEventBuilder.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/Expression/FeatureGroup.pm blib/lib/Bio/Expression/FeatureGroup.pm cp Bio/Graphics/Glyph/primers.pm blib/lib/Bio/Graphics/Glyph/primers.pm cp Bio/DB/GFF/Aggregator/ucsc_genscan.pm blib/lib/Bio/DB/GFF/Aggregator/ucsc_genscan.pm cp Bio/IdentifiableI.pm blib/lib/Bio/IdentifiableI.pm cp Bio/Graphics/Glyph/heterogeneous_segments.pm blib/lib/Bio/Graphics/Glyph/heterogeneous_segments.pm cp Bio/Ontology/InterProTerm.pm blib/lib/Bio/Ontology/InterProTerm.pm cp Bio/Graphics/Glyph/crossbox.pm blib/lib/Bio/Graphics/Glyph/crossbox.pm cp Bio/Tools/Blast/HTML.pm blib/lib/Bio/Tools/Blast/HTML.pm cp Bio/Tools/Grail.pm blib/lib/Bio/Tools/Grail.pm cp Bio/Coordinate/Chain.pm blib/lib/Bio/Coordinate/Chain.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/Tools/Blast/HSP.pm blib/lib/Bio/Tools/Blast/HSP.pm cp Bio/DB/FileCache.pm blib/lib/Bio/DB/FileCache.pm cp Bio/DB/GFF/Util/Binning.pm blib/lib/Bio/DB/GFF/Util/Binning.pm cp Bio/SearchIO/blast.pm blib/lib/Bio/SearchIO/blast.pm cp Bio/Tools/Primer/AssessorI.pm blib/lib/Bio/Tools/Primer/AssessorI.pm cp Bio/Species.pm blib/lib/Bio/Species.pm cp Bio/DB/GFF/Adaptor/biofetch_oracle.pm blib/lib/Bio/DB/GFF/Adaptor/biofetch_oracle.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/Tools/CodonTable.pm blib/lib/Bio/Tools/CodonTable.pm cp Bio/Matrix/PSM/PsmHeaderI.pm blib/lib/Bio/Matrix/PSM/PsmHeaderI.pm cp Bio/SeqIO/bsml.pm blib/lib/Bio/SeqIO/bsml.pm cp Bio/Tools/AlignFactory.pm blib/lib/Bio/Tools/AlignFactory.pm cp Bio/DB/QueryI.pm blib/lib/Bio/DB/QueryI.pm cp Bio/Graphics/Glyph/segments.pm blib/lib/Bio/Graphics/Glyph/segments.pm cp Bio/Annotation/DBLink.pm blib/lib/Bio/Annotation/DBLink.pm cp Bio/Seq/SeqWithQuality.pm blib/lib/Bio/Seq/SeqWithQuality.pm cp Bio/SearchIO/FastHitEventBuilder.pm blib/lib/Bio/SearchIO/FastHitEventBuilder.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/Search/Hit/BlastHit.pm blib/lib/Bio/Search/Hit/BlastHit.pm cp Bio/Graphics/Glyph/redgreen_segment.pm blib/lib/Bio/Graphics/Glyph/redgreen_segment.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/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/EventHandlerI.pm blib/lib/Bio/SearchIO/EventHandlerI.pm cp Bio/SearchIO/Writer/HitTableWriter.pm blib/lib/Bio/SearchIO/Writer/HitTableWriter.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/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/Cluster/SequenceFamily.pm blib/lib/Bio/Cluster/SequenceFamily.pm cp Bio/SeqIO/swiss.pm blib/lib/Bio/SeqIO/swiss.pm cp Bio/DB/Makefile.PL blib/lib/Bio/DB/Makefile.PL cp Bio/Tools/Analysis/DNA/ESEfinder.pm blib/lib/Bio/Tools/Analysis/DNA/ESEfinder.pm 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/Tools/Lucy.pm blib/lib/Bio/Tools/Lucy.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/Graphics/Glyph/xyplot.pm blib/lib/Bio/Graphics/Glyph/xyplot.pm cp Bio/Symbol/Alphabet.pm blib/lib/Bio/Symbol/Alphabet.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/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/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/Graphics/Glyph/ruler_arrow.pm blib/lib/Bio/Graphics/Glyph/ruler_arrow.pm cp Bio/Biblio/MedlineBookArticle.pm blib/lib/Bio/Biblio/MedlineBookArticle.pm cp Bio/Biblio/Patent.pm blib/lib/Bio/Biblio/Patent.pm cp Bio/Tools/Genemark.pm blib/lib/Bio/Tools/Genemark.pm cp Bio/Matrix/IO.pm blib/lib/Bio/Matrix/IO.pm cp Bio/Seq/RichSeq.pm blib/lib/Bio/Seq/RichSeq.pm cp Bio/DB/GFF/Aggregator.pm blib/lib/Bio/DB/GFF/Aggregator.pm cp Bio/DB/GFF.pm blib/lib/Bio/DB/GFF.pm cp Bio/SeqFeature/SiRNA/Pair.pm blib/lib/Bio/SeqFeature/SiRNA/Pair.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/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/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 bioscripts.pod blib/lib/bioscripts.pod cp Bio/DB/Registry.pm blib/lib/Bio/DB/Registry.pm cp Bio/Variation/VariantI.pm blib/lib/Bio/Variation/VariantI.pm cp Bio/Tools/Glimmer.pm blib/lib/Bio/Tools/Glimmer.pm cp Bio/Root/Utilities.pm blib/lib/Bio/Root/Utilities.pm cp Bio/Graphics/Glyph/line.pm blib/lib/Bio/Graphics/Glyph/line.pm cp Bio/Factory/SequenceFactoryI.pm blib/lib/Bio/Factory/SequenceFactoryI.pm cp Bio/Search/Hit/GenericHit.pm blib/lib/Bio/Search/Hit/GenericHit.pm cp Bio/Map/LinkageMap.pm blib/lib/Bio/Map/LinkageMap.pm cp Bio/Tools/RestrictionEnzyme.pm blib/lib/Bio/Tools/RestrictionEnzyme.pm cp Bio/OntologyIO/Handlers/InterProHandler.pm blib/lib/Bio/OntologyIO/Handlers/InterProHandler.pm cp Bio/AlignIO/stockholm.pm blib/lib/Bio/AlignIO/stockholm.pm cp Bio/PopGen/Individual.pm blib/lib/Bio/PopGen/Individual.pm cp Bio/DB/GFF/Adaptor/dbi/mysqlace.pm blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlace.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/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/Matrix/PhylipDist.pm blib/lib/Bio/Matrix/PhylipDist.pm cp Bio/Annotation/Comment.pm blib/lib/Bio/Annotation/Comment.