PATH=/home/fly1600/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin Start 2012-06-27T23:07:56 ActivePerl-1600 CPAN-1.9402 Going to read '/home/fly1600/var/cpan/Metadata' Database was generated on Thu, 28 Jun 2012 05:03:03 GMT Running make for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz Checksum for /net/nas/data/cpan/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz ok BioPerl-1.6.1 BioPerl-1.6.1/AUTHORS BioPerl-1.6.1/BioPerl.pm BioPerl-1.6.1/BUGS BioPerl-1.6.1/Build.PL BioPerl-1.6.1/Changes BioPerl-1.6.1/DEPENDENCIES BioPerl-1.6.1/DEPRECATED BioPerl-1.6.1/INSTALL BioPerl-1.6.1/INSTALL.SKIP BioPerl-1.6.1/INSTALL.WIN BioPerl-1.6.1/LICENSE BioPerl-1.6.1/Makefile.PL BioPerl-1.6.1/MANIFEST BioPerl-1.6.1/MANIFEST.SKIP BioPerl-1.6.1/META.yml BioPerl-1.6.1/README BioPerl-1.6.1/Bio BioPerl-1.6.1/Bio/AlignIO.pm BioPerl-1.6.1/Bio/AnalysisI.pm BioPerl-1.6.1/Bio/AnalysisParserI.pm BioPerl-1.6.1/Bio/AnalysisResultI.pm BioPerl-1.6.1/Bio/AnnotatableI.pm BioPerl-1.6.1/Bio/AnnotationCollectionI.pm 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BioPerl-1.6.1/t/Phenotype/MiniMIMentry.t BioPerl-1.6.1/t/Phenotype/OMIMentry.t BioPerl-1.6.1/t/Phenotype/OMIMentryAllelicVariant.t BioPerl-1.6.1/t/Phenotype/OMIMparser.t BioPerl-1.6.1/t/Phenotype/Phenotype.t BioPerl-1.6.1/t/PopGen BioPerl-1.6.1/t/PopGen/Coalescent.t BioPerl-1.6.1/t/PopGen/HtSNP.t BioPerl-1.6.1/t/PopGen/MK.t BioPerl-1.6.1/t/PopGen/PopGen.t BioPerl-1.6.1/t/PopGen/PopGenSims.t BioPerl-1.6.1/t/PopGen/TagHaplotype.t BioPerl-1.6.1/t/RemoteDB BioPerl-1.6.1/t/RemoteDB/BioFetch.t BioPerl-1.6.1/t/RemoteDB/CUTG.t BioPerl-1.6.1/t/RemoteDB/EMBL.t BioPerl-1.6.1/t/RemoteDB/EntrezGene.t BioPerl-1.6.1/t/RemoteDB/EUtilities.t BioPerl-1.6.1/t/RemoteDB/GenBank.t BioPerl-1.6.1/t/RemoteDB/GenPept.t BioPerl-1.6.1/t/RemoteDB/MeSH.t BioPerl-1.6.1/t/RemoteDB/RefSeq.t BioPerl-1.6.1/t/RemoteDB/SeqHound.t BioPerl-1.6.1/t/RemoteDB/SeqRead_fail.t BioPerl-1.6.1/t/RemoteDB/SeqVersion.t BioPerl-1.6.1/t/RemoteDB/SwissProt.t BioPerl-1.6.1/t/RemoteDB/Taxonomy.t BioPerl-1.6.1/t/RemoteDB/HIV BioPerl-1.6.1/t/RemoteDB/HIV/HIV.t BioPerl-1.6.1/t/RemoteDB/HIV/HIVAnnotProcessor.t BioPerl-1.6.1/t/RemoteDB/HIV/HIVQuery.t BioPerl-1.6.1/t/RemoteDB/HIV/HIVQueryHelper.t BioPerl-1.6.1/t/RemoteDB/Query BioPerl-1.6.1/t/RemoteDB/Query/GenBank.t BioPerl-1.6.1/t/Restriction BioPerl-1.6.1/t/Restriction/Analysis-refac.t BioPerl-1.6.1/t/Restriction/Analysis.t BioPerl-1.6.1/t/Restriction/Gel.t BioPerl-1.6.1/t/Restriction/IO.t BioPerl-1.6.1/t/Root BioPerl-1.6.1/t/Root/Exception.t BioPerl-1.6.1/t/Root/RootI.t BioPerl-1.6.1/t/Root/RootIO.t BioPerl-1.6.1/t/Root/Storable.t BioPerl-1.6.1/t/Root/Tempfile.t BioPerl-1.6.1/t/Root/Utilities.t BioPerl-1.6.1/t/SearchIO BioPerl-1.6.1/t/SearchIO/blast.t BioPerl-1.6.1/t/SearchIO/blast_pull.t BioPerl-1.6.1/t/SearchIO/blasttable.t BioPerl-1.6.1/t/SearchIO/blastxml.t BioPerl-1.6.1/t/SearchIO/CigarString.t BioPerl-1.6.1/t/SearchIO/cross_match.t BioPerl-1.6.1/t/SearchIO/erpin.t BioPerl-1.6.1/t/SearchIO/exonerate.t BioPerl-1.6.1/t/SearchIO/fasta.t BioPerl-1.6.1/t/SearchIO/gmap_f9.t BioPerl-1.6.1/t/SearchIO/hmmer.t BioPerl-1.6.1/t/SearchIO/hmmer_pull.t BioPerl-1.6.1/t/SearchIO/infernal.t BioPerl-1.6.1/t/SearchIO/megablast.t BioPerl-1.6.1/t/SearchIO/psl.t BioPerl-1.6.1/t/SearchIO/rnamotif.t BioPerl-1.6.1/t/SearchIO/SearchIO.t BioPerl-1.6.1/t/SearchIO/sim4.t BioPerl-1.6.1/t/SearchIO/SimilarityPair.t BioPerl-1.6.1/t/SearchIO/Tiling.t BioPerl-1.6.1/t/SearchIO/waba.t BioPerl-1.6.1/t/SearchIO/wise.t BioPerl-1.6.1/t/SearchIO/Writer BioPerl-1.6.1/t/SearchIO/Writer/GbrowseGFF.t BioPerl-1.6.1/t/SearchIO/Writer/HitTableWriter.t BioPerl-1.6.1/t/SearchIO/Writer/HSPTableWriter.t BioPerl-1.6.1/t/SearchIO/Writer/HTMLWriter.t BioPerl-1.6.1/t/Seq BioPerl-1.6.1/t/Seq/DBLink.t BioPerl-1.6.1/t/Seq/EncodedSeq.t BioPerl-1.6.1/t/Seq/LargeLocatableSeq.t BioPerl-1.6.1/t/Seq/LargePSeq.t BioPerl-1.6.1/t/Seq/LocatableSeq.t BioPerl-1.6.1/t/Seq/MetaSeq.t BioPerl-1.6.1/t/Seq/PrimaryQual.t BioPerl-1.6.1/t/Seq/PrimarySeq.t BioPerl-1.6.1/t/Seq/PrimedSeq.t BioPerl-1.6.1/t/Seq/Quality.t BioPerl-1.6.1/t/Seq/Seq.t BioPerl-1.6.1/t/Seq/WithQuality.t BioPerl-1.6.1/t/SeqFeature BioPerl-1.6.1/t/SeqFeature/FeatureIO.t BioPerl-1.6.1/t/SeqFeature/Location.t BioPerl-1.6.1/t/SeqFeature/LocationFactory.t BioPerl-1.6.1/t/SeqFeature/Primer.t BioPerl-1.6.1/t/SeqFeature/Range.t BioPerl-1.6.1/t/SeqFeature/RangeI.t BioPerl-1.6.1/t/SeqFeature/SeqAnalysisParser.t BioPerl-1.6.1/t/SeqFeature/SeqFeatAnnotated.t BioPerl-1.6.1/t/SeqFeature/SeqFeatCollection.t BioPerl-1.6.1/t/SeqFeature/SeqFeature.t BioPerl-1.6.1/t/SeqFeature/SeqFeaturePrimer.t BioPerl-1.6.1/t/SeqFeature/Unflattener.t BioPerl-1.6.1/t/SeqFeature/Unflattener2.t BioPerl-1.6.1/t/SeqIO BioPerl-1.6.1/t/SeqIO/abi.t BioPerl-1.6.1/t/SeqIO/ace.t BioPerl-1.6.1/t/SeqIO/agave.t BioPerl-1.6.1/t/SeqIO/alf.t BioPerl-1.6.1/t/SeqIO/asciitree.t BioPerl-1.6.1/t/SeqIO/bsml.t BioPerl-1.6.1/t/SeqIO/bsml_sax.t BioPerl-1.6.1/t/SeqIO/chadoxml.t BioPerl-1.6.1/t/SeqIO/chaos.t BioPerl-1.6.1/t/SeqIO/chaosxml.t BioPerl-1.6.1/t/SeqIO/ctf.t BioPerl-1.6.1/t/SeqIO/embl.t BioPerl-1.6.1/t/SeqIO/entrezgene.t BioPerl-1.6.1/t/SeqIO/excel.t BioPerl-1.6.1/t/SeqIO/exp.t BioPerl-1.6.1/t/SeqIO/fasta.t BioPerl-1.6.1/t/SeqIO/fastq.t BioPerl-1.6.1/t/SeqIO/flybase_chadoxml.t BioPerl-1.6.1/t/SeqIO/game.t BioPerl-1.6.1/t/SeqIO/gcg.t BioPerl-1.6.1/t/SeqIO/genbank.t BioPerl-1.6.1/t/SeqIO/Handler.t BioPerl-1.6.1/t/SeqIO/interpro.t BioPerl-1.6.1/t/SeqIO/kegg.t BioPerl-1.6.1/t/SeqIO/largefasta.t BioPerl-1.6.1/t/SeqIO/lasergene.t BioPerl-1.6.1/t/SeqIO/locuslink.t BioPerl-1.6.1/t/SeqIO/metafasta.t BioPerl-1.6.1/t/SeqIO/MultiFile.t BioPerl-1.6.1/t/SeqIO/Multiple_fasta.t BioPerl-1.6.1/t/SeqIO/phd.t BioPerl-1.6.1/t/SeqIO/pir.t BioPerl-1.6.1/t/SeqIO/pln.t BioPerl-1.6.1/t/SeqIO/qual.t BioPerl-1.6.1/t/SeqIO/raw.t BioPerl-1.6.1/t/SeqIO/scf.t BioPerl-1.6.1/t/SeqIO/SeqBuilder.t BioPerl-1.6.1/t/SeqIO/Splicedseq.t BioPerl-1.6.1/t/SeqIO/strider.t BioPerl-1.6.1/t/SeqIO/swiss.t BioPerl-1.6.1/t/SeqIO/tab.t BioPerl-1.6.1/t/SeqIO/table.t BioPerl-1.6.1/t/SeqIO/tigr.t BioPerl-1.6.1/t/SeqIO/tigrxml.t BioPerl-1.6.1/t/SeqIO/tinyseq.t BioPerl-1.6.1/t/SeqIO/ztr.t BioPerl-1.6.1/t/SeqTools BioPerl-1.6.1/t/SeqTools/Backtranslate.t BioPerl-1.6.1/t/SeqTools/CodonTable.t BioPerl-1.6.1/t/SeqTools/ECnumber.t BioPerl-1.6.1/t/SeqTools/GuessSeqFormat.t BioPerl-1.6.1/t/SeqTools/OddCodes.t BioPerl-1.6.1/t/SeqTools/SeqPattern.t BioPerl-1.6.1/t/SeqTools/SeqStats.t BioPerl-1.6.1/t/SeqTools/SeqUtils.t BioPerl-1.6.1/t/SeqTools/SeqWords.t BioPerl-1.6.1/t/Structure BioPerl-1.6.1/t/Structure/IO.t BioPerl-1.6.1/t/Structure/Structure.t BioPerl-1.6.1/t/Tools BioPerl-1.6.1/t/Tools/ePCR.t BioPerl-1.6.1/t/Tools/Est2Genome.t BioPerl-1.6.1/t/Tools/FootPrinter.t BioPerl-1.6.1/t/Tools/Geneid.t BioPerl-1.6.1/t/Tools/Genewise.t BioPerl-1.6.1/t/Tools/Genomewise.t BioPerl-1.6.1/t/Tools/Genpred.t BioPerl-1.6.1/t/Tools/GFF.t BioPerl-1.6.1/t/Tools/Hmmer.t BioPerl-1.6.1/t/Tools/IUPAC.t BioPerl-1.6.1/t/Tools/Lucy.t BioPerl-1.6.1/t/Tools/Match.t BioPerl-1.6.1/t/Tools/pICalculator.t BioPerl-1.6.1/t/Tools/Primer3.t BioPerl-1.6.1/t/Tools/Promoterwise.t BioPerl-1.6.1/t/Tools/Pseudowise.t BioPerl-1.6.1/t/Tools/QRNA.t BioPerl-1.6.1/t/Tools/RandDistFunctions.t BioPerl-1.6.1/t/Tools/RepeatMasker.t BioPerl-1.6.1/t/Tools/rnamotif.t BioPerl-1.6.1/t/Tools/Seg.t BioPerl-1.6.1/t/Tools/Sigcleave.t BioPerl-1.6.1/t/Tools/Signalp.t BioPerl-1.6.1/t/Tools/Sim4.t BioPerl-1.6.1/t/Tools/SiRNA.t BioPerl-1.6.1/t/Tools/TandemRepeatsFinder.t BioPerl-1.6.1/t/Tools/TargetP.t BioPerl-1.6.1/t/Tools/Tmhmm.t BioPerl-1.6.1/t/Tools/tRNAscanSE.t BioPerl-1.6.1/t/Tools/Alignment BioPerl-1.6.1/t/Tools/Alignment/Consed.t BioPerl-1.6.1/t/Tools/Analysis BioPerl-1.6.1/t/Tools/Analysis/DNA BioPerl-1.6.1/t/Tools/Analysis/DNA/ESEfinder.t BioPerl-1.6.1/t/Tools/Analysis/Protein BioPerl-1.6.1/t/Tools/Analysis/Protein/Domcut.t BioPerl-1.6.1/t/Tools/Analysis/Protein/ELM.t BioPerl-1.6.1/t/Tools/Analysis/Protein/GOR4.t BioPerl-1.6.1/t/Tools/Analysis/Protein/HNN.t BioPerl-1.6.1/t/Tools/Analysis/Protein/Mitoprot.t BioPerl-1.6.1/t/Tools/Analysis/Protein/NetPhos.t BioPerl-1.6.1/t/Tools/Analysis/Protein/Scansite.t BioPerl-1.6.1/t/Tools/Analysis/Protein/Sopma.t BioPerl-1.6.1/t/Tools/EMBOSS BioPerl-1.6.1/t/Tools/EMBOSS/Palindrome.t BioPerl-1.6.1/t/Tools/EUtilities BioPerl-1.6.1/t/Tools/EUtilities/egquery.t BioPerl-1.6.1/t/Tools/EUtilities/einfo.t BioPerl-1.6.1/t/Tools/EUtilities/elink_acheck.t BioPerl-1.6.1/t/Tools/EUtilities/elink_lcheck.t BioPerl-1.6.1/t/Tools/EUtilities/elink_llinks.t BioPerl-1.6.1/t/Tools/EUtilities/elink_ncheck.t BioPerl-1.6.1/t/Tools/EUtilities/elink_neighbor.t BioPerl-1.6.1/t/Tools/EUtilities/elink_neighbor_history.t BioPerl-1.6.1/t/Tools/EUtilities/elink_scores.t BioPerl-1.6.1/t/Tools/EUtilities/epost.t BioPerl-1.6.1/t/Tools/EUtilities/esearch.t BioPerl-1.6.1/t/Tools/EUtilities/espell.t BioPerl-1.6.1/t/Tools/EUtilities/esummary.t BioPerl-1.6.1/t/Tools/EUtilities/EUtilParameters.t BioPerl-1.6.1/t/Tools/Phylo BioPerl-1.6.1/t/Tools/Phylo/Gerp.t BioPerl-1.6.1/t/Tools/Phylo/Molphy.t BioPerl-1.6.1/t/Tools/Phylo/PAML.t BioPerl-1.6.1/t/Tools/Phylo/Phylip BioPerl-1.6.1/t/Tools/Phylo/Phylip/ProtDist.t BioPerl-1.6.1/t/Tools/Run BioPerl-1.6.1/t/Tools/Run/RemoteBlast.t BioPerl-1.6.1/t/Tools/Run/RemoteBlast_rpsblast.t BioPerl-1.6.1/t/Tools/Run/StandAloneBlast.t BioPerl-1.6.1/t/Tools/Run/WrapperBase.t BioPerl-1.6.1/t/Tools/Signalp BioPerl-1.6.1/t/Tools/Signalp/ExtendedSignalp.t BioPerl-1.6.1/t/Tools/Spidey BioPerl-1.6.1/t/Tools/Spidey/Spidey.t BioPerl-1.6.1/t/Tree BioPerl-1.6.1/t/Tree/Compatible.t BioPerl-1.6.1/t/Tree/Node.t BioPerl-1.6.1/t/Tree/RandomTreeFactory.t BioPerl-1.6.1/t/Tree/Tree.t BioPerl-1.6.1/t/Tree/TreeIO.t BioPerl-1.6.1/t/Tree/TreeStatistics.t BioPerl-1.6.1/t/Tree/PhyloNetwork BioPerl-1.6.1/t/Tree/PhyloNetwork/Factory.t BioPerl-1.6.1/t/Tree/PhyloNetwork/GraphViz.t BioPerl-1.6.1/t/Tree/PhyloNetwork/MuVector.t BioPerl-1.6.1/t/Tree/PhyloNetwork/PhyloNetwork.t BioPerl-1.6.1/t/Tree/PhyloNetwork/RandomFactory.t BioPerl-1.6.1/t/Tree/PhyloNetwork/TreeFactory.t BioPerl-1.6.1/t/Tree/TreeIO BioPerl-1.6.1/t/Tree/TreeIO/lintree.t BioPerl-1.6.1/t/Tree/TreeIO/newick.t BioPerl-1.6.1/t/Tree/TreeIO/nexus.t BioPerl-1.6.1/t/Tree/TreeIO/nhx.t BioPerl-1.6.1/t/Tree/TreeIO/phyloxml.t BioPerl-1.6.1/t/Tree/TreeIO/svggraph.t BioPerl-1.6.1/t/Tree/TreeIO/tabtree.t BioPerl-1.6.1/t/Variation BioPerl-1.6.1/t/Variation/AAChange.t BioPerl-1.6.1/t/Variation/AAReverseMutate.t BioPerl-1.6.1/t/Variation/Allele.t BioPerl-1.6.1/t/Variation/DNAMutation.t BioPerl-1.6.1/t/Variation/RNAChange.t BioPerl-1.6.1/t/Variation/SeqDiff.t BioPerl-1.6.1/t/Variation/SNP.t BioPerl-1.6.1/t/Variation/Variation_IO.t CPAN.pm: Going to build C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz >>> /home/fly1600/ap1600/bin/perl-static Makefile.PL # running Build.PL Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] Checking prerequisites... recommends: * Optional prerequisite Ace is not installed (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace) * Optional prerequisite Bio::ASN1::EntrezGene is not installed (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!]) * Optional prerequisite GraphViz is not installed (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Checking features: Network...................enabled BioDBSeqFeature_mysql.....enabled BioDBGFF..................enabled BioDBSeqFeature_BDB.......enabled BioDBSeqFeature_SQLite....enabled BioDBSeqFeature_Pg........enabled Do you want to run the Bio::DB::GFF or Bio::DB::SeqFeature::Store live database tests? y/n [n] - will not run the BioDBGFF or BioDBSeqFeature live database tests Install [a]ll BioPerl scripts, [n]one, or choose groups [i]nteractively? [a] - will install all scripts Do you want to run tests that require connection to servers across the internet (likely to cause some failures)? y/n [n] Could not get valid metadata. Error is: Invalid metadata structure. Errors: 'Perl_5' for 'license' does not have a URL scheme (resources -> license) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::FeatureIO::gff -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::WebAgent -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::EUtilParameters -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::OntologyIO::InterProParser -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Biblio::IO::medlinexml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::strider -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PhyloNetwork::RandomFactory -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Analysis::DNA::ESEfinder -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::game::gameSubs -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::FeatureIO::interpro -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::GFF::Adaptor::berkeleydb -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::entrezgene -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::tinyseq -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::chadoxml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::game::gameWriter -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::FileCache -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::bsml_sax -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Primer3 -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::GFF::Adaptor::ace -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PopGen::HtSNP -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tree::Compatible -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Ace -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Taxonomy::entrez -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::agave -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PopGen::TagHaplotype -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::SeqFeature::Store::FeatureFileLoader -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::* -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Analysis::Protein* -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SearchIO::blastxml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::EUtilities -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tree::Draw::Cladogram -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::SeqPattern -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::tigrxml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqFeature::Collection -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Draw::Pictogram -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SearchIO::Writer::BSMLResultWriter -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Query::HIVQuery -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::TreeIO::svggraph -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Biblio::eutils -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PhyloNetwork -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::SeqPattern::BackTranslate -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Query::GenBank -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Variation::IO::xml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PhyloNetwork::GraphViz -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqFeature::Annotated -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::NCBIHelper -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::HIV -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Analysis::DNA* -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Run::RemoteBlast -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::excel -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::ClusterIO::dbsnp -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Microarray::Tools::ReseqChip -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Biblio::soap -> requires) [Validation: 1.2] at /home/fly1600/var/megalib/Module/Build/Base.pm line 4568. Could not create MYMETA files - will not run internet-requiring tests Creating new 'Build' script for 'BioPerl' version '1.006001' >>> make /home/fly1600/ap1600/bin/perl-static Build --makefile_env_macros 1 Building BioPerl blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl blib/script/hivq.PLS -> blib/script/bp_hivq.pl blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl blib/script/flanks.PLS -> blib/script/bp_flanks.pl blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl blib/script/mutate.PLS -> blib/script/bp_mutate.pl blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl blib/script/bp_index.PLS -> blib/script/bp_index.pl blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl blib/script/einfo.PLS -> blib/script/bp_einfo.pl blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl blib/script/revtrans-motif.PLS -> blib/script/bp_revtrans-motif.pl blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl blib/script/biblio.PLS -> blib/script/bp_biblio.pl blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl blib/script/search2table.PLS -> blib/script/bp_search2table.pl blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl CJFIELDS/BioPerl-1.6.1.tar.gz make -- OK Running make test >>> make test TEST_VERBOSE=1 /home/fly1600/ap1600/bin/perl-static Build --makefile_env_macros 1 test Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS Changing sharpbang in blib/script/bp_sreformat.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/bp_sreformat.PLS.bak blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS Changing sharpbang in blib/script/seqconvert.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/seqconvert.PLS.bak blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl Copying scripts/DB-HIV/hivq.PLS -> blib/script/hivq.PLS Changing sharpbang in blib/script/hivq.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/hivq.PLS.bak blib/script/hivq.PLS -> blib/script/bp_hivq.pl Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS Changing sharpbang in blib/script/parse_hmmsearch.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/parse_hmmsearch.PLS.bak blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS Changing sharpbang in blib/script/bp_seqret.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/bp_seqret.PLS.bak blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS Changing sharpbang in blib/script/meta_gff.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/meta_gff.PLS.bak blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS Changing sharpbang in blib/script/tree2pag.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/tree2pag.PLS.bak blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS Changing sharpbang in blib/script/nexus2nh.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/nexus2nh.PLS.bak blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS Changing sharpbang in blib/script/filter_search.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/filter_search.PLS.bak blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS Changing sharpbang in blib/script/generate_histogram.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/generate_histogram.PLS.bak blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS Changing sharpbang in blib/script/heterogeneity_test.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/heterogeneity_test.PLS.bak blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS Changing sharpbang in blib/script/flanks.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/flanks.PLS.bak blib/script/flanks.PLS -> blib/script/bp_flanks.pl Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS Changing sharpbang in blib/script/load_gff.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/load_gff.PLS.bak blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS Changing sharpbang in blib/script/split_seq.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/split_seq.PLS.bak blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS Changing sharpbang in blib/script/biogetseq.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/biogetseq.PLS.bak blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS Changing sharpbang in blib/script/bp_fetch.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/bp_fetch.PLS.bak blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS Changing sharpbang in blib/script/mutate.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/mutate.PLS.bak blib/script/mutate.PLS -> blib/script/bp_mutate.pl Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS Changing sharpbang in blib/script/process_sgd.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/process_sgd.PLS.bak blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS Changing sharpbang in blib/script/bp_index.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/bp_index.PLS.bak blib/script/bp_index.PLS -> blib/script/bp_index.pl Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS Changing sharpbang in blib/script/dbsplit.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/dbsplit.PLS.bak blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS Changing sharpbang in blib/script/oligo_count.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/oligo_count.PLS.bak blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS Changing sharpbang in blib/script/hmmer_to_table.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/hmmer_to_table.PLS.bak blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS Changing sharpbang in blib/script/process_gadfly.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/process_gadfly.PLS.bak blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS Changing sharpbang in blib/script/bp_seqfeature_load.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/bp_seqfeature_load.PLS.bak blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS Changing sharpbang in blib/script/fastam9_to_table.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/fastam9_to_table.PLS.bak blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS Changing sharpbang in blib/script/seq_length.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/seq_length.PLS.bak blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS Changing sharpbang in blib/script/biofetch_genbank_proxy.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/biofetch_genbank_proxy.PLS.bak blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS Changing sharpbang in blib/script/extract_feature_seq.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/extract_feature_seq.PLS.bak blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS Changing sharpbang in blib/script/genbank2gff.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/genbank2gff.PLS.bak blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS Changing sharpbang in blib/script/taxid4species.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/taxid4species.PLS.bak blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS Changing sharpbang in blib/script/bulk_load_gff.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/bulk_load_gff.PLS.bak blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS Changing sharpbang in blib/script/search2gff.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/search2gff.PLS.bak blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS Changing sharpbang in blib/script/blast2tree.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/blast2tree.PLS.bak blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS Changing sharpbang in blib/script/make_mrna_protein.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/make_mrna_protein.PLS.bak blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS Changing sharpbang in blib/script/unflatten_seq.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/unflatten_seq.PLS.bak blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS Changing sharpbang in blib/script/search2tribe.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/search2tribe.PLS.bak blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS Changing sharpbang in blib/script/bioflat_index.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/bioflat_index.PLS.bak blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS Changing sharpbang in blib/script/pairwise_kaks.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/pairwise_kaks.PLS.bak blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS Changing sharpbang in blib/script/query_entrez_taxa.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/query_entrez_taxa.PLS.bak blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS Changing sharpbang in blib/script/bp_seqfeature_delete.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/bp_seqfeature_delete.PLS.bak blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS Changing sharpbang in blib/script/fast_load_gff.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/fast_load_gff.PLS.bak blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS Changing sharpbang in blib/script/chaos_plot.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/chaos_plot.PLS.bak blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS Changing sharpbang in blib/script/search2alnblocks.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/search2alnblocks.PLS.bak blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS Changing sharpbang in blib/script/bp_mrtrans.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/bp_mrtrans.PLS.bak blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS Changing sharpbang in blib/script/taxonomy2tree.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/taxonomy2tree.PLS.bak blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl Copying scripts/Bio-DB-EUtilities/einfo.PLS -> blib/script/einfo.PLS Changing sharpbang in blib/script/einfo.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/einfo.PLS.bak blib/script/einfo.PLS -> blib/script/bp_einfo.pl Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS Changing sharpbang in blib/script/download_query_genbank.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/download_query_genbank.PLS.bak blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS Changing sharpbang in blib/script/bp_nrdb.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/bp_nrdb.PLS.bak blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS Changing sharpbang in blib/script/mask_by_search.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/mask_by_search.PLS.bak blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS Changing sharpbang in blib/script/gccalc.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/gccalc.PLS.bak blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS Changing sharpbang in blib/script/composite_LD.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/composite_LD.PLS.bak blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS Changing sharpbang in blib/script/classify_hits_kingdom.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/classify_hits_kingdom.PLS.bak blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS Changing sharpbang in blib/script/aacomp.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/aacomp.PLS.bak blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl Copying scripts/utilities/revtrans-motif.PLS -> blib/script/revtrans-motif.PLS Changing sharpbang in blib/script/revtrans-motif.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/revtrans-motif.PLS.bak blib/script/revtrans-motif.PLS -> blib/script/bp_revtrans-motif.pl Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS Changing sharpbang in blib/script/process_wormbase.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/process_wormbase.PLS.bak blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS Changing sharpbang in blib/script/local_taxonomydb_query.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/local_taxonomydb_query.PLS.bak blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS Changing sharpbang in blib/script/biblio.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/biblio.PLS.bak blib/script/biblio.PLS -> blib/script/bp_biblio.pl Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS Changing sharpbang in blib/script/remote_blast.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/remote_blast.PLS.bak blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS Changing sharpbang in blib/script/seqretsplit.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/seqretsplit.PLS.bak blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS Changing sharpbang in blib/script/genbank2gff3.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/genbank2gff3.PLS.bak blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS Changing sharpbang in blib/script/search2table.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/search2table.PLS.bak blib/script/search2table.PLS -> blib/script/bp_search2table.pl Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS Changing sharpbang in blib/script/search2BSML.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/search2BSML.PLS.bak blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS Changing sharpbang in blib/script/translate_seq.PLS to /home/fly1600/ap1600/bin/perl-static Deleting blib/script/translate_seq.PLS.bak blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl t/Align/AlignStats.t ......................... 1..43 ok 1 - use Bio::Align::DNAStatistics; ok 2 - use Bio::Align::ProteinStatistics; ok 3 - use Bio::AlignIO; ok 4 - The object isa Bio::Align::AlignI ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 - The object isa Bio::Align::AlignI ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 - The object isa Bio::Align::AlignI ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 - The object isa Bio::Align::AlignI ok 38 - The object isa Bio::Matrix::PhylipDist ok 39 ok 40 ok 41 ok 42 - The object isa Bio::PrimarySeqI ok 43 ok t/Align/AlignUtil.t .......................... 1..33 ok 1 - use Bio::Align::Utilities; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - The object isa Bio::Align::AlignI ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok t/Align/SimpleAlign.t ........................ 1..179 ok 1 - use Bio::SimpleAlign; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqFeature::Generic; ok 4 - use Bio::Location::Simple; ok 5 - use Bio::Location::Split; ok 6 - The object isa Bio::AlignIO ok 7 - pfam input test ok 8 - match_line ok 9 - The object isa Bio::Align::AlignI ok 10 - num_sequences ok 11 - num_sequences ok 12 - select_noncont ok 13 - select_noncont ok 14 - num_sequences ok 15 - select_noncont ok 16 - select_noncont ok 17 - each_seq ok 18 - get_nse ok 19 - id ok 20 - num_gaps ok 21 - each_alphabetically ok 22 - column_from_residue_number ok 23 - display_name get/set ok 24 - display_name get ok 25 - consensus_string ok 26 - consensus_string ok 27 - consensus_string ok 28 ok 29 - each_seq_with_id ok 30 - is_flush ok 31 - id get/set ok 32 - length ok 33 - num_residues ok 34 - num_sequences ok 35 - overall_percentage_identity ok 36 - overall_percentage_identity ok 37 - overall_percentage_identity ok 38 - overall_percentage_identity ok 39 - average_percentage_identity ok 40 ok 41 - set_displayname_count ok 42 ok 43 - set_displayname_flat ok 44 ok 45 - set_displayname_normal ok 46 ok 47 ok 48 - uppercase, map_chars ok 49 - match_line ok 50 - remove_seqs ok 51 - remove_seqs ok 52 - add_seq ok 53 - add_seq ok 54 - get_seq_by_pos ok 55 - get_seq_by_pos ok 56 ok 57 ok 58 ok 59 - purge ok 60 - purge ok 61 - IO::String consensus_iupac ok 62 - IO::String write_aln normal ok 63 - IO::String write_aln slice ok 64 - IO::String write_aln slice ok 65 - IO::String write_aln slice ok 66 - IO::String write_aln slice ok 67 - IO::String write_aln slice ok 68 ok 69 - remove_columns by position ok 70 - remove_columns by position (wrong order) ok 71 - cigar_line ok 72 - cigar_line ok 73 - cigar_line ok 74 - cigar_line ok 75 - sort_alphabetically - before ok 76 ok 77 - sort_alphabetically - after ok 78 - remove_gaps ok 79 - remove_gaps all_gaps_only ok 80 - set_new_reference ok 81 - set_new_reference ok 82 - uniq_seq ok 83 - bug 2099 ok 84 - bug 2099 ok 85 - bug 2793 ok 86 - bug 2793 ok 87 - bug 2793 ok 88 - bug 2793 ok 89 - Bad sequence, bad! ok 90 - added 3 seqs ok 91 - first 2 features added ok 92 - 3rd feature added not ok 93 # TODO This should pass but dies; see bug 2842 # Failed (TODO) test at t/Align/SimpleAlign.t line 421. # died: Bio::Root::Exception ( # ------------- EXCEPTION: Bio::Root::Exception ------------- # MSG: In sequence one residue count gives end value 1. # Overriding value [0] with value 1 for Bio::LocatableSeq::end(). # ? # STACK: Error::throw # STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368 # STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:181 # STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:196 # STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1143 # STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421 # STACK: t/Align/SimpleAlign.t:421 # ----------------------------------------------------------- # ) ok 94 - slice 1 len ok 95 - correct masked seq ok 96 - correct masked seq ok 97 - correct masked seq not ok 98 # TODO This should pass but dies; see bug 2842 # Failed (TODO) test at t/Align/SimpleAlign.t line 421. # died: Bio::Root::Exception ( # ------------- EXCEPTION: Bio::Root::Exception ------------- # MSG: In sequence one residue count gives end value 3. # Overriding value [2] with value 3 for Bio::LocatableSeq::end(). # ? # STACK: Error::throw # STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368 # STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:181 # STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:196 # STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1143 # STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421 # STACK: t/Align/SimpleAlign.t:421 # ----------------------------------------------------------- # ) ok 99 - slice 2 len ok 100 - correct masked seq ok 101 - correct masked seq ok 102 - correct masked seq not ok 103 # TODO This should pass but dies; see bug 2842 # Failed (TODO) test at t/Align/SimpleAlign.t line 421. # died: Bio::Root::Exception ( # ------------- EXCEPTION: Bio::Root::Exception ------------- # MSG: In sequence one residue count gives end value 3. # Overriding value [1] with value 3 for Bio::LocatableSeq::end(). # ?? # STACK: Error::throw # STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368 # STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:181 # STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:196 # STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1143 # STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421 # STACK: t/Align/SimpleAlign.t:421 # ----------------------------------------------------------- # ) ok 104 - slice 3 len ok 105 - correct masked seq ok 106 - correct masked seq ok 107 - correct masked seq not ok 108 # TODO This should pass but dies; see bug 2842 # Failed (TODO) test at t/Align/SimpleAlign.t line 421. # died: Bio::Root::Exception ( # ------------- EXCEPTION: Bio::Root::Exception ------------- # MSG: In sequence one residue count gives end value 6. # Overriding value [4] with value 6 for Bio::LocatableSeq::end(). # ?? # STACK: Error::throw # STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368 # STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:181 # STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:196 # STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1143 # STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421 # STACK: t/Align/SimpleAlign.t:421 # ----------------------------------------------------------- # ) ok 109 - slice 4 len ok 110 - correct masked seq ok 111 - correct masked seq ok 112 - correct masked seq ok 113 - initial display id ok ok 114 - safe display id ok ok 115 - restored display id ok ok 116 - sort by list ok ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 - BIC:GGATCCATT[C/C]CTACT ok 124 - BIC:GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT ok 125 - BIC:G[G/C]ATCCATT[C/G]CTACT ok 126 - BIC:GGATCCATT[C/G]CTACT ok 127 - BIC:GGATCCATT[C/G]CTAC[T/A] ok 128 - BIC:GGATCCATT[C/G]CTA[C/G][T/A] ok 129 - BIC:GGATCCATT[C/G]CTACT ok 130 - BIC:GGATCCATT{C.C}CTACT ok 131 - BIC:GGAT{C.-}{C.-}ATT{C.C}CT{A.C}CT ok 132 - BIC:G{G.C}ATCCATT{C.G}CTACT ok 133 - BIC:GGATCCATT{C.G}CTACT ok 134 - BIC:GGATCCATT{C.G}CTAC{T.A} ok 135 - BIC:GGATCCATT{C.G}CTA{C.G}{T.A} ok 136 - BIC:GGATCCATT{C.G}CTACT ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 ok 156 ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 - The object isa Bio::SimpleAlign ok 175 - consensus string looks ok ok 176 - looks like correct unmasked alignment (from clustalw) ok 177 - looks like correct masked alignment (from clustalw) ok 178 ok 179 - align after looks ok ok t/Align/TreeBuild.t .......................... 1..13 ok 1 - use Bio::Align::DNAStatistics; ok 2 - use Bio::Align::ProteinStatistics; ok 3 - use Bio::Align::Utilities; ok 4 - use Bio::AlignIO; ok 5 - use Bio::Tree::DistanceFactory; ok 6 - use Bio::TreeIO; ok 7 - SimpleAlign object parsed out isa Bio::SimpleAlign ok 8 - Protein distance matrix retrieved isa Bio::Matrix::MatrixI ok 9 - Tree object gotten back isa Bio::Tree::TreeI ok 10 - NJ calculated Branch length ok 11 - NJ calculated Branch length ok 12 - Make sure two nodes are sister ok 13 - 10 replicates formulated ok t/Align/Utilities.t .......................... 1..13 ok 1 - use Bio::Align::Utilities; ok 2 - use Bio::SimpleAlign; ok 3 - use Bio::PrimarySeq; ok 4 - use Bio::LocatableSeq; ok 5 - use Bio::AlignIO; ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok t/AlignIO/AlignIO.t .......................... 