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/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/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/Phenotype/Measure.pm blib/lib/Bio/Phenotype/Measure.pm cp Bio/DB/GFF/RelSegment.pm blib/lib/Bio/DB/GFF/RelSegment.pm cp Bio/SeqFeature/Gene/Intron.pm blib/lib/Bio/SeqFeature/Gene/Intron.pm cp Bio/Tools/Eponine.pm blib/lib/Bio/Tools/Eponine.pm cp Bio/Map/OrderedPosition.pm blib/lib/Bio/Map/OrderedPosition.pm cp Bio/Annotation/TypeManager.pm blib/lib/Bio/Annotation/TypeManager.pm cp Bio/DB/GFF/Aggregator/ucsc_ensgene.pm blib/lib/Bio/DB/GFF/Aggregator/ucsc_ensgene.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/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/GenPept.pm blib/lib/Bio/DB/GenPept.pm cp Bio/Search/DatabaseI.pm blib/lib/Bio/Search/DatabaseI.pm cp Bio/Index/Blast.pm blib/lib/Bio/Index/Blast.pm cp Bio/SeqIO/game/featHandler.pm blib/lib/Bio/SeqIO/game/featHandler.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/Location/NarrowestCoordPolicy.pm blib/lib/Bio/Location/NarrowestCoordPolicy.pm cp Bio/Tools/pSW.pm blib/lib/Bio/Tools/pSW.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/Biblio/Book.pm blib/lib/Bio/Biblio/Book.pm cp Bio/SeqFeature/Gene/GeneStructure.pm blib/lib/Bio/SeqFeature/Gene/GeneStructure.pm cp Bio/SearchIO/Writer/HTMLResultWriter.pm blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm cp Bio/Tools/BPlite/Iteration.pm blib/lib/Bio/Tools/BPlite/Iteration.pm cp Bio/Tree/Statistics.pm blib/lib/Bio/Tree/Statistics.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/Graphics/Glyph/span.pm blib/lib/Bio/Graphics/Glyph/span.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/Root/Exception.pm blib/lib/Bio/Root/Exception.pm cp Bio/Factory/TreeFactoryI.pm blib/lib/Bio/Factory/TreeFactoryI.pm cp Bio/Assembly/IO/ace.pm blib/lib/Bio/Assembly/IO/ace.pm cp Bio/DB/Biblio/soap.pm blib/lib/Bio/DB/Biblio/soap.pm cp Bio/Root/Object.pm blib/lib/Bio/Root/Object.pm cp Bio/SeqIO/tab.pm blib/lib/Bio/SeqIO/tab.pm cp ./scripts_temp/bp_heterogeneity_test.pl blib/script/bp_heterogeneity_test.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_heterogeneity_test.pl cp ./scripts_temp/bp_biogetseq.pl blib/script/bp_biogetseq.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_biogetseq.pl cp ./scripts_temp/bp_biblio.pl blib/script/bp_biblio.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_biblio.pl cp ./scripts_temp/bp_extract_feature_seq.pl blib/script/bp_extract_feature_seq.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_extract_feature_seq.pl cp ./scripts_temp/bp_process_gadfly.pl blib/script/bp_process_gadfly.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_process_gadfly.pl cp ./scripts_temp/bp_aacomp.pl blib/script/bp_aacomp.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_aacomp.pl cp ./scripts_temp/bp_nrdb.pl blib/script/bp_nrdb.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_nrdb.pl cp ./scripts_temp/bp_mrtrans.pl blib/script/bp_mrtrans.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mrtrans.pl cp ./scripts_temp/bp_load_gff.pl blib/script/bp_load_gff.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_load_gff.pl cp ./scripts_temp/bp_process_sgd.pl blib/script/bp_process_sgd.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_process_sgd.pl cp ./scripts_temp/bp_gccalc.pl blib/script/bp_gccalc.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_gccalc.pl cp ./scripts_temp/bp_feature_draw.pl blib/script/bp_feature_draw.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_feature_draw.pl cp ./scripts_temp/bp_sreformat.pl blib/script/bp_sreformat.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_sreformat.pl cp ./scripts_temp/bp_oligo_count.pl blib/script/bp_oligo_count.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_oligo_count.pl cp ./scripts_temp/bp_translate_seq.pl blib/script/bp_translate_seq.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_translate_seq.pl cp ./scripts_temp/bp_flanks.pl blib/script/bp_flanks.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_flanks.pl cp ./scripts_temp/bp_index.pl blib/script/bp_index.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_index.pl cp ./scripts_temp/bp_seq_length.pl blib/script/bp_seq_length.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seq_length.pl cp ./scripts_temp/bp_search2alnblocks.pl blib/script/bp_search2alnblocks.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2alnblocks.pl cp ./scripts_temp/bp_search2tribe.pl blib/script/bp_search2tribe.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2tribe.pl cp ./scripts_temp/bp_generate_histogram.pl blib/script/bp_generate_histogram.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_generate_histogram.pl cp ./scripts_temp/bp_dbsplit.pl blib/script/bp_dbsplit.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_dbsplit.pl cp ./scripts_temp/bp_composite_LD.pl blib/script/bp_composite_LD.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_composite_LD.pl cp ./scripts_temp/bp_filter_search.pl blib/script/bp_filter_search.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_filter_search.pl cp ./scripts_temp/bp_mutate.pl blib/script/bp_mutate.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mutate.pl cp ./scripts_temp/bp_bioflat_index.pl blib/script/bp_bioflat_index.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_bioflat_index.pl cp ./scripts_temp/bp_seqconvert.pl blib/script/bp_seqconvert.