1..28 ok 1 - use Bio::AlignIO; ok 2 - input filehandle method test : metafasta ok 3 - input filehandle method test : po ok 4 - input filehandle method test : nexus ok 5 - input filehandle method test : clustalw ok 6 - input filehandle method test : prodom ok 7 - input filehandle method test : fasta ok 8 - input filehandle method test : arp ok 9 - input filehandle method test : xmfa ok 10 - input filehandle method test : mase ok 11 - input filehandle method test : psi ok 12 - input filehandle method test : phylip ok 13 - input filehandle method test : pfam ok 14 - input filehandle method test : selex ok 15 - input filehandle method test : stockholm ok 16 - input filehandle method test : msf ok 17 - filehandle output test : metafasta ok 18 - filehandle output test : po ok 19 - filehandle output test : nexus ok 20 - filehandle output test : clustalw ok 21 - filehandle output test : fasta ok 22 - filehandle output test : xmfa ok 23 - filehandle output test : psi ok 24 - filehandle output test : phylip ok 25 - filehandle output test : pfam ok 26 - filehandle output test : selex ok 27 - filehandle output test : stockholm ok 28 - filehandle output test : msf ok t/AlignIO/arp.t .............................. 1..48 ok 1 - use Bio::AlignIO::arp; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 - ARP get_nse() ok 5 ok 6 - ARP num_sequences() ok 7 - ARP id() ok 8 - ARP description() ok 9 - The object isa Bio::AnnotationCollectionI ok 10 - The object isa Bio::AnnotationI ok 11 ok 12 ok 13 ok 14 ok 15 - The object isa Bio::AlignIO ok 16 - The object isa Bio::Align::AlignI ok 17 - ARP get_nse() ok 18 - ARP num_sequences() ok 19 - ARP id() ok 20 - ARP description() ok 21 - The object isa Bio::AnnotationCollectionI ok 22 - The object isa Bio::AnnotationI ok 23 ok 24 ok 25 ok 26 ok 27 - The object isa Bio::Align::AlignI ok 28 - ARP get_nse() ok 29 - ARP num_sequences() ok 30 - ARP id() ok 31 - ARP description() ok 32 - The object isa Bio::AnnotationCollectionI ok 33 - The object isa Bio::AnnotationI ok 34 ok 35 ok 36 ok 37 ok 38 - The object isa Bio::Align::AlignI ok 39 - ARP get_nse() ok 40 - ARP num_sequences() ok 41 - ARP id() ok 42 - ARP description() ok 43 - The object isa Bio::AnnotationCollectionI ok 44 - The object isa Bio::AnnotationI ok 45 ok 46 ok 47 ok 48 ok t/AlignIO/bl2seq.t ........................... 1..3 ok 1 - use Bio::AlignIO::bl2seq; ok 2 - The object isa Bio::Align::AlignI ok 3 - BLAST bl2seq format test ok t/AlignIO/clustalw.t ......................... 1..6 ok 1 - use Bio::AlignIO::clustalw; ok 2 - The object isa Bio::Align::AlignI ok 3 - clustalw consensus_string test ok 4 - clustalw (.aln) output test ok 5 - The object isa Bio::Align::AlignI ok 6 - clustalw (.aln) input test ok t/AlignIO/emboss.t ........................... 1..37 ok 1 - use Bio::AlignIO::emboss; ok 2 - The object isa Bio::Align::AlignI ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 - The object isa Bio::Align::AlignI ok 11 ok 12 ok 13 ok 14 - The object isa Bio::Align::AlignI ok 15 ok 16 ok 17 ok 18 - The object isa Bio::Align::AlignI ok 19 ok 20 ok 21 - The object isa Bio::Align::AlignI ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 - The object isa Bio::Align::AlignI ok 33 ok 34 ok 35 ok 36 ok 37 ok t/AlignIO/fasta.t ............................ 1..10 ok 1 - use Bio::AlignIO::fasta; ok 2 - The object isa Bio::Align::AlignI ok 3 - fasta input test ok 4 - fasta input test for description ok 5 - fasta input test for id ok 6 - fasta input test for end ok 7 - fasta input test for description ok 8 - fasta output test ok 9 - filehandle input test ok 10 - filehandle output test ok t/AlignIO/largemultifasta.t .................. 1..7 ok 1 - use Bio::AlignIO::largemultifasta; ok 2 - The object isa Bio::Align::AlignI ok 3 - fasta input test ok 4 - fasta input test for description ok 5 - fasta input test for id ok 6 - fasta input test for description ok 7 - fasta output test ok t/AlignIO/maf.t .............................. 1..11 ok 1 - use Bio::AlignIO::maf; ok 2 - The object isa Bio::Align::AlignI ok 3 - maf input test ok 4 ok 5 - The object isa Bio::Align::AlignI ok 6 - maf input test ok 7 ok 8 - maf input test ok 9 ok 10 - maf input test ok 11 ok t/AlignIO/mase.t ............................. 1..3 ok 1 - use Bio::AlignIO::mase; ok 2 - The object isa Bio::Align::AlignI ok 3 - mase input test ok t/AlignIO/mega.t ............................. 1..6 ok 1 - use Bio::AlignIO::mega; ok 2 - The object isa Bio::Align::AlignI ok 3 ok 4 ok 5 ok 6 - mega output test ok t/AlignIO/meme.t ............................. 1..14 ok 1 - use Bio::AlignIO::meme; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 ok 5 ok 6 ok 7 ok 8 - The object isa Bio::AlignIO ok 9 - The object isa Bio::Align::AlignI ok 10 ok 11 ok 12 ok 13 ok 14 ok t/AlignIO/metafasta.t ........................ 1..4 ok 1 - use Bio::AlignIO::metafasta; ok 2 - The object isa Bio::Align::AlignI ok 3 - consensus_string on metafasta ok 4 - symbol_chars() using metafasta ok t/AlignIO/msf.t .............................. 1..4 ok 1 - use Bio::AlignIO::msf; ok 2 - The object isa Bio::Align::AlignI ok 3 - msf input test ok 4 - msf output test ok t/AlignIO/nexus.t ............................ 1..43 ok 1 - use Bio::AlignIO::nexus; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 ok 5 - nexus output test ok 6 - The object isa Bio::AlignIO ok 7 - The object isa Bio::Align::AlignI ok 8 - The object isa Bio::AlignIO ok 9 - The object isa Bio::Align::AlignI ok 10 - The object isa Bio::AlignIO ok 11 - The object isa Bio::Align::AlignI ok 12 - The object isa Bio::AlignIO ok 13 - The object isa Bio::Align::AlignI ok 14 - The object isa Bio::AlignIO ok 15 - The object isa Bio::Align::AlignI ok 16 - The object isa Bio::AlignIO ok 17 - The object isa Bio::Align::AlignI ok 18 - The object isa Bio::AlignIO ok 19 - The object isa Bio::Align::AlignI ok 20 - The object isa Bio::AlignIO ok 21 - The object isa Bio::Align::AlignI ok 22 - The object isa Bio::AlignIO ok 23 - The object isa Bio::Align::AlignI ok 24 - The object isa Bio::AlignIO ok 25 - The object isa Bio::Align::AlignI ok 26 - The object isa Bio::AlignIO ok 27 - The object isa Bio::Align::AlignI ok 28 - The object isa Bio::AlignIO ok 29 - The object isa Bio::Align::AlignI ok 30 - The object isa Bio::AlignIO ok 31 - The object isa Bio::Align::AlignI ok 32 - The object isa Bio::AlignIO ok 33 - The object isa Bio::Align::AlignI ok 34 - The object isa Bio::AlignIO ok 35 - The object isa Bio::Align::AlignI ok 36 - The object isa Bio::AlignIO ok 37 - The object isa Bio::Align::AlignI ok 38 - The object isa Bio::AlignIO ok 39 - The object isa Bio::Align::AlignI ok 40 - The object isa Bio::AlignIO ok 41 - The object isa Bio::Align::AlignI ok 42 - The object isa Bio::AlignIO ok 43 - The object isa Bio::Align::AlignI ok t/AlignIO/pfam.t ............................. 1..5 ok 1 - use Bio::AlignIO::pfam; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 ok 5 - pfam output test ok t/AlignIO/phylip.t ........................... 1..11 ok 1 - use Bio::AlignIO::phylip; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 ok 5 - phylip output test ok 6 - The object isa Bio::Align::AlignI ok 7 ok 8 - The object isa Bio::AlignIO ok 9 - The object isa Bio::Align::AlignI ok 10 ok 11 ok t/AlignIO/po.t ............................... 1..11 ok 1 - use Bio::AlignIO::po; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 ok 5 - The object isa Bio::AlignIO ok 6 - The object isa Bio::Align::AlignI ok 7 - po output test ok 8 - The object isa Bio::AlignIO ok 9 - The object isa Bio::Align::AlignI ok 10 ok 11 ok t/AlignIO/prodom.t ........................... 1..3 ok 1 - use Bio::AlignIO::prodom; ok 2 - The object isa Bio::Align::AlignI ok 3 - prodom input test ok t/AlignIO/psi.t .............................. 1..5 ok 1 - use Bio::AlignIO::psi; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 ok 5 ok t/AlignIO/selex.t ............................ 1..4 ok 1 - use Bio::AlignIO::selex; ok 2 - The object isa Bio::Align::AlignI ok 3 - selex format test ok 4 - selex output test ok t/AlignIO/stockholm.t ........................ 1..83 ok 1 - use Bio::AlignIO::stockholm; ok 2 - The object isa Bio::AlignIO ok 3 - The object isa Bio::Align::AlignI ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 - The object isa Bio::Annotation::Comment ok 10 - Stockholm annotation ok 11 - Stockholm annotation ok 12 - stockholm output test ok 13 - The object isa Bio::Align::AlignI ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 - Stockholm annotation isa Bio::Annotation::Reference ok 21 - Stockholm annotation ok 22 - Stockholm annotation ok 23 - Stockholm annotation ok 24 - Stockholm annotation ok 25 - The object isa Bio::Seq::MetaI ok 26 - Rfam meta data ok 27 - Rfam meta data ok 28 ok 29 - The object isa Bio::Align::AlignI ok 30 ok 31 ok 32 ok 33 ok 34 - The object isa Bio::Seq::MetaI ok 35 - Rfam meta data ok 36 - Rfam meta data ok 37 - The object isa Bio::AlignIO ok 38 ok 39 - The object isa Bio::Align::AlignI ok 40 ok 41 ok 42 ok 43 ok 44 - The object isa Bio::Annotation::SimpleValue ok 45 - Pfam annotation ok 46 ok 47 - The object isa Bio::Align::AlignI ok 48 ok 49 ok 50 ok 51 ok 52 - The object isa Bio::Align::AlignI ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 - The object isa Bio::Seq::MetaI ok 59 - Pfam aln meta data ok 60 - Pfam aln meta data ok 61 - Pfam aln meta data ok 62 - Pfam aln meta data ok 63 - Pfam aln meta data ok 64 - Pfam aln meta data ok 65 - Pfam seq meta data ok 66 - Pfam seq meta data ok 67 - Pfam seq meta data ok 68 - Pfam seq meta data ok 69 ok 70 - The object isa Bio::SeqFeatureI ok 71 - The object isa Bio::Seq::Meta ok 72 - The object isa Bio::AnnotationI ok 73 - The object isa Bio::Annotation::DBLink ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok t/AlignIO/xmfa.t ............................. 1..16 ok 1 - use Bio::AlignIO::xmfa; ok 2 - The object isa Bio::Align::AlignI ok 3 - xmfa input test ok 4 - xmfa input test for description ok 5 - xmfa input test for id ok 6 - xmfa input test for end ok 7 - xmfa input test for end ok 8 - xmfa alignment score ok 9 - The object isa Bio::Align::AlignI ok 10 - xmfa input test ok 11 - xmfa input test for description ok 12 - xmfa input test for id ok 13 - xmfa input test for end ok 14 - xmfa input test for end ok 15 - xmfa alignment score ok 16 - xmfa output test ok t/Alphabet.t ................................. 1..100 ok 1 - use Bio::Symbol::Alphabet; ok 2 - use Bio::Symbol::Symbol; ok 3 - use Bio::Symbol::DNAAlphabet; ok 4 - use Bio::Symbol::ProteinAlphabet; ok 5 - The object isa Bio::Symbol::Alphabet ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 - The object isa Bio::Symbol::AlphabetI ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 - The object isa Bio::Symbol::AlphabetI ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok t/Annotation/Annotation.t .................... 1..158 ok 1 - use Bio::Annotation::Collection; ok 2 - use Bio::Annotation::DBLink; ok 3 - use Bio::Annotation::Comment; ok 4 - use Bio::Annotation::Reference; ok 5 - use Bio::Annotation::SimpleValue; ok 6 - use Bio::Annotation::Target; ok 7 - use Bio::Annotation::AnnotationFactory; ok 8 - use Bio::Annotation::StructuredValue; ok 9 - use Bio::Annotation::TagTree; ok 10 - use Bio::Annotation::Tree; ok 11 - use Bio::Seq; ok 12 - use Bio::SimpleAlign; ok 13 - use Bio::Cluster::UniGene; ok 14 - The object isa Bio::AnnotationI ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 - The object isa Bio::AnnotationI ok 22 ok 23 ok 24 ok 25 - The object isa Bio::AnnotationCollectionI ok 26 ok 27 ok 28 - The object isa Bio::AnnotationI ok 29 ok 30 - The object isa Bio::AnnotationI ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 - The object isa Bio::AnnotationI ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 - The object isa Bio::AnnotationCollectionI ok 69 ok 70 ok 71 ok 72 ok 73 - The object isa Bio::Annotation::StructuredValue ok 74 ok 75 ok 76 ok 77 ok 78 - use Bio::Annotation::OntologyTerm; ok 79 - The object isa Bio::Ontology::Term ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 - The object isa Bio::AnnotatableI ok 86 - isa SeqFeatureI isa Bio::SeqFeatureI ok 87 - isa AnnotatableI isa Bio::AnnotatableI ok 88 - isa SeqFeatureI isa Bio::SeqFeatureI ok 89 - isa AnnotatableI isa Bio::AnnotatableI ok 90 - The object isa Bio::AnnotatableI ok 91 - The object isa Bio::AnnotatableI ok 92 - The object isa Bio::Factory::ObjectFactoryI ok 93 - The object isa Bio::Annotation::SimpleValue ok 94 ok 95 - The object isa Bio::Annotation::OntologyTerm ok 96 - Bio::Annotation::Comment ok 97 - The object isa Bio::Annotation::Comment ok 98 ok 99 - Bio::Annotation::Comment ok 100 - The object isa Bio::Annotation::Comment ok 101 - Bio::Annotation::Comment ok 102 - The object isa Bio::Annotation::Comment ok 103 ok 104 - The object isa Bio::Annotation::Target ok 105 ok 106 ok 107 - The object isa Bio::AnnotationI ok 108 - tree_id() ok 109 - tagname() ok 110 - The object isa Bio::AnnotatableI ok 111 - add tree to AlignI ok 112 - get seq from node id ok 113 ok 114 - The object isa Bio::Annotation::Tree ok 115 - The object isa Bio::AnnotationI ok 116 - default itext ok 117 - roundtrip ok 118 - itext ok 119 - spxr ok 120 - indent ok 121 - xml ok 122 - The object isa Data::Stag::StagI ok 123 ok 124 - child changes ok 125 - The object isa Data::Stag::StagI ok 126 ok 127 - child changes ok 128 - The object isa Data::Stag::StagI ok 129 ok 130 - child changes ok 131 - child changes in parent node ok 132 - no tags ok 133 - before Stag node ok 134 - after Stag node ok 135 - both stag nodes ok 136 - different instances ok 137 - before TagTree ok 138 - after TagTree ok 139 - both stag nodes ok 140 - different instances ok 141 - before TagTree ok 142 - after TagTree ok 143 - stag nodes ok 144 - same instance ok 145 - before TagTree ok 146 - after TagTree ok 147 - stag nodes ok 148 - different instance ok 149 - The object isa Bio::AnnotationI ok 150 - The object isa Data::Stag::StagI ok 151 - child changes ok 152 - The object isa Data::Stag::StagI ok 153 - child changes ok 154 - The object isa Data::Stag::StagI ok 155 - child changes ok 156 ok 157 ok 158 - The object isa Bio::Annotation::TagTree ok t/Annotation/AnnotationAdaptor.t ............. 1..23 ok 1 - use Bio::SeqFeature::Generic; ok 2 - use Bio::SeqFeature::AnnotationAdaptor; ok 3 - use Bio::Annotation::DBLink; ok 4 - use Bio::Annotation::Comment; ok 5 - use Bio::Annotation::SimpleValue; ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok t/Assembly/Assembly.t ........................ 1..51 ok 1 - use Bio::Assembly::IO; ok 2 - The object isa Bio::Assembly::IO not ok 3 # TODO phrap parser doesn't include the sequence string in the sequence objects. # Failed (TODO) test at t/Assembly/Assembly.t line 35. ok 4 - The object isa Bio::Assembly::Scaffold ok 5 ok 6 ok 7 - The object isa Bio::AnnotationCollectionI ok 8 - no annotations in Annotation collection? ok 9 ok 10 ok 11 - get_nof_singlets ok 12 - get_contig_seq_ids ok 13 - get_contig_ids ok 14 - get_singlet_ids ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 - get_nof_singlets ok 24 - get_contig_seq_ids ok 25 - get_contig_ids ok 26 - get_singlet_ids ok 27 ok 28 - the contig is a Bio::Assembly::Contig isa Bio::Assembly::Contig ok 29 ok 30 - get_nof_singlets ok 31 - the singlet is a Bio::Assembly::Contig isa Bio::Assembly::Contig ok 32 - the singlet is a Bio::Assembly::Singlet isa Bio::Assembly::Singlet ok 33 - get_contig_seq_ids ok 34 - get_contig_ids ok 35 - get_singlet_ids ok 36 - The object isa Bio::Assembly::Scaffold ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 - The object isa Bio::LocatableSeq ok 45 - The object isa Bio::Assembly::Contig ok 46 ok 47 ok 48 ok 49 - The object isa Bio::AnnotationCollectionI ok 50 - no annotations in Annotation collection? ok 51 ok t/Assembly/ContigSpectrum.t .................. 1..134 ok 1 - use Bio::Assembly::IO; ok 2 - use Bio::Assembly::Tools::ContigSpectrum; ok 3 - The object isa Bio::Assembly::IO ok 4 - The object isa Bio::Assembly::Scaffold ok 5 ok 6 - The object isa Bio::Assembly::Tools::ContigSpectrum 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 t/Biblio/Biblio.t ............................ 1..24 ok 1 - use Bio::Biblio; ok 2 - use Bio::Biblio::IO; ok 3 ok 4 ok 5 - citation 1 ok 6 - citation 2 ok 7 - citation 3 ok 8 - in callback ok 9 - in callback ok 10 - in callback ok 11 - calling callback ok 12 - citation 1 ok 13 - citation 2 ok 14 - citation 1 ok 15 - citation 2 ok 16 ok 17 - citation 1 ok 18 - citation 2 ok 19 - citation 3 ok 20 - citation 4 ok 21 - filehandle test ok 22 - filehandle test ok 23 - filehandle test ok 24 - filehandle test ok t/Biblio/References.t ........................ 1..537 ok 1 - use Bio::Biblio::Article; ok 2 - use Bio::Biblio::Book; ok 3 - use Bio::Biblio::BookArticle; ok 4 - use Bio::Biblio::Journal; ok 5 - use Bio::Biblio::JournalArticle; ok 6 - use Bio::Biblio::MedlineArticle; ok 7 - use Bio::Biblio::MedlineBook; ok 8 - use Bio::Biblio::MedlineBookArticle; ok 9 - use Bio::Biblio::MedlineJournal; ok 10 - use Bio::Biblio::MedlineJournalArticle; ok 11 - use Bio::Biblio::Organisation; ok 12 - use Bio::Biblio::Patent; ok 13 - use Bio::Biblio::Person; ok 14 - use Bio::Biblio::Proceeding; ok 15 - use Bio::Biblio::Provider; ok 16 - use Bio::Biblio::Ref; ok 17 - use Bio::Biblio::Service; ok 18 - use Bio::Biblio::TechReport; ok 19 - use Bio::Biblio::Thesis; ok 20 - use Bio::Biblio::WebResource; ok 21 - use Bio::Biblio::PubmedArticle; ok 22 - use Bio::Biblio::PubmedBookArticle; ok 23 - use Bio::Biblio::PubmedJournalArticle; ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 - set 'abstract' ok 48 - get 'abstract' ok 49 - set 'abstract_language' ok 50 - get 'abstract_language' ok 51 - set 'abstract_type' ok 52 - get 'abstract_type' ok 53 - set 'author_list_complete' ok 54 - get 'author_list_complete' ok 55 - set 'cross_references_list_complete' ok 56 - get 'cross_references_list_complete' ok 57 - set 'date' ok 58 - get 'date' ok 59 - set 'date_completed' ok 60 - get 'date_completed' ok 61 - set 'date_created' ok 62 - get 'date_created' ok 63 - set 'date_revised' ok 64 - get 'date_revised' ok 65 - set 'format' ok 66 - get 'format' ok 67 - set 'identifier' ok 68 - get 'identifier' ok 69 - set 'language' ok 70 - get 'language' ok 71 - set 'last_modified_date' ok 72 - get 'last_modified_date' ok 73 - set 'repository_subset' ok 74 - get 'repository_subset' ok 75 - set 'rights' ok 76 - get 'rights' ok 77 - set 'spatial_location' ok 78 - get 'spatial_location' ok 79 - set 'subject_headings_source' ok 80 - get 'subject_headings_source' ok 81 - set 'temporal_period' ok 82 - get 'temporal_period' ok 83 - set 'title' ok 84 - get 'title' ok 85 - set 'toc' ok 86 - get 'toc' ok 87 - set 'toc_type' ok 88 - get 'toc_type' ok 89 - set 'type' ok 90 - get 'type' ok 91 - set 'first_page' ok 92 - get 'first_page' ok 93 - set 'last_page' ok 94 - get 'last_page' ok 95 - set 'issue' ok 96 - get 'issue' ok 97 - set 'issue_supplement' ok 98 - get 'issue_supplement' ok 99 - set 'volume' ok 100 - get 'volume' ok 101 - set 'affiliation' ok 102 - get 'affiliation' ok 103 - set 'citation_owner' ok 104 - get 'citation_owner' ok 105 - set 'date_of_electronic_publication' ok 106 - get 'date_of_electronic_publication' ok 107 - set 'gene_symbols' ok 108 - get 'gene_symbols' ok 109 - set 'grant_list_complete' ok 110 - get 'grant_list_complete' ok 111 - set 'medline_date' ok 112 - get 'medline_date' ok 113 - set 'medline_id' ok 114 - get 'medline_id' ok 115 - set 'medline_page' ok 116 - get 'medline_page' ok 117 - set 'number_of_references' ok 118 - get 'number_of_references' ok 119 - set 'other_languages' ok 120 - get 'other_languages' ok 121 - set 'pmid' ok 122 - get 'pmid' ok 123 - set 'season' ok 124 - get 'season' ok 125 - set 'status' ok 126 - get 'status' ok 127 - set 'vernacular_title' ok 128 - get 'vernacular_title' ok 129 ok 130 - abstract ok 131 - abstract_language ok 132 - abstract_type ok 133 - author_list_complete ok 134 - cross_references_list_complete ok 135 - date ok 136 - date_completed ok 137 - date_created ok 138 - date_revised ok 139 - format ok 140 - identifier ok 141 - language ok 142 - last_modified_date ok 143 - repository_subset ok 144 - rights ok 145 - spatial_location ok 146 - subject_headings_source ok 147 - temporal_period ok 148 - title ok 149 - toc ok 150 - toc_type ok 151 - type ok 152 - first_page ok 153 - last_page ok 154 - issue ok 155 - issue_supplement ok 156 - volume ok 157 - affiliation ok 158 - citation_owner ok 159 - date_of_electronic_publication ok 160 - gene_symbols ok 161 - grant_list_complete ok 162 - medline_date ok 163 - medline_id ok 164 - medline_page ok 165 - number_of_references ok 166 - other_languages ok 167 - pmid ok 168 - season ok 169 - status ok 170 - vernacular_title ok 171 - get 'authors' ok 172 - get 'cross_references' ok 173 - get 'codes' ok 174 - get 'contributors' ok 175 - get 'keywords' ok 176 - get 'publisher' ok 177 - get 'subject_headings' ok 178 - get 'journal' ok 179 - get 'chemicals' ok 180 - get 'comment_ins' ok 181 - get 'comment_ons' ok 182 - get 'erratum_fors' ok 183 - get 'erratum_ins' ok 184 - get 'general_notes' ok 185 - get 'grants' ok 186 - get 'mesh_headings' ok 187 - get 'original_report_ins' ok 188 - get 'other_abstracts' ok 189 - get 'other_ids' ok 190 - get 'republished_froms' ok 191 - get 'republished_ins' ok 192 - get 'retraction_ins' ok 193 - get 'retraction_ofs' ok 194 - get 'summary_for_patients_ins' ok 195 - get 'update_ins' ok 196 - get 'update_ofs' ok 197 - get 'journal' ok 198 - add_author 1 ok 199 - add_author 2 ok 200 - get authors ok 201 - add_contributor 1 ok 202 - add_contributor 2 ok 203 - get contributors ok 204 - add_cross_reference 1 ok 205 - add_cross_reference 2 ok 206 - get cross_references ok 207 - get cross_references ok 208 - set 'abstract' ok 209 - get 'abstract' ok 210 - set 'abstract_language' ok 211 - get 'abstract_language' ok 212 - set 'abstract_type' ok 213 - get 'abstract_type' ok 214 - set 'author_list_complete' ok 215 - get 'author_list_complete' ok 216 - set 'cross_references_list_complete' ok 217 - get 'cross_references_list_complete' ok 218 - set 'date' ok 219 - get 'date' ok 220 - set 'date_completed' ok 221 - get 'date_completed' ok 222 - set 'date_created' ok 223 - get 'date_created' ok 224 - set 'date_revised' ok 225 - get 'date_revised' ok 226 - set 'format' ok 227 - get 'format' ok 228 - set 'identifier' ok 229 - get 'identifier' ok 230 - set 'language' ok 231 - get 'language' ok 232 - set 'last_modified_date' ok 233 - get 'last_modified_date' ok 234 - set 'repository_subset' ok 235 - get 'repository_subset' ok 236 - set 'rights' ok 237 - get 'rights' ok 238 - set 'spatial_location' ok 239 - get 'spatial_location' ok 240 - set 'subject_headings_source' ok 241 - get 'subject_headings_source' ok 242 - set 'temporal_period' ok 243 - get 'temporal_period' ok 244 - set 'title' ok 245 - get 'title' ok 246 - set 'toc' ok 247 - get 'toc' ok 248 - set 'toc_type' ok 249 - get 'toc_type' ok 250 - set 'type' ok 251 - get 'type' ok 252 - set 'first_page' ok 253 - get 'first_page' ok 254 - set 'last_page' ok 255 - get 'last_page' ok 256 - set 'affiliation' ok 257 - get 'affiliation' ok 258 - set 'citation_owner' ok 259 - get 'citation_owner' ok 260 - set 'date_of_electronic_publication' ok 261 - get 'date_of_electronic_publication' ok 262 - set 'gene_symbols' ok 263 - get 'gene_symbols' ok 264 - set 'grant_list_complete' ok 265 - get 'grant_list_complete' ok 266 - set 'medline_date' ok 267 - get 'medline_date' ok 268 - set 'medline_id' ok 269 - get 'medline_id' ok 270 - set 'medline_page' ok 271 - get 'medline_page' ok 272 - set 'number_of_references' ok 273 - get 'number_of_references' ok 274 - set 'other_languages' ok 275 - get 'other_languages' ok 276 - set 'pmid' ok 277 - get 'pmid' ok 278 - set 'season' ok 279 - get 'season' ok 280 - set 'status' ok 281 - get 'status' ok 282 - set 'vernacular_title' ok 283 - get 'vernacular_title' ok 284 ok 285 - abstract ok 286 - abstract_language ok 287 - abstract_type ok 288 - author_list_complete ok 289 - cross_references_list_complete ok 290 - date ok 291 - date_completed ok 292 - date_created ok 293 - date_revised ok 294 - format ok 295 - identifier ok 296 - language ok 297 - last_modified_date ok 298 - repository_subset ok 299 - rights ok 300 - spatial_location ok 301 - subject_headings_source ok 302 - temporal_period ok 303 - title ok 304 - toc ok 305 - toc_type ok 306 - type ok 307 - first_page ok 308 - last_page ok 309 - affiliation ok 310 - citation_owner ok 311 - date_of_electronic_publication ok 312 - gene_symbols ok 313 - grant_list_complete ok 314 - medline_date ok 315 - medline_id ok 316 - medline_page ok 317 - number_of_references ok 318 - other_languages ok 319 - pmid ok 320 - season ok 321 - status ok 322 - vernacular_title ok 323 - get 'authors' ok 324 - get 'cross_references' ok 325 - get 'codes' ok 326 - get 'contributors' ok 327 - get 'keywords' ok 328 - get 'publisher' ok 329 - get 'subject_headings' ok 330 - get 'book' ok 331 - get 'chemicals' ok 332 - get 'comment_ins' ok 333 - get 'comment_ons' ok 334 - get 'erratum_fors' ok 335 - get 'erratum_ins' ok 336 - get 'general_notes' ok 337 - get 'grants' ok 338 - get 'mesh_headings' ok 339 - get 'original_report_ins' ok 340 - get 'other_abstracts' ok 341 - get 'other_ids' ok 342 - get 'republished_froms' ok 343 - get 'republished_ins' ok 344 - get 'retraction_ins' ok 345 - get 'retraction_ofs' ok 346 - get 'summary_for_patients_ins' ok 347 - get 'update_ins' ok 348 - get 'update_ofs' ok 349 - get 'book' ok 350 - set 'abstract' ok 351 - get 'abstract' ok 352 - set 'abstract_language' ok 353 - get 'abstract_language' ok 354 - set 'abstract_type' ok 355 - get 'abstract_type' ok 356 - set 'author_list_complete' ok 357 - get 'author_list_complete' ok 358 - set 'cross_references_list_complete' ok 359 - get 'cross_references_list_complete' ok 360 - set 'date' ok 361 - get 'date' ok 362 - set 'date_completed' ok 363 - get 'date_completed' ok 364 - set 'date_created' ok 365 - get 'date_created' ok 366 - set 'date_revised' ok 367 - get 'date_revised' ok 368 - set 'format' ok 369 - get 'format' ok 370 - set 'identifier' ok 371 - get 'identifier' ok 372 - set 'language' ok 373 - get 'language' ok 374 - set 'last_modified_date' ok 375 - get 'last_modified_date' ok 376 - set 'repository_subset' ok 377 - get 'repository_subset' ok 378 - set 'rights' ok 379 - get 'rights' ok 380 - set 'spatial_location' ok 381 - get 'spatial_location' ok 382 - set 'subject_headings_source' ok 383 - get 'subject_headings_source' ok 384 - set 'temporal_period' ok 385 - get 'temporal_period' ok 386 - set 'title' ok 387 - get 'title' ok 388 - set 'toc' ok 389 - get 'toc' ok 390 - set 'toc_type' ok 391 - get 'toc_type' ok 392 - set 'type' ok 393 - get 'type' ok 394 - set 'edition' ok 395 - get 'edition' ok 396 - set 'isbn' ok 397 - get 'isbn' ok 398 - set 'series' ok 399 - get 'series' ok 400 - set 'volume' ok 401 - get 'volume' ok 402 ok 403 - abstract ok 404 - abstract_language ok 405 - abstract_type ok 406 - author_list_complete ok 407 - cross_references_list_complete ok 408 - date ok 409 - date_completed ok 410 - date_created ok 411 - date_revised ok 412 - format ok 413 - identifier ok 414 - language ok 415 - last_modified_date ok 416 - repository_subset ok 417 - rights ok 418 - spatial_location ok 419 - subject_headings_source ok 420 - temporal_period ok 421 - title ok 422 - toc ok 423 - toc_type ok 424 - type ok 425 - edition ok 426 - isbn ok 427 - series ok 428 - volume ok 429 - get 'authors' ok 430 - get 'cross_references' ok 431 - get 'codes' ok 432 - get 'contributors' ok 433 - get 'keywords' ok 434 - get 'publisher' ok 435 - get 'subject_headings' ok 436 - get 'editor' ok 437 - set 'abbreviation' ok 438 - get 'abbreviation' ok 439 - set 'issn' ok 440 - get 'issn' ok 441 - set 'name' ok 442 - get 'name' ok 443 - set 'coden' ok 444 - get 'coden' ok 445 - set 'country' ok 446 - get 'country' ok 447 - set 'medline_code' ok 448 - get 'medline_code' ok 449 - set 'medline_ta' ok 450 - get 'medline_ta' ok 451 - set 'nlm_unique_id' ok 452 - get 'nlm_unique_id' ok 453 ok 454 - abbreviation ok 455 - issn ok 456 - name ok 457 - coden ok 458 - country ok 459 - medline_code ok 460 - medline_ta ok 461 - nlm_unique_id ok 462 - set 'doc_number' ok 463 - get 'doc_number' ok 464 - set 'doc_office' ok 465 - get 'doc_office' ok 466 - set 'doc_type' ok 467 - get 'doc_type' ok 468 ok 469 - doc_number ok 470 - doc_office ok 471 - doc_type ok 472 - get 'applicants' ok 473 - set 'url' ok 474 - get 'url' ok 475 - set 'estimated_size' ok 476 - get 'estimated_size' ok 477 - set 'cost' ok 478 - get 'cost' ok 479 ok 480 - url ok 481 - estimated_size ok 482 - cost ok 483 - set 'type' ok 484 - get 'type' ok 485 - set 'affiliation' ok 486 - get 'affiliation' ok 487 - set 'email' ok 488 - get 'email' ok 489 - set 'firstname' ok 490 - get 'firstname' ok 491 - set 'forename' ok 492 - get 'forename' ok 493 - set 'initials' ok 494 - get 'initials' ok 495 - set 'lastname' ok 496 - get 'lastname' ok 497 - set 'middlename' ok 498 - get 'middlename' ok 499 - set 'postal_address' ok 500 - get 'postal_address' ok 501 - set 'suffix' ok 502 - get 'suffix' ok 503 ok 504 - type ok 505 - affiliation ok 506 - email ok 507 - firstname ok 508 - forename ok 509 - initials ok 510 - lastname ok 511 - middlename ok 512 - postal_address ok 513 - suffix ok 514 - set 'type' ok 515 - get 'type' ok 516 - set 'name' ok 517 - get 'name' ok 518 ok 519 - type ok 520 - name ok 521 - set 'type' ok 522 - get 'type' ok 523 - set 'name' ok 524 - get 'name' ok 525 ok 526 - type ok 527 - name ok 528 - set 'pubmed_status' ok 529 - get 'pubmed_status' ok 530 - set 'pubmed_provider_id' ok 531 - get 'pubmed_provider_id' ok 532 ok 533 - pubmed_status ok 534 - pubmed_provider_id ok 535 - get 'pubmed_history_list' ok 536 - get 'pubmed_article_id_list' ok 537 - get 'pubmed_url_list' ok t/Biblio/biofetch.t .......................... skipped: Network tests have not been requested t/Biblio/eutils.t ............................ skipped: Network tests have not been requested t/ClusterIO/ClusterIO.t ...................... 1..12 ok 1 - use Bio::ClusterIO; ok 2 - use Bio::Cluster::ClusterFactory; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 - The object isa Bio::Cluster::UniGeneI ok 12 - The object isa Bio::Cluster::UniGeneI ok t/ClusterIO/SequenceFamily.t ................. 1..19 ok 1 - use Bio::SeqIO; ok 2 - use Bio::Cluster::SequenceFamily; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok t/ClusterIO/unigene.t ........................ 1..73 ok 1 - use Bio::ClusterIO; ok 2 - new Bio::ClusterIO object defined ok 3 ok 4 - The object isa Bio::Cluster::UniGeneI ok 5 - The object isa Bio::ClusterI ok 6 - The object isa Bio::IdentifiableI ok 7 - The object isa Bio::DescribableI ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 - The object isa Bio::PrimarySeqI ok 49 ok 50 ok 51 - annotation object defined ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 - The object isa Bio::PrimarySeqI ok 67 ok 68 - next cluster ok 69 ok 70 ok 71 ok 72 ok 73 ok t/Coordinate/CoordinateGraph.t ............... 1..7 ok 1 - use Bio::Coordinate::Graph; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok t/Coordinate/CoordinateMapper.t .............. 1..175 ok 1 - use Bio::Location::Simple; ok 2 - use Bio::Coordinate::Pair; ok 3 - use Bio::Coordinate::Result::Match; ok 4 - use Bio::Coordinate::Result::Gap; ok 5 - use Bio::Coordinate::Chain; ok 6 - use Bio::Coordinate::Collection; ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - The object isa Bio::Coordinate::Result ok 15 - The object isa Bio::Location::SplitLocationI ok 16 ok 17 ok 18 ok 19 - The object isa Bio::LocationI ok 20 - The object isa Bio::Coordinate::Result::Match ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 - The object isa Bio::Coordinate::Result::Gap ok 38 - The object isa Bio::LocationI ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 - The object isa Bio::Coordinate::Result::Match ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 - Match: |314696| Test: 314696| ok 139 ok 140 ok 141 ok 142 - Match: |341| Test: 341| ok 143 ok 144 ok 145 ok 146 - Match: |315843| Test: 315843| ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 - Match: |627011| Test: 627011| ok 153 ok 154 ok 155 ok 156 - Match: |chr1| Test: chr1| ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok t/Coordinate/GeneCoordinateMapper.t .......... 1..116 ok 1 - use Bio::Location::Simple; ok 2 - use Bio::Coordinate::Pair; ok 3 - use Bio::Coordinate::ExtrapolatingPair; ok 4 - use Bio::Coordinate::GeneMapper; ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - The object isa Bio::Location::Simple ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 - The object isa Bio::Location::Simple ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok t/LiveSeq/Chain.t ............................ 1..45 ok 1 - use Bio::LiveSeq::Chain; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok t/LiveSeq/LiveSeq.t .......................... 1..48 ok 1 - use Bio::LiveSeq::IO::BioPerl; ok 2 ok 3 ok 4 - Bio::LiveSeq::Gene ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok t/LiveSeq/Mutation.t ......................... 1..19 ok 1 - use Bio::LiveSeq::Mutation; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok t/LiveSeq/Mutator.t .......................... 1..24 ok 1 - use Bio::LiveSeq::Mutator; ok 2 - use Bio::LiveSeq::IO::BioPerl; ok 3 - use Bio::Variation::IO; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok t/LocalDB/BioDBGFF.t ......................... 1..279 ok 1 - use Bio::DB::GFF; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 # skip fetch_feature_by_gid() not implemented by this adaptor ok 104 # skip fetch_feature_by_gid() not implemented by this adaptor ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 # skip delete_groups() not implemented by this adaptor ok 135 # skip delete_groups() not implemented by this adaptor ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 ok 156 ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok 176 ok 177 ok 178 ok 179 ok 180 ok 181 ok 182 ok 183 ok 184 ok 185 ok 186 ok 187 ok 188 ok 189 ok 190 ok 191 ok 192 ok 193 ok 194 ok 195 ok 196 ok 197 ok 198 ok 199 ok 200 ok 201 ok 202 ok 203 ok 204 ok 205 ok 206 ok 207 ok 208 ok 209 ok 210 ok 211 ok 212 ok 213 ok 214 ok 215 ok 216 ok 217 ok 218 ok 219 ok 220 ok 221 ok 222 ok 223 ok 224 ok 225 ok 226 ok 227 ok 228 ok 229 ok 230 ok 231 ok 232 ok 233 ok 234 ok 235 ok 236 ok 237 ok 238 ok 239 ok 240 ok 241 ok 242 # skip fetch_feature_by_gid() not implemented by this adaptor ok 243 # skip fetch_feature_by_gid() not implemented by this adaptor ok 244 ok 245 ok 246 ok 247 ok 248 ok 249 ok 250 # skip preferred groups are not supported by gff3 ok 251 # skip preferred groups are not supported by gff3 ok 252 # skip preferred groups are not supported by gff3 ok 253 ok 254 ok 255 ok 256 ok 257 ok 258 ok 259 ok 260 ok 261 ok 262 ok 263 ok 264 ok 265 ok 266 ok 267 ok 268 ok 269 ok 270 ok 271 ok 272 ok 273 # skip delete_groups() not implemented by this adaptor ok 274 # skip delete_groups() not implemented by this adaptor ok 275 ok 276 ok 277 ok 278 ok 279 ok t/LocalDB/BlastIndex.t ....................... 1..26 ok 1 - use Cwd; ok 2 - use Bio::SearchIO; ok 3 - use Bio::Index::Blast; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok t/LocalDB/DBFasta.t .......................... 1..15 ok 1 - use Bio::Root::IO; ok 2 - use File::Copy; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok t/LocalDB/DBQual.t ........................... 1..38 ok 1 - use Bio::Root::IO; ok 2 - use File::Copy; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 - The object isa Bio::Seq::PrimaryQual ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 - The object isa Bio::Seq::PrimaryQual ok 26 ok 27 ok 28 - The object isa Bio::Seq::PrimaryQual ok 29 ok 30 ok 31 ok 32 - The object isa Bio::Seq::PrimaryQual ok 33 ok 34 - The object isa Bio::Seq::PrimaryQual ok 35 ok 36 ok 37 ok 38 ok t/LocalDB/Flat.t ............................. 1..24 ok 1 - use Bio::DB::Flat; 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 t/LocalDB/Index.t ............................ 1..64 ok 1 - use Bio::Index::Fasta; ok 2 - use Bio::Index::Qual; ok 3 - use Bio::Index::SwissPfam; ok 4 - use Bio::Index::EMBL; ok 5 - use Bio::Index::GenBank; ok 6 - use Bio::Index::Swissprot; ok 7 - use Bio::DB::InMemoryCache; ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 - The object isa Bio::PrimarySeqI ok 17 ok 18 ok 19 ok 20 - The object isa Bio::SeqI 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/LocalDB/Registry.t ......................... 1..14 ok 1 - use Bio::DB::Registry; ok 2 - use Bio::DB::Flat; ok 3 ok 4 ok 5 ok 6 # skip Network tests have not been requested ok 7 # skip Network tests have not been requested ok 8 # skip Network tests have not been requested ok 9 # skip Network tests have not been requested ok 10 # skip Network tests have not been requested ok 11 # skip Network tests have not been requested ok 12 # skip Network tests have not been requested ok 13 # skip Network tests have not been requested ok 14 # skip Network tests have not been requested ok Use of qw(...) as parentheses is deprecated at Bio/DB/SeqFeature/Store/LoadHelper.pm line 72. t/LocalDB/SeqFeature.t ....................... 