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqconvert.pl cp ./scripts_temp/bp_local_taxonomydb_query.pl blib/script/bp_local_taxonomydb_query.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_local_taxonomydb_query.pl cp ./scripts_temp/bp_process_ncbi_human.pl blib/script/bp_process_ncbi_human.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_process_ncbi_human.pl cp ./scripts_temp/bp_fetch.pl blib/script/bp_fetch.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_fetch.pl cp ./scripts_temp/bp_search2gff.pl blib/script/bp_search2gff.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2gff.pl cp ./scripts_temp/bp_process_wormbase.pl blib/script/bp_process_wormbase.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_process_wormbase.pl cp ./scripts_temp/bp_fast_load_gff.pl blib/script/bp_fast_load_gff.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_fast_load_gff.pl cp ./scripts_temp/bp_split_seq.pl blib/script/bp_split_seq.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_split_seq.pl cp ./scripts_temp/bp_bulk_load_gff.pl blib/script/bp_bulk_load_gff.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_bulk_load_gff.pl cp ./scripts_temp/bp_pg_bulk_load_gff.pl blib/script/bp_pg_bulk_load_gff.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_pg_bulk_load_gff.pl cp ./scripts_temp/bp_blast2tree.pl blib/script/bp_blast2tree.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_blast2tree.pl cp ./scripts_temp/bp_chaos_plot.pl blib/script/bp_chaos_plot.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_chaos_plot.pl cp ./scripts_temp/bp_search2BSML.pl blib/script/bp_search2BSML.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2BSML.pl cp ./scripts_temp/bp_remote_blast.pl blib/script/bp_remote_blast.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_remote_blast.pl cp ./scripts_temp/bp_frend.pl blib/script/bp_frend.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_frend.pl cp ./scripts_temp/bp_mask_by_search.pl blib/script/bp_mask_by_search.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mask_by_search.pl cp ./scripts_temp/bp_search_overview.pl blib/script/bp_search_overview.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search_overview.pl cp ./scripts_temp/bp_genbank2gff.pl blib/script/bp_genbank2gff.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_genbank2gff.pl cp ./scripts_temp/bp_pairwise_kaks.pl blib/script/bp_pairwise_kaks.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_pairwise_kaks.pl cp ./scripts_temp/bp_biofetch_genbank_proxy.pl blib/script/bp_biofetch_genbank_proxy.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_biofetch_genbank_proxy.pl cp ./scripts_temp/bp_taxid4species.pl blib/script/bp_taxid4species.pl /export/home/fly818/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_taxid4species.pl BIRNEY/bioperl-1.4.tar.gz make -- OK Running make test >>> make test TEST_VERBOSE=1 PERL_DL_NONLAZY=1 /export/home/fly818/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(1, 'blib/lib', 'blib/arch')" t/*.t 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 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 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 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 GD or Text::Shellwords modules are not installed. This means that Bio::Graphics module is unusable. Skipping tests. t/BioGraphics.t .............. 1..14 ok 1 # unable to run all of the Bio::Graphics tests ok 2 # unable to run all of the Bio::Graphics tests ok 3 # unable to run all of the Bio::Graphics tests ok 4 # unable to run all of the Bio::Graphics tests ok 5 # unable to run all of the Bio::Graphics tests ok 6 # unable to run all of the Bio::Graphics tests ok 7 # unable to run all of the Bio::Graphics tests ok 8 # unable to run all of the Bio::Graphics tests ok 9 # unable to run all of the Bio::Graphics tests ok 10 # unable to run all of the Bio::Graphics tests ok 11 # unable to run all of the Bio::Graphics tests ok 12 # unable to run all of the Bio::Graphics tests ok 13 # unable to run all of the Bio::Graphics tests ok 14 # unable to run all of the Bio::Graphics tests ok 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 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 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 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 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 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 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 t/CoordinateGraph.t .......... 1..7 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 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 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 t/DB.t ....................... 