1..69 ok 1 - use Bio::DB::SeqFeature::Store; ok 2 - use Bio::DB::SeqFeature::Store::GFF3Loader; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 - feature names should be case insensitive 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 - The object isa Bio::Location::Split 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 - keyword search; 1 term ok 69 - keyword search; 2 terms ok Use of qw(...) as parentheses is deprecated at Bio/Matrix/PSM/SiteMatrix.pm line 346. t/LocalDB/transfac_pro.t ..................... 1..115 ok 1 - use Bio::Matrix::PSM::IO; ok 2 - use Bio::DB::TFBS; ok 3 - use Bio::DB::Taxonomy; ok 4 ok 5 ok 6 ok 7 ok 8 - The object isa Bio::Annotation::Reference 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 - The object isa Bio::Seq 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 - The object isa Bio::Matrix::PSM::SiteMatrix ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 - The object isa Bio::SimpleAlign 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 - The object isa Bio::SeqI ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 - The object isa Bio::Map::TranscriptionFactor ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok t/Map/Cyto.t ................................. 1..110 ok 1 - use Bio::Map::CytoMap; ok 2 - use Bio::Map::CytoPosition; ok 3 - use Bio::Map::CytoMarker; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - The object isa Bio::Map::CytoPosition ok 15 ok 16 ok 17 ok 18 - The object isa Bio::Range ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok t/Map/Linkage.t .............................. 1..18 ok 1 - use Bio::Map::LinkagePosition; ok 2 - use Bio::Map::Microsatellite; ok 3 - use Bio::Map::LinkageMap; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok t/Map/Map.t .................................. 1..267 ok 1 - use Bio::Map::SimpleMap; ok 2 - use Bio::Map::Marker; ok 3 - use Bio::Map::Position; ok 4 - use Bio::Map::Relative; ok 5 - use Bio::Map::Mappable; ok 6 ok 7 ok 8 ok 9 ok 10 - Length is 0 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 - use Bio::Map::Gene; ok 152 - use Bio::Map::GeneMap; ok 153 - use Bio::Map::TranscriptionFactor; ok 154 - use Bio::Map::GeneRelative; ok 155 - use Bio::Map::GenePosition; ok 156 - use Bio::Map::Prediction; ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok 176 ok 177 ok 178 ok 179 ok 180 ok 181 ok 182 ok 183 ok 184 ok 185 ok 186 ok 187 ok 188 ok 189 ok 190 ok 191 ok 192 ok 193 ok 194 ok 195 ok 196 ok 197 ok 198 ok 199 ok 200 ok 201 ok 202 ok 203 ok 204 ok 205 ok 206 ok 207 ok 208 ok 209 ok 210 ok 211 ok 212 ok 213 ok 214 ok 215 ok 216 ok 217 ok 218 ok 219 ok 220 ok 221 ok 222 ok 223 ok 224 ok 225 ok 226 ok 227 ok 228 ok 229 ok 230 ok 231 ok 232 ok 233 ok 234 ok 235 ok 236 ok 237 ok 238 ok 239 ok 240 ok 241 ok 242 ok 243 ok 244 ok 245 ok 246 ok 247 ok 248 ok 249 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 250 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 251 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 252 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 253 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 254 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 255 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 256 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 257 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 258 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 259 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 260 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 261 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 262 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 263 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 264 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 265 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 266 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok 267 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed ok t/Map/MapIO.t ................................ 1..51 ok 1 - use Bio::MapIO; ok 2 ok 3 - The object isa Bio::Map::MapI ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok t/Map/MicrosatelliteMarker.t ................. 1..8 ok 1 - use Bio::Map::SimpleMap; ok 2 - use Bio::Map::Position; ok 3 - use Bio::Map::Microsatellite; ok 4 ok 5 ok 6 ok 7 ok 8 ok t/Map/Physical.t ............................. 1..39 ok 1 - use Bio::Map::Physical; ok 2 - use Bio::MapIO; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 - code holds and returns a string, definition requires a boolean ok 13 - code holds and returns a string, definition requires a boolean 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 Use of qw(...) as parentheses is deprecated at Bio/Matrix/PSM/SiteMatrix.pm line 346. t/Matrix/IO/masta.t .......................... 1..16 ok 1 - use Bio::Matrix::PSM::IO; 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 Use of qw(...) as parentheses is deprecated at Bio/Matrix/PSM/SiteMatrix.pm line 346. t/Matrix/IO/psm.t ............................ 1..63 ok 1 - use Bio::Matrix::PSM::IO; 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/Matrix/InstanceSite.t ...................... 1..6 ok 1 - use Bio::Matrix::PSM::InstanceSite; ok 2 ok 3 ok 4 ok 5 ok 6 ok t/Matrix/Matrix.t ............................ 1..77 ok 1 - use Bio::Matrix::Generic; ok 2 - use Bio::Matrix::IO; 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 - The object isa Bio::Matrix::Scoring ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 - The object isa Bio::Matrix::Scoring 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 t/Matrix/ProtMatrix.t ........................ 1..14 ok 1 - use Bio::Matrix::PSM::ProtMatrix; 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 Use of qw(...) as parentheses is deprecated at Bio/Matrix/PSM/SiteMatrix.pm line 346. t/Matrix/ProtPsm.t ........................... 1..14 ok 1 - use Bio::Matrix::PSM::IO; ok 2 ok 3 ok 4 ok 5 # skip TODO: Module incomplete ok 6 # skip TODO: Module incomplete ok 7 # skip TODO: Module incomplete ok 8 # skip TODO: Module incomplete ok 9 # skip TODO: Module incomplete ok 10 # skip TODO: Module incomplete ok 11 # skip TODO: Module incomplete ok 12 # skip TODO: Module incomplete ok 13 # skip TODO: Module incomplete ok 14 # skip TODO: Module incomplete ok Use of qw(...) as parentheses is deprecated at Bio/Matrix/PSM/SiteMatrix.pm line 346. t/Matrix/SiteMatrix.t ........................ 1..14 ok 1 - use Bio::Matrix::PSM::SiteMatrix; 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/Ontology/GOterm.t .......................... 1..62 ok 1 - use Bio::Ontology::GOterm; ok 2 - use Bio::Ontology::Ontology; ok 3 - use Bio::Annotation::DBLink; ok 4 - The object isa Bio::Ontology::GOterm 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 t/Ontology/GraphAdaptor.t .................... 1..28 ok 1 - use Bio::Ontology::SimpleGOEngine::GraphAdaptor; 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 t/Ontology/IO/go.t ........................... 1..102 ok 1 - use Bio::OntologyIO; ok 2 ok 3 - The object isa Bio::Ontology::OntologyI ok 4 ok 5 - The object isa Bio::Ontology::OntologyEngineI 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 t/Ontology/IO/interpro.t ..................... 1..47 ok 1 - use Bio::OntologyIO; ok 2 ok 3 ok 4 ok 5 ok 6 - term Integrins alpha chain in ontology InterPro ok 7 ok 8 - term post-translational modification in ontology InterPro ok 9 ok 10 - term Repeat in ontology InterPro ok 11 ok 12 - term Binding Site in ontology InterPro ok 13 ok 14 - term Cdc20/Fizzy in ontology InterPro ok 15 ok 16 - term Kringle in ontology InterPro ok 17 ok 18 - term Helix-turn-helix, AraC type in ontology InterPro ok 19 ok 20 - term Active Site in ontology InterPro ok 21 ok 22 - term Active Site in ontology InterPro ok 23 ok 24 - term Binding Site in ontology InterPro ok 25 ok 26 - term Domain in ontology InterPro ok 27 ok 28 - term Family in ontology InterPro ok 29 ok 30 - term Repeat in ontology InterPro ok 31 ok 32 - term post-translational modification in ontology InterPro 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/Ontology/IO/obo.t .......................... 1..83 ok 1 - use Bio::OntologyIO; ok 2 - use Bio::Ontology::RelationshipType; 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 - got a ontology IO handler isa Bio::OntologyIO ok 47 - got ontology parser2 isa Bio::Ontology::Ontology ok 48 - got OBO engine object isa Bio::Ontology::OBOEngine ok 49 - got ontology parser2 isa Bio::Ontology::Ontology ok 50 - got OBO engine object isa Bio::Ontology::OBOEngine ok 51 - got ontology parser2 isa Bio::Ontology::Ontology ok 52 - got OBO engine object isa Bio::Ontology::OBOEngine ok 53 - Gene ontology ok 54 - biological process ok 55 - molecular function ok 56 - Got root ok 57 - Got root ok 58 - Got regulates # from gene_ontology ok 59 - Got # positively regulates from gene_ontology ok 60 - Got # regulates from biological_process ok 61 - Got # positively regulates from biological_process ok 62 - Got predicates for gene_ontology ok 63 - Got predicates for biological_process ok 64 - Got regulates predicate ok 65 - Got positively regulates predicate ok 66 - Got relationships for biological_process ok 67 - Got relationships for molecular_function ok 68 - Got is a relationship from # molecular_function ok 69 - Got term object isa Bio::Ontology::Term ok 70 - Got term id ok 71 - Got term name ok 72 - Got regulated object isa Bio::Ontology::Term ok 73 - Got regulated term1 id ok 74 - Got term1 object isa Bio::Ontology::Term ok 75 - Got back the child ok 76 - Got term object isa Bio::Ontology::Term ok 77 - Got term id ok 78 - Got term name ok 79 - Got regulated object isa Bio::Ontology::Term ok 80 - Got regulated term1 id ok 81 - Got identical regulation ok 82 - Got term1 object isa Bio::Ontology::Term ok 83 - Got back the child ok t/Ontology/Ontology.t ........................ 1..52 ok 1 - use Bio::OntologyIO; ok 2 - use Bio::Ontology::RelationshipType; 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 t/Ontology/OntologyEngine.t .................. 1..27 ok 1 - use Bio::Ontology::Term; ok 2 - use Bio::Ontology::Relationship; ok 3 - use Bio::Ontology::RelationshipType; ok 4 - use Bio::Ontology::SimpleOntologyEngine; ok 5 - use Bio::Ontology::Ontology; ok 6 - The object isa Bio::Ontology::OntologyEngineI 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 t/Ontology/OntologyStore.t ................... skipped: Network tests have not been requested t/Ontology/Relationship.t .................... 1..12 ok 1 - use Bio::Ontology::Relationship; ok 2 - use Bio::Ontology::GOterm; ok 3 - use Bio::Ontology::RelationshipType; ok 4 - The object isa Bio::Ontology::RelationshipType ok 5 - The object isa Bio::Ontology::GOterm ok 6 - The object isa Bio::Ontology::GOterm ok 7 - The object isa Bio::Ontology::Relationship ok 8 ok 9 ok 10 ok 11 ok 12 ok t/Ontology/RelationshipType.t ................ 1..23 ok 1 - use Bio::Ontology::RelationshipType; ok 2 - use Bio::Ontology::Ontology; ok 3 - The object isa Bio::Ontology::RelationshipType ok 4 - The object isa Bio::Ontology::TermI 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/Ontology/Term.t ............................ 1..54 ok 1 - use Bio::Ontology::Term; ok 2 - use Bio::Ontology::TermFactory; ok 3 - use Bio::Annotation::DBLink; ok 4 - The object isa Bio::Ontology::TermI 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 - The object isa Bio::Ontology::TermI ok 45 ok 46 - The object isa Bio::Ontology::TermI ok 47 - The object isa Bio::Ontology::GOterm ok 48 ok 49 ok 50 - The object isa Bio::Ontology::TermI ok 51 - The object isa Bio::AnnotationI ok 52 ok 53 ok 54 ok t/Perl.t ..................................... 1..29 ok 1 - use Bio::Perl; ok 2 ok 3 - The object isa Bio::SeqI ok 4 ok 5 - The object isa Bio::SeqI ok 6 ok 7 - The object isa Bio::SeqI ok 8 - The object isa Bio::SeqI ok 9 ok 10 ok 11 - The object isa Bio::SeqI ok 12 ok 13 - The object isa Bio::SeqI ok 14 ok 15 - The object isa Bio::PrimarySeqI ok 16 ok 17 ok 18 ok 19 ok 20 # skip Network tests have not been requested ok 21 # skip Network tests have not been requested ok 22 # skip Network tests have not been requested ok 23 # skip Network tests have not been requested ok 24 # skip Network tests have not been requested ok 25 # skip Network tests have not been requested ok 26 # skip Network tests have not been requested ok 27 # skip Network tests have not been requested ok 28 # skip Network tests have not been requested ok 29 # skip Network tests have not been requested ok t/Phenotype/Correlate.t ...................... 1..17 ok 1 - use Bio::Phenotype::Correlate; ok 2 - use Bio::Species; ok 3 - The object isa Bio::Phenotype::Correlate 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/Phenotype/MeSH.t ........................... 1..24 ok 1 - use Bio::Phenotype::MeSH::Term; ok 2 - use Bio::Phenotype::MeSH::Twig; 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 t/Phenotype/Measure.t ........................ 1..21 ok 1 - use Bio::Phenotype::Measure; ok 2 - The object isa Bio::Phenotype::Measure 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/Phenotype/MiniMIMentry.t ................... 1..15 ok 1 - use Bio::Phenotype::OMIM::MiniMIMentry; ok 2 - The object isa Bio::Phenotype::OMIM::MiniMIMentry 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/Phenotype/OMIMentry.t ...................... 1..153 ok 1 - use Bio::Phenotype::OMIM::OMIMentry; ok 2 - use Bio::Phenotype::OMIM::MiniMIMentry; ok 3 - use Bio::Species; ok 4 - use Bio::Annotation::Reference; ok 5 - use Bio::Map::CytoPosition; ok 6 - use Bio::Phenotype::Correlate; ok 7 - use Bio::Phenotype::Measure; ok 8 - use Bio::Annotation::DBLink; ok 9 - The object isa Bio::Phenotype::OMIM::OMIMentry 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 - operator overloading in AnnotationI is deprecated ok 80 - operator overloading in AnnotationI is deprecated ok 81 ok 82 ok 83 - operator overloading in AnnotationI is deprecated ok 84 - operator overloading in AnnotationI is deprecated 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 - operator overloading in AnnotationI is deprecated ok 137 - operator overloading in AnnotationI is deprecated ok 138 ok 139 ok 140 - operator overloading in AnnotationI is deprecated ok 141 - operator overloading in AnnotationI is deprecated 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 t/Phenotype/OMIMentryAllelicVariant.t ........ 1..27 ok 1 - use Bio::Phenotype::OMIM::OMIMentryAllelicVariant; ok 2 - The object isa Bio::Phenotype::OMIM::OMIMentryAllelicVariant 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 t/Phenotype/OMIMparser.t ..................... 1..175 ok 1 - use Bio::Phenotype::OMIM::OMIMparser; ok 2 - The object isa Bio::Phenotype::OMIM::OMIMparser ok 3 - The object isa Bio::Phenotype::OMIM::OMIMentry 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 - The object isa Bio::Phenotype::OMIM::MiniMIMentry 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 - The object isa Bio::Phenotype::OMIM::OMIMentry 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 - The object isa Bio::Phenotype::OMIM::MiniMIMentry 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 - missing linebreak caught ok t/Phenotype/Phenotype.t ...................... 1..116 ok 1 - use Bio::Phenotype::Phenotype; ok 2 - use Bio::Species; ok 3 - use Bio::Annotation::Reference; ok 4 - use Bio::Map::CytoPosition; ok 5 - use Bio::Phenotype::Correlate; ok 6 - use Bio::Phenotype::Measure; ok 7 - use Bio::Annotation::DBLink; ok 8 - The object isa Bio::Phenotype::PhenotypeI ok 9 - The object isa Bio::Phenotype::Phenotype 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 - operator overloading in AnnotationI is deprecated ok 43 - operator overloading in AnnotationI is deprecated ok 44 ok 45 ok 46 - operator overloading in AnnotationI is deprecated ok 47 - operator overloading in AnnotationI is deprecated 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 - operator overloading in AnnotationI is deprecated ok 100 - operator overloading in AnnotationI is deprecated ok 101 ok 102 ok 103 - operator overloading in AnnotationI is deprecated ok 104 - operator overloading in AnnotationI is deprecated 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 # Failed test 'POD test for Bio/Tree/Statistics.pm' # at /home/fly1600/var/megalib/Test/Pod.pm line 182. Wide character in print at /home/fly1600/var/megalib/Test/Builder.pm line 1759. # Bio/Tree/Statistics.pm (215): Non-ASCII character seen before =encoding in 'deï¬ning'. Assuming UTF-8 # Failed test 'POD test for Bio/Tools/GuessSeqFormat.pm' # at /home/fly1600/var/megalib/Test/Pod.pm line 182. # Bio/Tools/GuessSeqFormat.pm (226): Non-ASCII character seen before =encoding in 'Kähäri,'. Assuming ISO8859-1 # Failed test 'POD test for Bio/Tools/Geneid.pm' # at /home/fly1600/var/megalib/Test/Pod.pm line 182. # Bio/Tools/Geneid.pm (38): Non-ASCII character seen before =encoding in 'Guigó'. Assuming ISO8859-1 # Failed test 'POD test for examples/biblio/biblio-eutils-example.pl' # at /home/fly1600/var/megalib/Test/Pod.pm line 182. # examples/biblio/biblio-eutils-example.pl (109): Non-ASCII character seen before =encoding in 'Kubícková'. Assuming ISO8859-1 # Failed test 'POD test for Bio/Tools/Run/WrapperBase.pm' # at /home/fly1600/var/megalib/Test/Pod.pm line 182. # Bio/Tools/Run/WrapperBase.pm (182): Non-ASCII character seen before =encoding in 'NB:ÊThis'. Assuming ISO8859-1 # Looks like you failed 5 tests of 999. t/PodSyntax.t ................................ 