1..78 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 not ok 30 # Test 30 got: 'Bio::Seq::RichSeq=HASH(0xa1c258)' (t/DB.t at line 144) # Expected: 'O39869' not ok 31 # Test 31 got: '9PICO' (t/DB.t at line 145) # Expected: 'UNK' ok 32 ok 33 ok 34 # skip ok 35 ok 36 ok 37 ok 38 ok 39 # could not connect to swissprot ok 40 # could not connect to swissprot ok 41 # could not connect to swissprot ok 42 # could not connect to swissprot ok 43 # could not connect to swissprot ok 44 # could not connect to swissprot ok 45 # could not connect to swissprot ok 46 # could not connect to swissprot ok 47 # could not connect to swissprot ok 48 # could not connect to swissprot ok 49 # could not connect to swissprot ok 50 # could not connect to swissprot ok 51 # could not connect to swissprot ok 52 # could not connect to swissprot ok 53 # could not connect to swissprot ok 54 # could not connect to swissprot ok 55 # could not connect to swissprot ok 56 # could not connect to swissprot ok 57 # could not connect to swissprot ok 58 # could not connect to swissprot ok 59 # could not connect to swissprot ok 60 # could not connect to swissprot ok 61 # could not connect to swissprot ok 62 # could not connect to swissprot ok 63 # could not connect to swissprot ok 64 # could not connect to swissprot ok 65 # could not connect to swissprot ok 66 # could not connect to swissprot ok 67 # could not connect to swissprot ok 68 # could not connect to swissprot ok 69 # could not connect to swissprot ok 70 # could not connect to swissprot ok 71 # could not connect to swissprot ok 72 # could not connect to swissprot ok 73 # could not connect to swissprot ok 74 # could not connect to swissprot ok 75 # could not connect to swissprot ok 76 # could not connect to swissprot ok 77 # could not connect to swissprot ok 78 # could not connect to swissprot Failed 2/78 subtests (less 1 skipped subtest: 75 okay) t/DBCUTG.t ................... 1..22 ok 1 ok 2 ok 3 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 4 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 5 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 6 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 7 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 8 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 9 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 10 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 11 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 12 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 13 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 14 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 15 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 16 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 17 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 18 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 19 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 20 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 21 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 22 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok AnyDBM_File doesn't define an EXISTS method at Bio/DB/Fasta.pm line 577 t/DBFasta.t .................. 1..12 ok 1 ok 2 ok 3 ok 4 Dubious, test returned 255 (wstat 65280, 0xff00) Failed 8/12 subtests t/DNAMutation.t .............. 1..36 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 t/Domcut.t ................... 1..25 ok 1 ok 2 ok 3 ok 4 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 5 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 6 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 7 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 8 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 9 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 10 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 11 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 12 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 13 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 14 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 15 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 16 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 17 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 18 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 19 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 20 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 21 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 22 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 23 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 24 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 25 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok t/ECnumber.t ................. 1..26 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 -------------------- WARNING --------------------- MSG: Bio::Tools::Analysis::Protein::ELM Request Error: 400 URL must be absolute Content-Type: text/plain Client-Date: Sat, 13 Jun 2009 05:38:36 GMT Client-Warning: Internal response 400 URL must be absolute --------------------------------------------------- t/ELM.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 # unable to run all of the tests depending on web access ok 12 # unable to run all of the tests depending on web access ok 13 # unable to run all of the tests depending on web access ok 14 # unable to run all of the tests depending on web access ok t/EMBL_DB.t .................. 1..15 ok 1 ok 2 ok 3 ok 4 ok 5 not ok 6 # Test 6 got: 'embl|J02231|J02231' (t/EMBL_DB.t at line 67) # Expected: qr/(?-xism:embl.+BUM)/ ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 not ok 13 # Test 13 got: '1611' (t/EMBL_DB.t at line 95) # Expected: '408' not ok 14 # Test 14 got: '408' (t/EMBL_DB.t at line 96) # Expected: '1611' ok 15 Failed 3/15 subtests t/EMBOSS_Tools.