1..999 ok 1 - POD test for Bio/DBLinkContainerI.pm ok 2 - POD test for Bio/PrimarySeq.pm ok 3 - POD test for Bio/SeqFeatureI.pm ok 4 - POD test for Bio/WebAgent.pm ok 5 - POD test for Bio/Species.pm ok 6 - POD test for Bio/AnnotatableI.pm ok 7 - POD test for Bio/SimpleAlign.pm ok 8 - POD test for Bio/UpdateableSeqI.pm ok 9 - POD test for Bio/MapIO.pm ok 10 - POD test for Bio/ParameterBaseI.pm ok 11 - POD test for Bio/Seq.pm ok 12 - POD test for Bio/LocatableSeq.pm ok 13 - POD test for Bio/Biblio.pm ok 14 - POD test for Bio/ClusterIO.pm ok 15 - POD test for Bio/SeqI.pm ok 16 - POD test for Bio/HandlerBaseI.pm ok 17 - POD test for Bio/OntologyIO.pm ok 18 - POD test for Bio/SearchDist.pm ok 19 - POD test for Bio/SeqUtils.pm ok 20 - POD test for Bio/SearchIO.pm ok 21 - POD test for Bio/LocationI.pm ok 22 - POD test for Bio/Taxonomy.pm ok 23 - POD test for Bio/Taxon.pm ok 24 - POD test for Bio/Perl.pm ok 25 - POD test for Bio/IdCollectionI.pm ok 26 - POD test for Bio/AnalysisResultI.pm ok 27 - POD test for Bio/AnnotationCollectionI.pm ok 28 - POD test for Bio/SimpleAnalysisI.pm ok 29 - POD test for Bio/AnalysisI.pm ok 30 - POD test for Bio/TreeIO.pm ok 31 - POD test for Bio/FeatureIO.pm ok 32 - POD test for Bio/DasI.pm ok 33 - POD test for Bio/PullParserI.pm ok 34 - POD test for Bio/AnnotationI.pm ok 35 - POD test for Bio/AnalysisParserI.pm ok 36 - POD test for Bio/DescribableI.pm ok 37 - POD test for Bio/ClusterI.pm ok 38 - POD test for Bio/PrimarySeqI.pm ok 39 - POD test for Bio/FeatureHolderI.pm ok 40 - POD test for Bio/SeqAnalysisParserI.pm ok 41 - POD test for Bio/SeqIO.pm ok 42 - POD test for Bio/PhyloNetwork.pm ok 43 - POD test for Bio/Range.pm ok 44 - POD test for Bio/AlignIO.pm ok 45 - POD test for Bio/RangeI.pm ok 46 - POD test for Bio/IdentifiableI.pm ok 47 - POD test for examples/bioperl.pl (no pod) ok 48 - POD test for examples/rev_and_trans.pl (no pod) ok 49 - POD test for examples/generate_random_seq.pl (no pod) ok 50 - POD test for examples/make_primers.pl (no pod) ok 51 - POD test for examples/revcom_dir.pl (no pod) ok 52 - POD test for examples/subsequence.cgi (no pod) ok 53 - POD test for examples/longorf.pl ok 54 - POD test for maintenance/pod.pl ok 55 - POD test for maintenance/dependencies.pl ok 56 - POD test for maintenance/check_NAME.pl ok 57 - POD test for maintenance/authors.pl ok 58 - POD test for maintenance/ncbi_blast_switches.pl (no pod) ok 59 - POD test for maintenance/check_URLs.pl ok 60 - POD test for maintenance/module_usage.pl (no pod) ok 61 - POD test for maintenance/deprecated.pl ok 62 - POD test for maintenance/cvs2cl_by_file.pl ok 63 - POD test for maintenance/version.pl ok 64 - POD test for maintenance/modules.pl ok 65 - POD test for maintenance/symlink_script.pl ok 66 - POD test for Bio/OntologyIO/soflat.pm ok 67 - POD test for Bio/OntologyIO/obo.pm ok 68 - POD test for Bio/OntologyIO/InterProParser.pm ok 69 - POD test for Bio/OntologyIO/simplehierarchy.pm ok 70 - POD test for Bio/OntologyIO/goflat.pm ok 71 - POD test for Bio/OntologyIO/dagflat.pm ok 72 - POD test for Bio/Map/Relative.pm ok 73 - POD test for Bio/Map/PositionHandler.pm ok 74 - POD test for Bio/Map/MappableI.pm ok 75 - POD test for Bio/Map/GeneMap.pm ok 76 - POD test for Bio/Map/TranscriptionFactor.pm ok 77 - POD test for Bio/Map/SimpleMap.pm ok 78 - POD test for Bio/Map/CytoMarker.pm ok 79 - POD test for Bio/Map/CytoPosition.pm ok 80 - POD test for Bio/Map/Prediction.pm ok 81 - POD test for Bio/Map/Mappable.pm ok 82 - POD test for Bio/Map/RelativeI.pm ok 83 - POD test for Bio/Map/GenePosition.pm ok 84 - POD test for Bio/Map/PositionWithSequence.pm ok 85 - POD test for Bio/Map/Position.pm ok 86 - POD test for Bio/Map/Gene.pm ok 87 - POD test for Bio/Map/Marker.pm ok 88 - POD test for Bio/Map/Physical.pm ok 89 - POD test for Bio/Map/Contig.pm ok 90 - POD test for Bio/Map/OrderedPosition.pm ok 91 - POD test for Bio/Map/EntityI.pm ok 92 - POD test for Bio/Map/FPCMarker.pm ok 93 - POD test for Bio/Map/CytoMap.pm ok 94 - POD test for Bio/Map/MarkerI.pm ok 95 - POD test for Bio/Map/GeneRelative.pm ok 96 - POD test for Bio/Map/LinkageMap.pm ok 97 - POD test for Bio/Map/PositionHandlerI.pm ok 98 - POD test for Bio/Map/Microsatellite.pm ok 99 - POD test for Bio/Map/MapI.pm ok 100 - POD test for Bio/Map/PositionI.pm ok 101 - POD test for Bio/Map/OrderedPositionWithDistance.pm ok 102 - POD test for Bio/Map/Clone.pm ok 103 - POD test for Bio/Map/LinkagePosition.pm ok 104 - POD test for Bio/Search/GenericStatistics.pm ok 105 - POD test for Bio/Search/GenericDatabase.pm ok 106 - POD test for Bio/Search/StatisticsI.pm ok 107 - POD test for Bio/Search/DatabaseI.pm ok 108 - POD test for Bio/Search/Processor.pm ok 109 - POD test for Bio/Search/BlastStatistics.pm ok 110 - POD test for Bio/Search/SearchUtils.pm ok 111 - POD test for Bio/Search/BlastUtils.pm ok 112 - POD test for Bio/Matrix/MatrixI.pm ok 113 - POD test for Bio/Matrix/Generic.pm ok 114 - POD test for Bio/Matrix/Scoring.pm ok 115 - POD test for Bio/Matrix/IO.pm ok 116 - POD test for Bio/Matrix/Mlagan.pm ok 117 - POD test for Bio/Matrix/PhylipDist.pm ok 118 - POD test for Bio/Tree/AlleleNode.pm ok 119 - POD test for Bio/Tree/Compatible.pm ok 120 - POD test for Bio/Tree/TreeI.pm ok 121 - POD test for Bio/Tree/RandomFactory.pm ok 122 - POD test for Bio/Tree/AnnotatableNode.pm ok 123 - POD test for Bio/Tree/DistanceFactory.pm ok 124 - POD test for Bio/Tree/NodeI.pm ok 125 - POD test for Bio/Tree/NodeNHX.pm ok 126 - POD test for Bio/Tree/Node.pm not ok 127 - POD test for Bio/Tree/Statistics.pm ok 128 - POD test for Bio/Tree/Tree.pm ok 129 - POD test for Bio/Tree/TreeFunctionsI.pm ok 130 - POD test for Bio/PopGen/HtSNP.pm ok 131 - POD test for Bio/PopGen/IndividualI.pm ok 132 - POD test for Bio/PopGen/PopulationI.pm ok 133 - POD test for Bio/PopGen/PopStats.pm ok 134 - POD test for Bio/PopGen/GenotypeI.pm ok 135 - POD test for Bio/PopGen/Utilities.pm ok 136 - POD test for Bio/PopGen/TagHaplotype.pm ok 137 - POD test for Bio/PopGen/Genotype.pm ok 138 - POD test for Bio/PopGen/IO.pm ok 139 - POD test for Bio/PopGen/Marker.pm ok 140 - POD test for Bio/PopGen/MarkerI.pm ok 141 - POD test for Bio/PopGen/Individual.pm ok 142 - POD test for Bio/PopGen/Statistics.pm ok 143 - POD test for Bio/PopGen/Population.pm ok 144 - POD test for Bio/Event/EventGeneratorI.pm ok 145 - POD test for Bio/Event/EventHandlerI.pm ok 146 - POD test for Bio/Tools/AlignFactory.pm ok 147 - POD test for Bio/Tools/RNAMotif.pm ok 148 - POD test for Bio/Tools/PrositeScan.pm ok 149 - POD test for Bio/Tools/ECnumber.pm ok 150 - POD test for Bio/Tools/pSW.pm ok 151 - POD test for Bio/Tools/Pseudowise.pm ok 152 - POD test for Bio/Tools/Grail.pm not ok 153 - POD test for Bio/Tools/GuessSeqFormat.pm ok 154 - POD test for Bio/Tools/RandomDistFunctions.pm ok 155 - POD test for Bio/Tools/MZEF.pm ok 156 - POD test for Bio/Tools/SeqPattern.pm ok 157 - POD test for Bio/Tools/FootPrinter.pm ok 158 - POD test for Bio/Tools/EUtilities.pm ok 159 - POD test for Bio/Tools/Fgenesh.pm ok 160 - POD test for Bio/Tools/ERPIN.pm ok 161 - POD test for Bio/Tools/Est2Genome.pm ok 162 - POD test for Bio/Tools/Prints.pm ok 163 - POD test for Bio/Tools/isPcr.pm ok 164 - POD test for Bio/Tools/Lucy.pm ok 165 - POD test for Bio/Tools/Seg.pm ok 166 - POD test for Bio/Tools/Promoterwise.pm not ok 167 - POD test for Bio/Tools/Geneid.pm ok 168 - POD test for Bio/Tools/Protparam.pm ok 169 - POD test for Bio/Tools/IUPAC.pm ok 170 - POD test for Bio/Tools/dpAlign.pm ok 171 - POD test for Bio/Tools/SiRNA.pm ok 172 - POD test for Bio/Tools/QRNA.pm ok 173 - POD test for Bio/Tools/Primer3.pm ok 174 - POD test for Bio/Tools/CodonTable.pm ok 175 - POD test for Bio/Tools/Infernal.pm ok 176 - POD test for Bio/Tools/GFF.pm ok 177 - POD test for Bio/Tools/Glimmer.pm ok 178 - POD test for Bio/Tools/tRNAscanSE.pm ok 179 - POD test for Bio/Tools/ipcress.pm ok 180 - POD test for Bio/Tools/Genemark.pm ok 181 - POD test for Bio/Tools/Coil.pm ok 182 - POD test for Bio/Tools/Blat.pm ok 183 - POD test for Bio/Tools/Match.pm ok 184 - POD test for Bio/Tools/SeqStats.pm ok 185 - POD test for Bio/Tools/Gel.pm ok 186 - POD test for Bio/Tools/Genscan.pm ok 187 - POD test for Bio/Tools/TargetP.pm ok 188 - POD test for Bio/Tools/SeqWords.pm ok 189 - POD test for Bio/Tools/Sigcleave.pm ok 190 - POD test for Bio/Tools/EPCR.pm ok 191 - POD test for Bio/Tools/pICalculator.pm ok 192 - POD test for Bio/Tools/RepeatMasker.pm ok 193 - POD test for Bio/Tools/Tmhmm.pm ok 194 - POD test for Bio/Tools/Signalp.pm ok 195 - POD test for Bio/Tools/ESTScan.pm ok 196 - POD test for Bio/Tools/Eponine.pm ok 197 - POD test for Bio/Tools/Profile.pm ok 198 - POD test for Bio/Tools/AnalysisResult.pm ok 199 - POD test for Bio/Tools/Hmmpfam.pm ok 200 - POD test for Bio/Tools/Genewise.pm ok 201 - POD test for Bio/Tools/Genomewise.pm ok 202 - POD test for Bio/Tools/OddCodes.pm ok 203 - POD test for Bio/Tools/TandemRepeatsFinder.pm ok 204 - POD test for Bio/Location/Split.pm ok 205 - POD test for Bio/Location/FuzzyLocationI.pm ok 206 - POD test for Bio/Location/SplitLocationI.pm ok 207 - POD test for Bio/Location/Atomic.pm ok 208 - POD test for Bio/Location/NarrowestCoordPolicy.pm ok 209 - POD test for Bio/Location/AvWithinCoordPolicy.pm ok 210 - POD test for Bio/Location/CoordinatePolicyI.pm ok 211 - POD test for Bio/Location/Fuzzy.pm ok 212 - POD test for Bio/Location/Simple.pm ok 213 - POD test for Bio/Location/WidestCoordPolicy.pm ok 214 - POD test for Bio/Restriction/EnzymeI.pm ok 215 - POD test for Bio/Restriction/EnzymeCollection.pm ok 216 - POD test for Bio/Restriction/Enzyme.pm ok 217 - POD test for Bio/Restriction/IO.pm ok 218 - POD test for Bio/Restriction/Analysis.pm ok 219 - POD test for Bio/Annotation/OntologyTerm.pm ok 220 - POD test for Bio/Annotation/StructuredValue.pm ok 221 - POD test for Bio/Annotation/DBLink.pm ok 222 - POD test for Bio/Annotation/AnnotationFactory.pm ok 223 - POD test for Bio/Annotation/SimpleValue.pm ok 224 - POD test for Bio/Annotation/Comment.pm ok 225 - POD test for Bio/Annotation/Collection.pm ok 226 - POD test for Bio/Annotation/TagTree.pm ok 227 - POD test for Bio/Annotation/Reference.pm ok 228 - POD test for Bio/Annotation/TypeManager.pm ok 229 - POD test for Bio/Annotation/Target.pm ok 230 - POD test for Bio/Annotation/Relation.pm ok 231 - POD test for Bio/Annotation/Tree.pm ok 232 - POD test for Bio/SeqFeature/PositionProxy.pm ok 233 - POD test for Bio/SeqFeature/CollectionI.pm ok 234 - POD test for Bio/SeqFeature/FeaturePair.pm ok 235 - POD test for Bio/SeqFeature/Generic.pm ok 236 - POD test for Bio/SeqFeature/Lite.pm ok 237 - POD test for Bio/SeqFeature/Primer.pm ok 238 - POD test for Bio/SeqFeature/Similarity.pm ok 239 - POD test for Bio/SeqFeature/Collection.pm ok 240 - POD test for Bio/SeqFeature/Computation.pm ok 241 - POD test for Bio/SeqFeature/TypedSeqFeatureI.pm ok 242 - POD test for Bio/SeqFeature/AnnotationAdaptor.pm ok 243 - POD test for Bio/SeqFeature/Annotated.pm ok 244 - POD test for Bio/SeqFeature/SimilarityPair.pm ok 245 - POD test for Bio/SeqEvolution/EvolutionI.pm ok 246 - POD test for Bio/SeqEvolution/Factory.pm ok 247 - POD test for Bio/SeqEvolution/DNAPoint.pm ok 248 - POD test for Bio/Factory/DriverFactory.pm ok 249 - POD test for Bio/Factory/ObjectFactory.pm ok 250 - POD test for Bio/Factory/SequenceStreamI.pm ok 251 - POD test for Bio/Factory/TreeFactoryI.pm ok 252 - POD test for Bio/Factory/MapFactoryI.pm ok 253 - POD test for Bio/Factory/SequenceFactoryI.pm ok 254 - POD test for Bio/Factory/SeqAnalysisParserFactory.pm ok 255 - POD test for Bio/Factory/ApplicationFactoryI.pm ok 256 - POD test for Bio/Factory/AnalysisI.pm ok 257 - POD test for Bio/Factory/ObjectFactoryI.pm ok 258 - POD test for Bio/Factory/LocationFactoryI.pm ok 259 - POD test for Bio/Factory/SeqAnalysisParserFactoryI.pm ok 260 - POD test for Bio/Factory/SequenceProcessorI.pm ok 261 - POD test for Bio/Factory/ObjectBuilderI.pm ok 262 - POD test for Bio/Factory/FTLocationFactory.pm ok 263 - POD test for Bio/MapIO/mapmaker.pm ok 264 - POD test for Bio/MapIO/fpc.pm ok 265 - POD test for Bio/AlignIO/xmfa.pm ok 266 - POD test for Bio/AlignIO/meme.pm ok 267 - POD test for Bio/AlignIO/selex.pm ok 268 - POD test for Bio/AlignIO/po.pm ok 269 - POD test for Bio/AlignIO/largemultifasta.pm ok 270 - POD test for Bio/AlignIO/metafasta.pm ok 271 - POD test for Bio/AlignIO/maf.pm ok 272 - POD test for Bio/AlignIO/mase.pm ok 273 - POD test for Bio/AlignIO/fasta.pm ok 274 - POD test for Bio/AlignIO/phylip.pm ok 275 - POD test for Bio/AlignIO/nexus.pm ok 276 - POD test for Bio/AlignIO/prodom.pm ok 277 - POD test for Bio/AlignIO/msf.pm ok 278 - POD test for Bio/AlignIO/emboss.pm ok 279 - POD test for Bio/AlignIO/pfam.pm ok 280 - POD test for Bio/AlignIO/proda.pm ok 281 - POD test for Bio/AlignIO/clustalw.pm ok 282 - POD test for Bio/AlignIO/arp.pm ok 283 - POD test for Bio/AlignIO/bl2seq.pm ok 284 - POD test for Bio/AlignIO/mega.pm ok 285 - POD test for Bio/AlignIO/stockholm.pm ok 286 - POD test for Bio/AlignIO/psi.pm ok 287 - POD test for Bio/LiveSeq/Transcript.pm ok 288 - POD test for Bio/LiveSeq/Repeat_Unit.pm ok 289 - POD test for Bio/LiveSeq/DNA.pm ok 290 - POD test for Bio/LiveSeq/ChainI.pm ok 291 - POD test for Bio/LiveSeq/SeqI.pm ok 292 - POD test for Bio/LiveSeq/Repeat_Region.pm ok 293 - POD test for Bio/LiveSeq/Prim_Transcript.pm ok 294 - POD test for Bio/LiveSeq/Gene.pm ok 295 - POD test for Bio/LiveSeq/AARange.pm ok 296 - POD test for Bio/LiveSeq/Translation.pm ok 297 - POD test for Bio/LiveSeq/Mutation.pm ok 298 - POD test for Bio/LiveSeq/Exon.pm ok 299 - POD test for Bio/LiveSeq/Intron.pm ok 300 - POD test for Bio/LiveSeq/Mutator.pm ok 301 - POD test for Bio/LiveSeq/Chain.pm ok 302 - POD test for Bio/LiveSeq/Range.pm ok 303 - POD test for Bio/FeatureIO/interpro.pm ok 304 - POD test for Bio/FeatureIO/vecscreen_simple.pm ok 305 - POD test for Bio/FeatureIO/bed.pm ok 306 - POD test for Bio/FeatureIO/gtf.pm ok 307 - POD test for Bio/FeatureIO/gff.pm ok 308 - POD test for Bio/FeatureIO/ptt.pm ok 309 - POD test for Bio/PhyloNetwork/FactoryX.pm ok 310 - POD test for Bio/PhyloNetwork/TreeFactory.pm ok 311 - POD test for Bio/PhyloNetwork/RandomFactory.pm ok 312 - POD test for Bio/PhyloNetwork/TreeFactoryMulti.pm ok 313 - POD test for Bio/PhyloNetwork/GraphViz.pm ok 314 - POD test for Bio/PhyloNetwork/Factory.pm ok 315 - POD test for Bio/PhyloNetwork/muVector.pm ok 316 - POD test for Bio/PhyloNetwork/TreeFactoryX.pm ok 317 - POD test for Bio/MolEvol/CodonModel.pm ok 318 - POD test for Bio/Expression/Contact.pm ok 319 - POD test for Bio/Expression/ProbeI.pm ok 320 - POD test for Bio/Expression/FeatureI.pm ok 321 - POD test for Bio/Expression/DataSet.pm ok 322 - POD test for Bio/Expression/Sample.pm ok 323 - POD test for Bio/Expression/FeatureGroup.pm ok 324 - POD test for Bio/Expression/Platform.pm ok 325 - POD test for Bio/Cluster/FamilyI.pm ok 326 - POD test for Bio/Cluster/SequenceFamily.pm ok 327 - POD test for Bio/Cluster/ClusterFactory.pm ok 328 - POD test for Bio/Cluster/UniGene.pm ok 329 - POD test for Bio/Cluster/UniGeneI.pm ok 330 - POD test for Bio/Biblio/Book.pm ok 331 - POD test for Bio/Biblio/Proceeding.pm ok 332 - POD test for Bio/Biblio/MedlineBookArticle.pm ok 333 - POD test for Bio/Biblio/Provider.pm ok 334 - POD test for Bio/Biblio/PubmedJournalArticle.pm ok 335 - POD test for Bio/Biblio/BiblioBase.pm ok 336 - POD test for Bio/Biblio/Thesis.pm ok 337 - POD test for Bio/Biblio/Ref.pm ok 338 - POD test for Bio/Biblio/Organisation.pm ok 339 - POD test for Bio/Biblio/MedlineJournal.pm ok 340 - POD test for Bio/Biblio/Article.pm ok 341 - POD test for Bio/Biblio/IO.pm ok 342 - POD test for Bio/Biblio/MedlineJournalArticle.pm ok 343 - POD test for Bio/Biblio/WebResource.pm ok 344 - POD test for Bio/Biblio/TechReport.pm ok 345 - POD test for Bio/Biblio/PubmedArticle.pm ok 346 - POD test for Bio/Biblio/MedlineArticle.pm ok 347 - POD test for Bio/Biblio/Journal.pm ok 348 - POD test for Bio/Biblio/Person.pm ok 349 - POD test for Bio/Biblio/BookArticle.pm ok 350 - POD test for Bio/Biblio/JournalArticle.pm ok 351 - POD test for Bio/Biblio/Patent.pm ok 352 - POD test for Bio/Biblio/Service.pm ok 353 - POD test for Bio/Biblio/MedlineBook.pm ok 354 - POD test for Bio/Biblio/PubmedBookArticle.pm ok 355 - POD test for Bio/Assembly/Singlet.pm ok 356 - POD test for Bio/Assembly/Scaffold.pm ok 357 - POD test for Bio/Assembly/ContigAnalysis.pm ok 358 - POD test for Bio/Assembly/IO.pm ok 359 - POD test for Bio/Assembly/Contig.pm ok 360 - POD test for Bio/Assembly/ScaffoldI.pm ok 361 - POD test for Bio/CodonUsage/IO.pm ok 362 - POD test for Bio/CodonUsage/Table.pm ok 363 - POD test for Bio/SearchIO/blast_pull.pm ok 364 - POD test for Bio/SearchIO/gmap_f9.pm ok 365 - POD test for Bio/SearchIO/fasta.pm ok 366 - POD test for Bio/SearchIO/psl.pm ok 367 - POD test for Bio/SearchIO/cross_match.pm ok 368 - POD test for Bio/SearchIO/blast.pm ok 369 - POD test for Bio/SearchIO/hmmer.pm ok 370 - POD test for Bio/SearchIO/sim4.pm ok 371 - POD test for Bio/SearchIO/FastHitEventBuilder.pm ok 372 - POD test for Bio/SearchIO/infernal.pm ok 373 - POD test for Bio/SearchIO/waba.pm ok 374 - POD test for Bio/SearchIO/blastxml.pm ok 375 - POD test for Bio/SearchIO/wise.pm ok 376 - POD test for Bio/SearchIO/IteratedSearchResultEventBuilder.pm ok 377 - POD test for Bio/SearchIO/SearchWriterI.pm ok 378 - POD test for Bio/SearchIO/rnamotif.pm ok 379 - POD test for Bio/SearchIO/axt.pm ok 380 - POD test for Bio/SearchIO/erpin.pm ok 381 - POD test for Bio/SearchIO/EventHandlerI.pm ok 382 - POD test for Bio/SearchIO/SearchResultEventBuilder.pm ok 383 - POD test for Bio/SearchIO/exonerate.pm ok 384 - POD test for Bio/SearchIO/megablast.pm ok 385 - POD test for Bio/SearchIO/hmmer_pull.pm ok 386 - POD test for Bio/SearchIO/blasttable.pm ok 387 - POD test for Bio/SeqIO/interpro.pm ok 388 - POD test for Bio/SeqIO/scf.pm ok 389 - POD test for Bio/SeqIO/FTHelper.pm ok 390 - POD test for Bio/SeqIO/raw.pm ok 391 - POD test for Bio/SeqIO/lasergene.pm ok 392 - POD test for Bio/SeqIO/qual.pm ok 393 - POD test for Bio/SeqIO/entrezgene.pm ok 394 - POD test for Bio/SeqIO/strider.pm ok 395 - POD test for Bio/SeqIO/largefasta.pm ok 396 - POD test for Bio/SeqIO/metafasta.pm ok 397 - POD test for Bio/SeqIO/tab.pm ok 398 - POD test for Bio/SeqIO/fasta.pm ok 399 - POD test for Bio/SeqIO/exp.pm ok 400 - POD test for Bio/SeqIO/table.pm ok 401 - POD test for Bio/SeqIO/swissdriver.pm ok 402 - POD test for Bio/SeqIO/tigrxml.pm ok 403 - POD test for Bio/SeqIO/tinyseq.pm ok 404 - POD test for Bio/SeqIO/pln.pm ok 405 - POD test for Bio/SeqIO/chaosxml.pm ok 406 - POD test for Bio/SeqIO/abi.pm ok 407 - POD test for Bio/SeqIO/genbank.pm ok 408 - POD test for Bio/SeqIO/asciitree.pm ok 409 - POD test for Bio/SeqIO/bsml.pm ok 410 - POD test for Bio/SeqIO/chadoxml.pm ok 411 - POD test for Bio/SeqIO/tigr.pm ok 412 - POD test for Bio/SeqIO/pir.pm ok 413 - POD test for Bio/SeqIO/swiss.pm ok 414 - POD test for Bio/SeqIO/MultiFile.pm ok 415 - POD test for Bio/SeqIO/phd.pm ok 416 - POD test for Bio/SeqIO/locuslink.pm ok 417 - POD test for Bio/SeqIO/bsml_sax.pm ok 418 - POD test for Bio/SeqIO/ctf.pm ok 419 - POD test for Bio/SeqIO/kegg.pm ok 420 - POD test for Bio/SeqIO/agave.pm ok 421 - POD test for Bio/SeqIO/embldriver.pm ok 422 - POD test for Bio/SeqIO/gbdriver.pm ok 423 - POD test for Bio/SeqIO/ace.pm ok 424 - POD test for Bio/SeqIO/ztr.pm ok 425 - POD test for Bio/SeqIO/embl.pm ok 426 - POD test for Bio/SeqIO/excel.pm ok 427 - POD test for Bio/SeqIO/chaos.pm ok 428 - POD test for Bio/SeqIO/gcg.pm ok 429 - POD test for Bio/SeqIO/alf.pm ok 430 - POD test for Bio/SeqIO/flybase_chadoxml.pm ok 431 - POD test for Bio/SeqIO/game.pm ok 432 - POD test for Bio/SeqIO/fastq.pm ok 433 - POD test for Bio/Root/HTTPget.pm ok 434 - POD test for Bio/Root/Exception.pm ok 435 - POD test for Bio/Root/Utilities.pm ok 436 - POD test for Bio/Root/RootI.pm ok 437 - POD test for Bio/Root/Version.pm ok 438 - POD test for Bio/Root/IO.pm ok 439 - POD test for Bio/Root/Test.pm ok 440 - POD test for Bio/Root/Root.pm ok 441 - POD test for Bio/Root/Build.pm ok 442 - POD test for Bio/Root/Storable.pm ok 443 - POD test for Bio/DB/GenericWebAgent.pm ok 444 - POD test for Bio/DB/Registry.pm ok 445 - POD test for Bio/DB/Fasta.pm ok 446 - POD test for Bio/DB/EMBL.pm ok 447 - POD test for Bio/DB/Expression.pm ok 448 - POD test for Bio/DB/GenBank.pm ok 449 - POD test for Bio/DB/UpdateableSeqI.pm ok 450 - POD test for Bio/DB/EUtilities.pm ok 451 - POD test for Bio/DB/ReferenceI.pm ok 452 - POD test for Bio/DB/Failover.pm ok 453 - POD test for Bio/DB/SeqI.pm ok 454 - POD test for Bio/DB/WebDBSeqI.pm ok 455 - POD test for Bio/DB/NCBIHelper.pm ok 456 - POD test for Bio/DB/RefSeq.pm ok 457 - POD test for Bio/DB/LocationI.pm ok 458 - POD test for Bio/DB/Taxonomy.pm ok 459 - POD test for Bio/DB/DBFetch.pm ok 460 - POD test for Bio/DB/GenPept.pm ok 461 - POD test for Bio/DB/BiblioI.pm ok 462 - POD test for Bio/DB/SeqFeature.pm ok 463 - POD test for Bio/DB/RandomAccessI.pm ok 464 - POD test for Bio/DB/CUTG.pm ok 465 - POD test for Bio/DB/GFF.pm ok 466 - POD test for Bio/DB/Flat.pm ok 467 - POD test for Bio/DB/FileCache.pm ok 468 - POD test for Bio/DB/Qual.pm ok 469 - POD test for Bio/DB/EntrezGene.pm ok 470 - POD test for Bio/DB/HIV.pm ok 471 - POD test for Bio/DB/Universal.pm ok 472 - POD test for Bio/DB/BioFetch.pm ok 473 - POD test for Bio/DB/InMemoryCache.pm ok 474 - POD test for Bio/DB/Ace.pm ok 475 - POD test for Bio/DB/SeqVersion.pm ok 476 - POD test for Bio/DB/TFBS.pm ok 477 - POD test for Bio/DB/QueryI.pm ok 478 - POD test for Bio/DB/SwissProt.pm ok 479 - POD test for Bio/DB/MeSH.pm ok 480 - POD test for Bio/DB/SeqHound.pm ok 481 - POD test for Bio/Symbol/AlphabetI.pm ok 482 - POD test for Bio/Symbol/Symbol.pm ok 483 - POD test for Bio/Symbol/SymbolI.pm ok 484 - POD test for Bio/Symbol/Alphabet.pm ok 485 - POD test for Bio/Symbol/DNAAlphabet.pm ok 486 - POD test for Bio/Symbol/ProteinAlphabet.pm ok 487 - POD test for Bio/Das/FeatureTypeI.pm ok 488 - POD test for Bio/Das/SegmentI.pm ok 489 - POD test for Bio/Variation/VariantI.pm ok 490 - POD test for Bio/Variation/RNAChange.pm ok 491 - POD test for Bio/Variation/DNAMutation.pm ok 492 - POD test for Bio/Variation/SNP.pm ok 493 - POD test for Bio/Variation/IO.pm ok 494 - POD test for Bio/Variation/SeqDiff.pm ok 495 - POD test for Bio/Variation/AAReverseMutate.pm ok 496 - POD test for Bio/Variation/Allele.pm ok 497 - POD test for Bio/Variation/AAChange.pm ok 498 - POD test for Bio/Structure/StructureI.pm ok 499 - POD test for Bio/Structure/Residue.pm ok 500 - POD test for Bio/Structure/Atom.pm ok 501 - POD test for Bio/Structure/IO.pm ok 502 - POD test for Bio/Structure/Entry.pm ok 503 - POD test for Bio/Structure/Chain.pm ok 504 - POD test for Bio/Structure/Model.pm ok 505 - POD test for Bio/Coordinate/ResultI.pm ok 506 - POD test for Bio/Coordinate/Result.pm ok 507 - POD test for Bio/Coordinate/MapperI.pm ok 508 - POD test for Bio/Coordinate/ExtrapolatingPair.pm ok 509 - POD test for Bio/Coordinate/Collection.pm ok 510 - POD test for Bio/Coordinate/Graph.pm ok 511 - POD test for Bio/Coordinate/Utils.pm ok 512 - POD test for Bio/Coordinate/GeneMapper.pm ok 513 - POD test for Bio/Coordinate/Chain.pm ok 514 - POD test for Bio/Coordinate/Pair.pm ok 515 - POD test for Bio/Align/Utilities.pm ok 516 - POD test for Bio/Align/AlignI.pm ok 517 - POD test for Bio/Align/PairwiseStatistics.pm ok 518 - POD test for Bio/Align/StatisticsI.pm ok 519 - POD test for Bio/Align/ProteinStatistics.pm ok 520 - POD test for Bio/Align/DNAStatistics.pm ok 521 - POD test for Bio/TreeIO/TreeEventBuilder.pm ok 522 - POD test for Bio/TreeIO/newick.pm ok 523 - POD test for Bio/TreeIO/nexus.pm ok 524 - POD test for Bio/TreeIO/nhx.pm ok 525 - POD test for Bio/TreeIO/svggraph.pm ok 526 - POD test for Bio/TreeIO/phyloxml.pm ok 527 - POD test for Bio/TreeIO/pag.pm ok 528 - POD test for Bio/TreeIO/tabtree.pm ok 529 - POD test for Bio/TreeIO/lintree.pm ok 530 - POD test for Bio/TreeIO/cluster.pm ok 531 - POD test for Bio/Taxonomy/Taxon.pm ok 532 - POD test for Bio/Taxonomy/FactoryI.pm ok 533 - POD test for Bio/Taxonomy/Node.pm ok 534 - POD test for Bio/Taxonomy/Tree.pm ok 535 - POD test for Bio/Seq/PrimaryQual.pm ok 536 - POD test for Bio/Seq/SeqFactory.pm ok 537 - POD test for Bio/Seq/LargeSeq.pm ok 538 - POD test for Bio/Seq/SeqFastaSpeedFactory.pm ok 539 - POD test for Bio/Seq/SeqBuilder.pm ok 540 - POD test for Bio/Seq/Quality.pm ok 541 - POD test for Bio/Seq/PrimedSeq.pm ok 542 - POD test for Bio/Seq/RichSeq.pm ok 543 - POD test for Bio/Seq/LargeLocatableSeq.pm ok 544 - POD test for Bio/Seq/TraceI.pm ok 545 - POD test for Bio/Seq/QualI.pm ok 546 - POD test for Bio/Seq/SeqWithQuality.pm ok 547 - POD test for Bio/Seq/LargeSeqI.pm ok 548 - POD test for Bio/Seq/SequenceTrace.pm ok 549 - POD test for Bio/Seq/Meta.pm ok 550 - POD test for Bio/Seq/MetaI.pm ok 551 - POD test for Bio/Seq/BaseSeqProcessor.pm ok 552 - POD test for Bio/Seq/LargePrimarySeq.pm ok 553 - POD test for Bio/Seq/RichSeqI.pm ok 554 - POD test for Bio/Seq/EncodedSeq.pm ok 555 - POD test for Bio/ClusterIO/dbsnp.pm ok 556 - POD test for Bio/ClusterIO/unigene.pm ok 557 - POD test for Bio/Phenotype/PhenotypeI.pm ok 558 - POD test for Bio/Phenotype/Correlate.pm ok 559 - POD test for Bio/Phenotype/Measure.pm ok 560 - POD test for Bio/Phenotype/Phenotype.pm ok 561 - POD test for Bio/Ontology/TermFactory.pm ok 562 - POD test for Bio/Ontology/InterProTerm.pm ok 563 - POD test for Bio/Ontology/TermI.pm ok 564 - POD test for Bio/Ontology/Ontology.pm ok 565 - POD test for Bio/Ontology/OntologyEngineI.pm ok 566 - POD test for Bio/Ontology/Path.pm ok 567 - POD test for Bio/Ontology/OntologyStore.pm ok 568 - POD test for Bio/Ontology/PathI.pm ok 569 - POD test for Bio/Ontology/RelationshipI.pm ok 570 - POD test for Bio/Ontology/OBOterm.pm ok 571 - POD test for Bio/Ontology/Term.pm ok 572 - POD test for Bio/Ontology/RelationshipFactory.pm ok 573 - POD test for Bio/Ontology/RelationshipType.pm ok 574 - POD test for Bio/Ontology/Relationship.pm ok 575 - POD test for Bio/Ontology/OntologyI.pm ok 576 - POD test for Bio/Ontology/OBOEngine.pm ok 577 - POD test for Bio/Ontology/DocumentRegistry.pm ok 578 - POD test for Bio/Ontology/SimpleOntologyEngine.pm ok 579 - POD test for Bio/Ontology/GOterm.pm ok 580 - POD test for Bio/Index/Blast.pm ok 581 - POD test for Bio/Index/Fasta.pm ok 582 - POD test for Bio/Index/EMBL.pm ok 583 - POD test for Bio/Index/GenBank.pm ok 584 - POD test for Bio/Index/BlastTable.pm ok 585 - POD test for Bio/Index/Stockholm.pm ok 586 - POD test for Bio/Index/Fastq.pm ok 587 - POD test for Bio/Index/SwissPfam.pm ok 588 - POD test for Bio/Index/Hmmer.pm ok 589 - POD test for Bio/Index/AbstractSeq.pm ok 590 - POD test for Bio/Index/Qual.pm ok 591 - POD test for Bio/Index/Swissprot.pm ok 592 - POD test for Bio/Index/Abstract.pm ok 593 - POD test for scripts/popgen/composite_LD.PLS ok 594 - POD test for scripts/popgen/heterogeneity_test.PLS ok 595 - POD test for scripts/seqstats/chaos_plot.PLS ok 596 - POD test for scripts/seqstats/aacomp.PLS ok 597 - POD test for scripts/seqstats/oligo_count.PLS ok 598 - POD test for scripts/seqstats/gccalc.PLS ok 599 - POD test for scripts/biblio/biblio.PLS ok 600 - POD test for scripts/DB-HIV/hivq.PLS ok 601 - POD test for scripts/tree/blast2tree.PLS ok 602 - POD test for scripts/tree/tree2pag.PLS ok 603 - POD test for scripts/tree/nexus2nh.PLS ok 604 - POD test for scripts/seq/unflatten_seq.PLS ok 605 - POD test for scripts/seq/split_seq.PLS ok 606 - POD test for scripts/seq/seqconvert.PLS ok 607 - POD test for scripts/seq/make_mrna_protein.PLS ok 608 - POD test for scripts/seq/seqretsplit.PLS ok 609 - POD test for scripts/seq/extract_feature_seq.PLS ok 610 - POD test for scripts/seq/translate_seq.PLS ok 611 - POD test for scripts/utilities/pairwise_kaks.PLS ok 612 - POD test for scripts/utilities/mutate.PLS ok 613 - POD test for scripts/utilities/download_query_genbank.PLS ok 614 - POD test for scripts/utilities/search2tribe.PLS ok 615 - POD test for scripts/utilities/bp_sreformat.PLS ok 616 - POD test for scripts/utilities/revtrans-motif.PLS ok 617 - POD test for scripts/utilities/search2gff.PLS ok 618 - POD test for scripts/utilities/bp_mrtrans.PLS ok 619 - POD test for scripts/utilities/search2alnblocks.PLS ok 620 - POD test for scripts/utilities/mask_by_search.PLS ok 621 - POD test for scripts/utilities/search2BSML.PLS ok 622 - POD test for scripts/utilities/dbsplit.PLS ok 623 - POD test for scripts/utilities/seq_length.PLS ok 624 - POD test for scripts/utilities/remote_blast.PLS ok 625 - POD test for scripts/utilities/bp_nrdb.PLS ok 626 - POD test for scripts/searchio/hmmer_to_table.PLS ok 627 - POD test for scripts/searchio/search2table.PLS ok 628 - POD test for scripts/searchio/parse_hmmsearch.PLS ok 629 - POD test for scripts/searchio/fastam9_to_table.PLS ok 630 - POD test for scripts/searchio/filter_search.PLS ok 631 - POD test for scripts/Bio-DB-GFF/bulk_load_gff.PLS ok 632 - POD test for scripts/Bio-DB-GFF/load_gff.PLS ok 633 - POD test for scripts/Bio-DB-GFF/fast_load_gff.PLS ok 634 - POD test for scripts/Bio-DB-GFF/meta_gff.PLS ok 635 - POD test for scripts/Bio-DB-GFF/genbank2gff.PLS ok 636 - POD test for scripts/Bio-DB-GFF/process_wormbase.PLS ok 637 - POD test for scripts/Bio-DB-GFF/generate_histogram.PLS ok 638 - POD test for scripts/Bio-DB-GFF/process_gadfly.PLS ok 639 - POD test for scripts/Bio-DB-GFF/genbank2gff3.PLS ok 640 - POD test for scripts/Bio-DB-GFF/process_sgd.PLS ok 641 - POD test for scripts/index/bp_fetch.PLS ok 642 - POD test for scripts/index/bp_index.PLS ok 643 - POD test for scripts/index/bp_seqret.PLS ok 644 - POD test for scripts/DB/biofetch_genbank_proxy.PLS ok 645 - POD test for scripts/DB/bioflat_index.PLS ok 646 - POD test for scripts/DB/flanks.PLS ok 647 - POD test for scripts/DB/biogetseq.PLS ok 648 - POD test for scripts/taxa/taxonomy2tree.PLS ok 649 - POD test for scripts/taxa/local_taxonomydb_query.PLS ok 650 - POD test for scripts/taxa/taxid4species.PLS ok 651 - POD test for scripts/taxa/classify_hits_kingdom.PLS ok 652 - POD test for scripts/taxa/query_entrez_taxa.PLS ok 653 - POD test for scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS (no pod) ok 654 - POD test for scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS (no pod) ok 655 - POD test for scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS (no pod) ok 656 - POD test for scripts/Bio-DB-EUtilities/einfo.PLS ok 657 - POD test for examples/popgen/parse_calc_stats.pl (no pod) ok 658 - POD test for examples/structure/structure-io.pl (no pod) ok 659 - POD test for examples/quality/svgtrace.pl (no pod) ok 660 - POD test for examples/biblio/biblio_soap.pl (no pod) not ok 661 - POD test for examples/biblio/biblio-eutils-example.pl ok 662 - POD test for examples/biblio/biblio-soap-example.pl ok 663 - POD test for examples/liveseq/change_gene.pl (no pod) ok 664 - POD test for examples/db/get_seqs.pl (no pod) ok 665 - POD test for examples/db/gb2features.pl (no pod) ok 666 - POD test for examples/db/dbfetch ok 667 - POD test for examples/db/rfetch.pl (no pod) ok 668 - POD test for examples/db/use_registry.pl (no pod) ok 669 - POD test for examples/db/getGenBank.pl (no pod) ok 670 - POD test for examples/db/est_tissue_query.pl (no pod) ok 671 - POD test for examples/tools/parse_codeml.pl (no pod) ok 672 - POD test for examples/tools/reverse-translate.pl ok 673 - POD test for examples/tools/run_genscan.pl (no pod) ok 674 - POD test for examples/tools/seq_pattern.pl (no pod) ok 675 - POD test for examples/tools/gb_to_gff.pl (no pod) ok 676 - POD test for examples/tools/run_primer3.pl ok 677 - POD test for examples/tools/psw.pl (no pod) ok 678 - POD test for examples/tools/standaloneblast.pl (no pod) ok 679 - POD test for examples/tools/extract_genes.pl ok 680 - POD test for examples/tools/gff2ps.pl ok 681 - POD test for examples/contributed/nmrpdb_parse.pl (no pod) ok 682 - POD test for examples/contributed/rebase2list.pl (no pod) ok 683 - POD test for examples/contributed/prosite2perl.pl (no pod) ok 684 - POD test for examples/tree/paup2phylip.pl (no pod) ok 685 - POD test for examples/sirna/rnai_finder.cgi ok 686 - POD test for examples/align/aligntutorial.pl (no pod) ok 687 - POD test for examples/align/align_on_codons.pl (no pod) ok 688 - POD test for examples/align/clustalw.pl (no pod) ok 689 - POD test for examples/align/simplealign.pl (no pod) ok 690 - POD test for examples/tk/hitdisplay.pl (no pod) ok 691 - POD test for examples/tk/gsequence.pl (no pod) ok 692 - POD test for examples/searchio/hspwriter.pl (no pod) ok 693 - POD test for examples/searchio/resultwriter.pl (no pod) ok 694 - POD test for examples/searchio/custom_writer.pl (no pod) ok 695 - POD test for examples/searchio/hitwriter.pl (no pod) ok 696 - POD test for examples/searchio/rawwriter.pl (no pod) ok 697 - POD test for examples/searchio/waba2gff.pl (no pod) ok 698 - POD test for examples/searchio/blast_example.pl (no pod) ok 699 - POD test for examples/searchio/htmlwriter.pl (no pod) ok 700 - POD test for examples/searchio/psiblast_features.pl (no pod) ok 701 - POD test for examples/searchio/waba2gff3.pl ok 702 - POD test for examples/searchio/psiblast_iterations.pl (no pod) ok 703 - POD test for examples/Bio-DB-GFF/load_ucsc.pl (no pod) ok 704 - POD test for examples/cluster/dbsnp.pl (no pod) ok 705 - POD test for examples/root/exceptions2.pl (no pod) ok 706 - POD test for examples/root/exceptions1.pl (no pod) ok 707 - POD test for examples/root/exceptions3.pl (no pod) ok 708 - POD test for examples/root/exceptions4.pl (no pod) ok 709 - POD test for Bio/OntologyIO/Handlers/BaseSAXHandler.pm ok 710 - POD test for Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm ok 711 - POD test for Bio/OntologyIO/Handlers/InterProHandler.pm ok 712 - POD test for Bio/Search/Tiling/MapTiling.pm ok 713 - POD test for Bio/Search/Tiling/MapTileUtils.pm ok 714 - POD test for Bio/Search/Tiling/TilingI.pm ok 715 - POD test for Bio/Search/Result/ResultI.pm ok 716 - POD test for Bio/Search/Result/HmmpfamResult.pm ok 717 - POD test for Bio/Search/Result/PullResultI.pm ok 718 - POD test for Bio/Search/Result/ResultFactory.pm ok 719 - POD test for Bio/Search/Result/WABAResult.pm ok 720 - POD test for Bio/Search/Result/BlastPullResult.pm ok 721 - POD test for Bio/Search/Result/GenericResult.pm ok 722 - POD test for Bio/Search/Result/BlastResult.pm ok 723 - POD test for Bio/Search/Result/HMMERResult.pm ok 724 - POD test for Bio/Search/Result/CrossMatchResult.pm ok 725 - POD test for Bio/Search/Iteration/GenericIteration.pm ok 726 - POD test for Bio/Search/Iteration/IterationI.pm ok 727 - POD test for Bio/Search/Hit/HMMERHit.pm ok 728 - POD test for Bio/Search/Hit/Fasta.pm ok 729 - POD test for Bio/Search/Hit/PullHitI.pm ok 730 - POD test for Bio/Search/Hit/GenericHit.pm ok 731 - POD test for Bio/Search/Hit/BlastPullHit.pm ok 732 - POD test for Bio/Search/Hit/HmmpfamHit.pm ok 733 - POD test for Bio/Search/Hit/BlastHit.pm ok 734 - POD test for Bio/Search/Hit/HitI.pm ok 735 - POD test for Bio/Search/Hit/ModelHit.pm ok 736 - POD test for Bio/Search/Hit/HitFactory.pm ok 737 - POD test for Bio/Search/Hit/PsiBlastHit.pm ok 738 - POD test for Bio/Search/HSP/WABAHSP.pm ok 739 - POD test for Bio/Search/HSP/PullHSPI.pm ok 740 - POD test for Bio/Search/HSP/BlastPullHSP.pm ok 741 - POD test for Bio/Search/HSP/HmmpfamHSP.pm ok 742 - POD test for Bio/Search/HSP/HMMERHSP.pm ok 743 - POD test for Bio/Search/HSP/HSPI.pm ok 744 - POD test for Bio/Search/HSP/BlastHSP.pm ok 745 - POD test for Bio/Search/HSP/FastaHSP.pm ok 746 - POD test for Bio/Search/HSP/PsiBlastHSP.pm ok 747 - POD test for Bio/Search/HSP/HSPFactory.pm ok 748 - POD test for Bio/Search/HSP/PSLHSP.pm ok 749 - POD test for Bio/Search/HSP/GenericHSP.pm ok 750 - POD test for Bio/Search/HSP/ModelHSP.pm ok 751 - POD test for Bio/Matrix/PSM/SiteMatrixI.pm ok 752 - POD test for Bio/Matrix/PSM/InstanceSiteI.pm ok 753 - POD test for Bio/Matrix/PSM/SiteMatrix.pm ok 754 - POD test for Bio/Matrix/PSM/IO.pm ok 755 - POD test for Bio/Matrix/PSM/Psm.pm ok 756 - POD test for Bio/Matrix/PSM/ProtPsm.pm ok 757 - POD test for Bio/Matrix/PSM/PsmHeader.pm ok 758 - POD test for Bio/Matrix/PSM/PsmHeaderI.pm ok 759 - POD test for Bio/Matrix/PSM/ProtMatrix.pm ok 760 - POD test for Bio/Matrix/PSM/PsmI.pm ok 761 - POD test for Bio/Matrix/PSM/InstanceSite.pm ok 762 - POD test for Bio/Matrix/IO/phylip.pm ok 763 - POD test for Bio/Matrix/IO/mlagan.pm ok 764 - POD test for Bio/Matrix/IO/scoring.pm ok 765 - POD test for Bio/Tree/Draw/Cladogram.pm ok 766 - POD test for Bio/PopGen/Simulation/Coalescent.pm ok 767 - POD test for Bio/PopGen/Simulation/GeneticDrift.pm ok 768 - POD test for Bio/PopGen/IO/hapmap.pm ok 769 - POD test for Bio/PopGen/IO/prettybase.pm ok 770 - POD test for Bio/PopGen/IO/phase.pm ok 771 - POD test for Bio/PopGen/IO/csv.pm ok 772 - POD test for Bio/Tools/Alignment/Trim.pm ok 773 - POD test for Bio/Tools/Alignment/Consed.pm ok 774 - POD test for Bio/Tools/EUtilities/Summary.pm ok 775 - POD test for Bio/Tools/EUtilities/History.pm ok 776 - POD test for Bio/Tools/EUtilities/Query.pm ok 777 - POD test for Bio/Tools/EUtilities/Link.pm ok 778 - POD test for Bio/Tools/EUtilities/EUtilDataI.pm ok 779 - POD test for Bio/Tools/EUtilities/Info.pm ok 780 - POD test for Bio/Tools/EUtilities/EUtilParameters.pm ok 781 - POD test for Bio/Tools/EUtilities/Cookie.pm ok 782 - POD test for Bio/Tools/EUtilities/HistoryI.pm ok 783 - POD test for Bio/Tools/Phylo/PAML.pm ok 784 - POD test for Bio/Tools/Phylo/Gumby.pm ok 785 - POD test for Bio/Tools/Phylo/Molphy.pm ok 786 - POD test for Bio/Tools/Phylo/Gerp.pm ok 787 - POD test for Bio/Tools/SeqPattern/Backtranslate.pm ok 788 - POD test for Bio/Tools/Primer/AssessorI.pm ok 789 - POD test for Bio/Tools/Primer/Feature.pm ok 790 - POD test for Bio/Tools/Primer/Pair.pm ok 791 - POD test for Bio/Tools/EMBOSS/Palindrome.pm ok 792 - POD test for Bio/Tools/Sim4/Exon.pm ok 793 - POD test for Bio/Tools/Sim4/Results.pm ok 794 - POD test for Bio/Tools/Run/StandAloneWUBlast.pm ok 795 - POD test for Bio/Tools/Run/StandAloneBlast.pm ok 796 - POD test for Bio/Tools/Run/ParametersI.pm not ok 797 - POD test for Bio/Tools/Run/WrapperBase.pm ok 798 - POD test for Bio/Tools/Run/StandAloneNCBIBlast.pm ok 799 - POD test for Bio/Tools/Run/RemoteBlast.pm ok 800 - POD test for Bio/Tools/Run/GenericParameters.pm ok 801 - POD test for Bio/Tools/Spidey/Exon.pm ok 802 - POD test for Bio/Tools/Spidey/Results.pm ok 803 - POD test for Bio/Tools/Analysis/SimpleAnalysisBase.pm ok 804 - POD test for Bio/Tools/Prediction/Gene.pm ok 805 - POD test for Bio/Tools/Prediction/Exon.pm ok 806 - POD test for Bio/Tools/Signalp/ExtendedSignalp.pm ok 807 - POD test for Bio/Tools/HMMER/Domain.pm ok 808 - POD test for