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 t/EncodedSeq.t ............... 1..37 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 t/ePCR.t ..................... 1..23 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 t/ESEfinder.t ................ 1..12 ok 1 ok 2 ok 3 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 4 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 5 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 6 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 7 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 8 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 9 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 10 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 11 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 12 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok t/est2genome.t ............... 1..60 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 t/Exception.t ................ 1..8 ok 1 ok 2 Setting test data (Eeny meeny miney moe.) ok 3 ok 4 Executing method bar() in TestObject Throwing a Bio::TestException ok 5 ok 6 ok 7 ok 8 ok t/Exonerate.t ................ 1..45 ok 1 ok 2 ok 3 # no query length available in default output ok 4 ok 5 # no hit length available in default output 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 # no query length available in default output ok 26 ok 27 # no hit length available in default output 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 DB_File not loaded. This means flat.t test cannot be executed. Skipping t/flat.t ..................... 1..16 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 14 # DB_File not installed ok 15 # DB_File not installed ok 16 # DB_File not installed ok t/FootPrinter.t .............. 1..26 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 t/game.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/GDB.t ...................... 1..11 ok 1 # GDB test skipped to avoid timeouts ok 2 # GDB test skipped to avoid timeouts ok 3 # GDB test skipped to avoid timeouts ok 4 # GDB test skipped to avoid timeouts ok 5 # GDB test skipped to avoid timeouts ok 6 # GDB test skipped to avoid timeouts ok 7 # GDB test skipped to avoid timeouts ok 8 # GDB test skipped to avoid timeouts ok 9 # GDB test skipped to avoid timeouts ok 10 # GDB test skipped to avoid timeouts ok 11 # GDB test skipped to avoid timeouts ok -------------------- WARNING --------------------- MSG: sorted sublocation array requested but root location doesn't define seq_id (at least one sublocation does!) --------------------------------------------------- -------------------- WARNING --------------------- MSG: sorted sublocation array requested but root location doesn't define seq_id (at least one sublocation does!) --------------------------------------------------- Use of uninitialized value in concatenation (.) or string at /export/home/fly818/var/cpan/build/bioperl-1.4-jXjcCH/blib/lib/Bio/Coordinate/GeneMapper.pm line 814. t/GeneCoordinateMapper.t ..... 1..113 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 t/Geneid.t ................... 1..26 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 t/Genewise.t ................. 1..51 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 # skip ok 34 # skip ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok t/Genomewise.t ............... 1..20 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 t/Genpred.t .................. 1..56 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 Filehandle GEN0 opened only for output at /export/home/fly818/var/cpan/build/bioperl-1.4-jXjcCH/blib/lib/Bio/Root/IO.pm line 440. Filehandle GEN1 opened only for output at /export/home/fly818/var/cpan/build/bioperl-1.4-jXjcCH/blib/lib/Bio/Root/IO.pm line 440. t/GFF.t ...................... 1..32 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 t/GOR4.t ..................... 1..11 ok 1 ok 2 ok 3 ok 4 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 5 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 6 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 7 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 8 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 9 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 10 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 11 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok t/GOterm.t ................... 1..59 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 t/GuessSeqFormat.t ........... 1..46 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 t/hmmer.t .................... 1..136 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 t/HNN.t ...................... 1..13 ok 1 ok 2 ok 3 ok 4 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 5 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 6 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 7 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 8 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 9 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 10 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 11 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 12 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 13 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok t/Index.t .................... 1..32 ok 1 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 2 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 3 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 4 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 5 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 6 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 7 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 8 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 9 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 10 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 11 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 12 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 13 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 14 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 15 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 16 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 17 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 18 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 19 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 20 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 21 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 22 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 23 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 24 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 25 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 26 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 27 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 28 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 29 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 30 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 31 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok 32 # DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed ok t/InstanceSite.t ............. 1..6 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok t/InterProParser.t ........... 1..47 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 t/IUPAC.t .................... 1..1 ok 1 ok t/largefasta.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/largepseq.t ................ 1..22 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 t/LinkageMap.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 t/LiveSeq.t .................. 1..48 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 t/LocatableSeq.t ............. 1..80 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 t/Location.t ................. 1..72 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 t/LocationFactory.t .......... 1..177 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 171 ok 172 ok 173 ok 174 ok 175 ok 176 ok 177 ok t/LocusLink.t ................ 1..23 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 t/lucy.t ..................... 1..22 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 t/Map.t ...................... 1..48 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 t/MapIO.t .................... 1..23 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 t/Matrix.t ................... 1..64 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 t/Measure.t .................. 1..20 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 Use of uninitialized value in substitution (s///) at /export/home/fly818/var/cpan/build/bioperl-1.4-jXjcCH/blib/lib/Bio/DB/MeSH.pm line 263. Use of uninitialized value in regexp compilation at /export/home/fly818/var/cpan/build/bioperl-1.4-jXjcCH/blib/lib/Bio/DB/MeSH.pm line 277. Use of uninitialized value in regexp compilation at /export/home/fly818/var/cpan/build/bioperl-1.4-jXjcCH/blib/lib/Bio/DB/MeSH.pm line 277. Use of uninitialized value in regexp compilation at /export/home/fly818/var/cpan/build/bioperl-1.4-jXjcCH/blib/lib/Bio/DB/MeSH.pm line 277. t/MeSH.t ..................... 1..26 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 not ok 26 # Test 26 got: '0' (t/MeSH.t at line 97) # Expected: '2' Failed 1/26 subtests t/MetaSeq.t .................. 1..73 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 t/MicrosatelliteMarker.t ..... 1..6 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok t/MiniMIMentry.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 t/MitoProt.t ................. 1..8 ok 1 ok 2 ok 3 ok 4 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 5 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 6 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 7 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 8 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok t/Molphy.t ................... 1..17 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 t/multiple_fasta.t ........... 1..8 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok t/Mutation.t ................. 1..18 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 t/Mutator.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 t/NetPhos.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 t/Node.t ..................... 1..17 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 t/OddCodes.t ................. 1..10 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok t/OMIMentry.t ................ 1..145 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 t/OMIMentryAllelicVariant.t .. 1..26 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 t/OMIMparser.t ............... 1..173 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 171 ok 172 ok 173 ok set_attribute: not a compat02 graph at /export/home/fly818/var/megalib/Graph.pm line 2453, line 10. t/Ontology.t ................. 1..50 Dubious, test returned 255 (wstat 65280, 0xff00) Failed 50/50 subtests t/OntologyEngine.t ........... 1..22 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 t/PAML.t ..................... 1..116 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 Use of uninitialized value in substitution (s///) at /export/home/fly818/var/cpan/build/bioperl-1.4-jXjcCH/blib/lib/Bio/SeqIO/swiss.pm line 855, line 45. t/Perl.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 t/phd.t ...................... 1..5 ok 1 ok 2 ok 3 ok 4 ok 5 ok t/Phenotype.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 t/PhylipDist.t ............... 1..19 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 t/pICalculator.t ............. 1..36 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 t/Pictogram.t ................ 1..3 ok 1 ok 2 ok 3 ok t/PopGen.t ................... 1..74 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 # -0.001 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 # Fst not calculated yet 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 # 0.16273 ok 55 # 0.16273 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 # 0.72985 ok 67 # 0.72985 ok 68 # 0.72985 ok 69 # 0.72985 ok 70 ok 71 ok 72 ok 73 ok 74 ok t/PopGenSims.t ............... 1..22 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 t/primaryqual.t .............. 1..31 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 t/PrimarySeq.t ............... 1..35 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 t/primedseq.t ................ 1..9 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok t/Primer.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 t/primer3.t .................. 1..10 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok t/Promoterwise.t ............. 1..6 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok t/ProtDist.t ................. 1..46 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 t/psm.t ...................... 1..42 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 t/QRNA.t ..................... 1..29 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 t/qual.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 t/RandDistFunctions.t ........ 1..4 ok 1 ok 2 ok 3 ok 4 ok t/RandomTreeFactory.t ........ 1..3 ok 1 ok 2 ok 3 ok t/Range.t .................... 1..32 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 t/RangeI.t ................... 1..19 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 t/RefSeq.t ................... 1..13 ok 1 ok 2 ok 3 ok 4 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 5 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 6 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 7 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 8 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 9 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 10 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 11 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 12 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok 13 # Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test ok DB_File and BerkeleyDB not found. Skipping DB_File tests t/Registry.t ................. 1..6 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok t/Relationship.t ............. 1..9 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok t/RelationshipType.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/RemoteBlast.t .............. 1..6 ok 1 ok 2 ok 3 # Skip to avoid timeout ok 4 # Skip to avoid timeout ok 5 # Skip to avoid timeout ok 6 # Skip to avoid timeout ok t/RepeatMasker.t ............. 1..6 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok t/RestrictionAnalysis.t ...... 1..150 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 t/RestrictionEnzyme.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 t/RestrictionIO.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 t/RNAChange.t ................ 1..29 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 t/RootI.t .................... 1..10 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok t/RootIO.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/RootStorable.t ............. 1..34 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 t/Scansite.t ................. 1..12 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 # set env BIOPERLDEBUG to run tests over web ok 8 # set env BIOPERLDEBUG to run tests over web ok 9 # set env BIOPERLDEBUG to run tests over web ok 10 # set env BIOPERLDEBUG to run tests over web ok 11 # set env BIOPERLDEBUG to run tests over web ok 12 # set env BIOPERLDEBUG to run tests over web ok Terminated make: *** [test_dynamic] Error 143 Timeout (max run time is 300s) /export/home/fly818/bin/perl killed by signal 15