Bio/Tools/HMMER/Set.pm ok 809 - POD test for Bio/Tools/HMMER/Results.pm ok 810 - POD test for Bio/Restriction/Enzyme/MultiSite.pm ok 811 - POD test for Bio/Restriction/Enzyme/MultiCut.pm ok 812 - POD test for Bio/Restriction/IO/prototype.pm ok 813 - POD test for Bio/Restriction/IO/bairoch.pm ok 814 - POD test for Bio/Restriction/IO/base.pm ok 815 - POD test for Bio/Restriction/IO/itype2.pm ok 816 - POD test for Bio/Restriction/IO/withrefm.pm ok 817 - POD test for Bio/SeqFeature/SiRNA/Oligo.pm ok 818 - POD test for Bio/SeqFeature/SiRNA/Pair.pm ok 819 - POD test for Bio/SeqFeature/Gene/Transcript.pm ok 820 - POD test for Bio/SeqFeature/Gene/ExonI.pm ok 821 - POD test for Bio/SeqFeature/Gene/Promoter.pm ok 822 - POD test for Bio/SeqFeature/Gene/UTR.pm ok 823 - POD test for Bio/SeqFeature/Gene/Poly_A_site.pm ok 824 - POD test for Bio/SeqFeature/Gene/Exon.pm ok 825 - POD test for Bio/SeqFeature/Gene/Intron.pm ok 826 - POD test for Bio/SeqFeature/Gene/TranscriptI.pm ok 827 - POD test for Bio/SeqFeature/Gene/GeneStructureI.pm ok 828 - POD test for Bio/SeqFeature/Gene/NC_Feature.pm ok 829 - POD test for Bio/SeqFeature/Gene/GeneStructure.pm ok 830 - POD test for Bio/SeqFeature/Tools/Unflattener.pm ok 831 - POD test for Bio/SeqFeature/Tools/TypeMapper.pm ok 832 - POD test for Bio/SeqFeature/Tools/IDHandler.pm ok 833 - POD test for Bio/SeqFeature/Tools/FeatureNamer.pm ok 834 - POD test for Bio/AlignIO/Handler/GenericAlignHandler.pm ok 835 - POD test for Bio/LiveSeq/IO/BioPerl.pm ok 836 - POD test for Bio/LiveSeq/IO/Loader.pm ok 837 - POD test for Bio/Expression/FeatureSet/FeatureSetMas50.pm ok 838 - POD test for Bio/Expression/FeatureGroup/FeatureGroupMas50.pm ok 839 - POD test for Bio/Biblio/IO/pubmedxml.pm ok 840 - POD test for Bio/Biblio/IO/medlinexml.pm ok 841 - POD test for Bio/Biblio/IO/medline2ref.pm ok 842 - POD test for Bio/Biblio/IO/pubmed2ref.pm ok 843 - POD test for Bio/Assembly/Tools/ContigSpectrum.pm ok 844 - POD test for Bio/Assembly/IO/phrap.pm ok 845 - POD test for Bio/Assembly/IO/tigr.pm ok 846 - POD test for Bio/Assembly/IO/ace.pm ok 847 - POD test for Bio/SearchIO/Writer/BSMLResultWriter.pm ok 848 - POD test for Bio/SearchIO/Writer/HSPTableWriter.pm ok 849 - POD test for Bio/SearchIO/Writer/ResultTableWriter.pm ok 850 - POD test for Bio/SearchIO/Writer/GbrowseGFF.pm ok 851 - POD test for Bio/SearchIO/Writer/TextResultWriter.pm ok 852 - POD test for Bio/SearchIO/Writer/HTMLResultWriter.pm ok 853 - POD test for Bio/SearchIO/Writer/HitTableWriter.pm ok 854 - POD test for Bio/SearchIO/XML/PsiBlastHandler.pm ok 855 - POD test for Bio/SearchIO/XML/BlastHandler.pm ok 856 - POD test for Bio/SeqIO/game/seqHandler.pm ok 857 - POD test for Bio/SeqIO/game/gameSubs.pm ok 858 - POD test for Bio/SeqIO/game/gameHandler.pm ok 859 - POD test for Bio/SeqIO/game/gameWriter.pm ok 860 - POD test for Bio/SeqIO/game/featHandler.pm ok 861 - POD test for Bio/SeqIO/Handler/GenericRichSeqHandler.pm ok 862 - POD test for Bio/SeqIO/tinyseq/tinyseqHandler.pm ok 863 - POD test for Bio/Root/Test/Warn.pm ok 864 - POD test for Bio/DB/SeqVersion/gi.pm ok 865 - POD test for Bio/DB/Query/GenBank.pm ok 866 - POD test for Bio/DB/Query/HIVQuery.pm ok 867 - POD test for Bio/DB/Query/WebQuery.pm ok 868 - POD test for Bio/DB/SeqFeature/NormalizedTableFeatureI.pm ok 869 - POD test for Bio/DB/SeqFeature/NormalizedFeatureI.pm ok 870 - POD test for Bio/DB/SeqFeature/Segment.pm ok 871 - POD test for Bio/DB/SeqFeature/NormalizedFeature.pm ok 872 - POD test for Bio/DB/SeqFeature/Store.pm ok 873 - POD test for Bio/DB/GFF/Homol.pm ok 874 - POD test for Bio/DB/GFF/Typename.pm ok 875 - POD test for Bio/DB/GFF/Segment.pm ok 876 - POD test for Bio/DB/GFF/RelSegment.pm ok 877 - POD test for Bio/DB/GFF/Featname.pm ok 878 - POD test for Bio/DB/GFF/Feature.pm ok 879 - POD test for Bio/DB/GFF/Aggregator.pm ok 880 - POD test for Bio/DB/Flat/BinarySearch.pm ok 881 - POD test for Bio/DB/Flat/BDB.pm ok 882 - POD test for Bio/DB/Expression/geo.pm ok 883 - POD test for Bio/DB/Biblio/soap.pm ok 884 - POD test for Bio/DB/Biblio/biofetch.pm ok 885 - POD test for Bio/DB/Biblio/eutils.pm ok 886 - POD test for Bio/DB/TFBS/transfac_pro.pm ok 887 - POD test for Bio/DB/HIV/HIVQueryHelper.pm ok 888 - POD test for Bio/DB/HIV/HIVAnnotProcessor.pm ok 889 - POD test for Bio/DB/Taxonomy/entrez.pm ok 890 - POD test for Bio/DB/Taxonomy/flatfile.pm ok 891 - POD test for Bio/DB/Taxonomy/list.pm ok 892 - POD test for Bio/Variation/IO/xml.pm ok 893 - POD test for Bio/Variation/IO/flat.pm ok 894 - POD test for Bio/Structure/IO/pdb.pm ok 895 - POD test for Bio/Coordinate/Result/Gap.pm ok 896 - POD test for Bio/Coordinate/Result/Match.pm ok 897 - POD test for Bio/Seq/Meta/Array.pm ok 898 - POD test for Bio/Phenotype/MeSH/Twig.pm ok 899 - POD test for Bio/Phenotype/MeSH/Term.pm ok 900 - POD test for Bio/Phenotype/OMIM/MiniMIMentry.pm ok 901 - POD test for Bio/Phenotype/OMIM/OMIMparser.pm ok 902 - POD test for Bio/Phenotype/OMIM/OMIMentry.pm ok 903 - POD test for Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm ok 904 - POD test for Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm ok 905 - POD test for Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm ok 906 - POD test for examples/root/lib/TestObject.pm ok 907 - POD test for examples/root/lib/TestInterface.pm ok 908 - POD test for Bio/Matrix/PSM/IO/meme.pm ok 909 - POD test for Bio/Matrix/PSM/IO/psiblast.pm ok 910 - POD test for Bio/Matrix/PSM/IO/transfac.pm ok 911 - POD test for Bio/Matrix/PSM/IO/mast.pm ok 912 - POD test for Bio/Matrix/PSM/IO/masta.pm ok 913 - POD test for Bio/Tools/SiRNA/Ruleset/saigo.pm ok 914 - POD test for Bio/Tools/SiRNA/Ruleset/tuschl.pm ok 915 - POD test for Bio/Tools/EUtilities/Info/FieldInfo.pm ok 916 - POD test for Bio/Tools/EUtilities/Info/LinkInfo.pm ok 917 - POD test for Bio/Tools/EUtilities/Query/GlobalQuery.pm ok 918 - POD test for Bio/Tools/EUtilities/Summary/ItemContainerI.pm ok 919 - POD test for Bio/Tools/EUtilities/Summary/DocSum.pm ok 920 - POD test for Bio/Tools/EUtilities/Summary/Item.pm ok 921 - POD test for Bio/Tools/EUtilities/Link/LinkSet.pm ok 922 - POD test for Bio/Tools/EUtilities/Link/UrlLink.pm ok 923 - POD test for Bio/Tools/Phylo/Molphy/Result.pm ok 924 - POD test for Bio/Tools/Phylo/Phylip/ProtDist.pm ok 925 - POD test for Bio/Tools/Phylo/PAML/Result.pm ok 926 - POD test for Bio/Tools/Phylo/PAML/ModelResult.pm ok 927 - POD test for Bio/Tools/Primer/Assessor/Base.pm ok 928 - POD test for Bio/Tools/Analysis/DNA/ESEfinder.pm ok 929 - POD test for Bio/Tools/Analysis/Protein/HNN.pm ok 930 - POD test for Bio/Tools/Analysis/Protein/Sopma.pm ok 931 - POD test for Bio/Tools/Analysis/Protein/Domcut.pm ok 932 - POD test for Bio/Tools/Analysis/Protein/Mitoprot.pm ok 933 - POD test for Bio/Tools/Analysis/Protein/NetPhos.pm ok 934 - POD test for Bio/Tools/Analysis/Protein/Scansite.pm ok 935 - POD test for Bio/Tools/Analysis/Protein/ELM.pm ok 936 - POD test for Bio/Tools/Analysis/Protein/GOR4.pm ok 937 - POD test for Bio/DB/SeqFeature/Store/LoadHelper.pm ok 938 - POD test for Bio/DB/SeqFeature/Store/bdb.pm ok 939 - POD test for Bio/DB/SeqFeature/Store/memory.pm ok 940 - POD test for Bio/DB/SeqFeature/Store/FeatureFileLoader.pm ok 941 - POD test for Bio/DB/SeqFeature/Store/berkeleydb3.pm ok 942 - POD test for Bio/DB/SeqFeature/Store/berkeleydb.pm ok 943 - POD test for Bio/DB/SeqFeature/Store/Loader.pm ok 944 - POD test for Bio/DB/SeqFeature/Store/GFF3Loader.pm ok 945 - POD test for Bio/DB/SeqFeature/Store/GFF2Loader.pm ok 946 - POD test for Bio/DB/GFF/Aggregator/processed_transcript.pm ok 947 - POD test for Bio/DB/GFF/Aggregator/alignment.pm ok 948 - POD test for Bio/DB/GFF/Aggregator/ucsc_acembly.pm ok 949 - POD test for Bio/DB/GFF/Aggregator/ucsc_unigene.pm ok 950 - POD test for Bio/DB/GFF/Aggregator/none.pm ok 951 - POD test for Bio/DB/GFF/Aggregator/clone.pm ok 952 - POD test for Bio/DB/GFF/Aggregator/ucsc_ensgene.pm ok 953 - POD test for Bio/DB/GFF/Aggregator/ucsc_sanger22.pm ok 954 - POD test for Bio/DB/GFF/Aggregator/orf.pm ok 955 - POD test for Bio/DB/GFF/Aggregator/so_transcript.pm ok 956 - POD test for Bio/DB/GFF/Aggregator/ucsc_twinscan.pm ok 957 - POD test for Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm ok 958 - POD test for Bio/DB/GFF/Aggregator/match.pm ok 959 - POD test for Bio/DB/GFF/Aggregator/gene.pm ok 960 - POD test for Bio/DB/GFF/Aggregator/transcript.pm ok 961 - POD test for Bio/DB/GFF/Aggregator/coding.pm ok 962 - POD test for Bio/DB/GFF/Aggregator/ucsc_softberry.pm ok 963 - POD test for Bio/DB/GFF/Aggregator/ucsc_refgene.pm ok 964 - POD test for Bio/DB/GFF/Aggregator/ucsc_genscan.pm ok 965 - POD test for Bio/DB/GFF/Adaptor/memory.pm ok 966 - POD test for Bio/DB/GFF/Adaptor/biofetch.pm ok 967 - POD test for Bio/DB/GFF/Adaptor/biofetch_oracle.pm ok 968 - POD test for Bio/DB/GFF/Adaptor/dbi.pm ok 969 - POD test for Bio/DB/GFF/Adaptor/berkeleydb.pm ok 970 - POD test for Bio/DB/GFF/Adaptor/ace.pm ok 971 - POD test for Bio/DB/GFF/Util/Rearrange.pm ok 972 - POD test for Bio/DB/GFF/Util/Binning.pm ok 973 - POD test for Bio/DB/Flat/BDB/fasta.pm ok 974 - POD test for Bio/DB/Flat/BDB/genbank.pm ok 975 - POD test for Bio/DB/Flat/BDB/swiss.pm ok 976 - POD test for Bio/DB/Flat/BDB/embl.pm ok 977 - POD test for Bio/Structure/SecStr/STRIDE/Res.pm ok 978 - POD test for Bio/Structure/SecStr/DSSP/Res.pm ok 979 - POD test for examples/root/lib/Bio/PrimarySeq.pm ok 980 - POD test for examples/root/lib/Bio/Seq.pm ok 981 - POD test for examples/root/lib/Bio/SeqI.pm ok 982 - POD test for examples/root/lib/Bio/PrimarySeqI.pm ok 983 - POD test for Bio/DB/SeqFeature/Store/DBI/Iterator.pm ok 984 - POD test for Bio/DB/SeqFeature/Store/DBI/SQLite.pm ok 985 - POD test for Bio/DB/SeqFeature/Store/DBI/mysql.pm ok 986 - POD test for Bio/DB/SeqFeature/Store/DBI/Pg.pm ok 987 - POD test for Bio/DB/GFF/Adaptor/dbi/pg.pm ok 988 - POD test for Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm ok 989 - POD test for Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm ok 990 - POD test for Bio/DB/GFF/Adaptor/dbi/oracle.pm ok 991 - POD test for Bio/DB/GFF/Adaptor/dbi/caching_handle.pm ok 992 - POD test for Bio/DB/GFF/Adaptor/dbi/mysql.pm ok 993 - POD test for Bio/DB/GFF/Adaptor/dbi/iterator.pm ok 994 - POD test for Bio/DB/GFF/Adaptor/dbi/oracleace.pm ok 995 - POD test for Bio/DB/GFF/Adaptor/dbi/mysqlace.pm ok 996 - POD test for Bio/DB/GFF/Adaptor/dbi/pg_fts.pm ok 997 - POD test for Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm ok 998 - POD test for Bio/DB/GFF/Adaptor/memory/feature_serializer.pm ok 999 - POD test for Bio/DB/GFF/Adaptor/memory/iterator.pm Dubious, test returned 5 (wstat 1280, 0x500) Failed 5/999 subtests t/PopGen/Coalescent.t ........................ 1..13 ok 1 - use Bio::PopGen::Simulation::Coalescent; ok 2 - use Bio::PopGen::Statistics; ok 3 - use Bio::TreeIO; ok 4 ok 5 ok 6 - pi ok 7 - theta ok 8 - tajimaD ok 9 - all the mutations should be polymorphic (by definition) ok 10 - fu and li D ok 11 - fu and li D* ok 12 - fu and li F ok 13 - fu and li F ok t/PopGen/HtSNP.t ............................. 1..8 ok 1 - use Bio::PopGen::HtSNP; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok t/PopGen/MK.t ................................ 1..46 ok 1 - use Bio::AlignIO; ok 2 - use Bio::PopGen::Statistics; ok 3 - use Bio::PopGen::Utilities; ok 4 - The object isa Bio::PopGen::Statistics ok 5 - The object isa Bio::SimpleAlign ok 6 - The object isa Bio::PopGen::Population ok 7 - Marker Names ok 8 - Number of Inds ok 9 - number of ingroup sequences ok 10 - number of outgroup1 sequences ok 11 - number of outgroup2 sequences ok 12 - NSpoly ok 13 - NSfixed ok 14 - Spoly ok 15 - Sfixed ok 16 - McDonald Kreitman ok 17 - NSpoly ok 18 - NSfixed ok 19 - Spoly ok 20 - Sfixed ok 21 - McDonald Kreitman ok 22 - NSpoly ok 23 - NSfixed ok 24 - Spoly ok 25 - Sfixed ok 26 - The object isa Bio::SimpleAlign ok 27 - The object isa Bio::PopGen::Population ok 28 - Marker Names ok 29 - Number of Inds ok 30 - number of ingroup sequences ok 31 - number of outgroup1 sequences ok 32 - number of outgroup2 sequences ok 33 - NSpoly ok 34 - NSfixed ok 35 - Spoly ok 36 - Sfixed ok 37 - McDonald Kreitman ok 38 - NSpoly ok 39 - NSfixed ok 40 - Spoly ok 41 - Sfixed ok 42 - McDonald Kreitman ok 43 - NSpoly ok 44 - NSfixed ok 45 - Spoly ok 46 - Sfixed ok t/PopGen/PopGen.t ............................ 1..100 ok 1 - use Bio::PopGen::Individual; ok 2 - use Bio::PopGen::Genotype; ok 3 - use Bio::PopGen::Population; ok 4 - use Bio::PopGen::IO; ok 5 - use Bio::PopGen::PopStats; ok 6 - use Bio::AlignIO; ok 7 - use Bio::PopGen::Statistics; ok 8 - use Bio::PopGen::Utilities; 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 - mrsa,mssa aflp1 ok 38 - all pops, aflp1 ok 39 - mrsa,envpop aflp1,aflp2 ok 40 ok 41 ok 42 ok 43 - mssa,mrsa all_bands ok 44 - env,mssa mkr1 ok 45 - env,mssa,mrsa all bands ok 46 - env,mssa,mrsa mkr2 ok 47 - mrsa,nc all_bands 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 - Pi on 3-allele data ok 100 - Theta on 3-allele data ok t/PopGen/PopGenSims.t ........................ 1..23 ok 1 - use Bio::PopGen::Simulation::GeneticDrift; ok 2 - Allele freqs should sum to 1 ok 3 - Allele freqs should sum to 1 ok 4 - Allele freqs should sum to 1 ok 5 - Allele freqs should sum to 1 ok 6 - Allele freqs should sum to 1 ok 7 - Allele freqs should sum to 1 ok 8 - Allele freqs should sum to 1 ok 9 - Allele freqs should sum to 1 ok 10 - Allele freqs should sum to 1 ok 11 - Allele freqs should sum to 1 ok 12 ok 13 - All frequencies should be <= 1 ok 14 - Allele freqs should sum to 1 ok 15 - Allele freqs should sum to 1 ok 16 - Allele freqs should sum to 1 ok 17 - Allele freqs should sum to 1 ok 18 - Allele freqs should sum to 1 ok 19 - Allele freqs should sum to 1 ok 20 - Allele freqs should sum to 1 ok 21 - Allele freqs should sum to 1 ok 22 - Allele freqs should sum to 1 ok 23 - Allele freqs should sum to 1 ok t/PopGen/TagHaplotype.t ...................... 1..3 ok 1 - use Bio::PopGen::TagHaplotype; ok 2 ok 3 ok t/RemoteDB/BioFetch.t ........................ skipped: Network tests have not been requested t/RemoteDB/CUTG.t ............................ 1..37 ok 1 - use Bio::DB::CUTG; ok 2 - use Bio::CodonUsage::Table; ok 3 - use Bio::CodonUsage::IO; ok 4 - use Bio::SeqIO; ok 5 - use Bio::Tools::SeqStats; 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 # skip Network tests have not been requested ok 25 # skip Network tests have not been requested ok 26 # skip Network tests have not been requested ok 27 # skip Network tests have not been requested ok 28 # skip Network tests have not been requested ok 29 # skip Network tests have not been requested ok 30 # skip Network tests have not been requested ok 31 # skip Network tests have not been requested ok 32 # skip Network tests have not been requested ok 33 # skip Network tests have not been requested ok 34 # skip Network tests have not been requested ok 35 # skip Network tests have not been requested ok 36 # skip Network tests have not been requested ok 37 # skip Network tests have not been requested ok t/RemoteDB/EMBL.t ............................ skipped: Network tests have not been requested t/RemoteDB/EUtilities.t ...................... skipped: Network tests have not been requested t/RemoteDB/EntrezGene.t ...................... skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed t/RemoteDB/GenBank.t ......................... skipped: Network tests have not been requested t/RemoteDB/GenPept.t ......................... skipped: Network tests have not been requested t/RemoteDB/HIV/HIV.t ......................... 1..30 ok 1 - use Bio::DB::HIV; ok 2 - use Bio::DB::WebDBSeqI; ok 3 - use Bio::DB::HIV::HIVAnnotProcessor; ok 4 - The object isa Bio::DB::HIV ok 5 - The object isa Bio::Root::Root ok 6 - Bio::DB::HIV->can(...) ok 7 - Bio::DB::HIV->can(...) ok 8 - Bio::DB::HIV->can(...) ok 9 - lanl_base set in default object ok 10 - map_db set in default object ok 11 - make_search_if set in default object ok 12 - search_ set in default object ok 13 - url_base_address set in default object ok 14 - default sequence request format (fasta) ok 15 - sorry till implemented ok 16 - sorry till implemented ok 17 - HIVQuery type exception check ok 18 # skip Network tests have not been requested ok 19 # skip Network tests have not been requested ok 20 # skip Network tests have not been requested ok 21 # skip Network tests have not been requested ok 22 # skip Network tests have not been requested ok 23 # skip Network tests have not been requested ok 24 # skip Network tests have not been requested ok 25 # skip Network tests have not been requested ok 26 # skip Network tests have not been requested ok 27 # skip Network tests have not been requested ok 28 # skip Network tests have not been requested ok 29 # skip Network tests have not been requested ok 30 # skip Network tests have not been requested ok t/RemoteDB/HIV/HIVAnnotProcessor.t ........... 1..11 ok 1 - use Bio::Seq; ok 2 - use Bio::SeqIO; ok 3 - use Bio::DB::HIV::HIVAnnotProcessor; ok 4 - The object isa Bio::DB::HIV::HIVAnnotProcessor ok 5 - The object isa Bio::Root::Root ok 6 - Bio::DB::HIV::HIVAnnotProcessor->can(...) ok 7 - Bio::DB::HIV::HIVAnnotProcessor->can('hiv_query') ok 8 - bad type set exception ok 9 - attach stream ok 10 - write exception ok 11 - access stream ok t/RemoteDB/HIV/HIVQuery.t .................... 1..41 ok 1 - use Bio::DB::Query::HIVQuery; ok 2 - use Bio::DB::HIV; ok 3 - use Bio::Annotation::Collection; ok 4 - use Bio::Annotation::Comment; ok 5 - use Bio::Annotation::Reference; ok 6 - use Bio::DB::HIV::HIVQueryHelper; ok 7 - The object isa Bio::DB::Query::HIVQuery ok 8 - The object isa Bio::Root::Root ok 9 - Bio::DB::Query::HIVQuery->can(...) ok 10 - Bio::DB::Query::HIVQuery->can(...) ok 11 - Bio::DB::Query::HIVQuery->can(...) ok 12 - _map_db_uri set in default object ok 13 - _make_search_if_uri set in default object ok 14 - _search_uri set in default object ok 15 - _schema_file set in default object ok 16 - _run_option set in default object ok 17 - annotations container available ok 18 - query syntax check 1 ok 19 - query syntax check 2 ok 20 - query syntax check 3 ok 21 - query parser check ok 22 - multiquery parse check ok 23 - use HTML::Parser; ok 24 - help html to file ok 25 - help html parsed ok 26 - bad field exception check ok 27 - bad match data exception check ok 28 - empty field not ok exception check ok 29 - uninitialized schema exception check ok 30 - query not run (level 1) warning check ok 31 - query not run (level 2) warning check ok 32 # skip Network tests have not been requested ok 33 # skip Network tests have not been requested ok 34 # skip Network tests have not been requested ok 35 # skip Network tests have not been requested ok 36 # skip Network tests have not been requested ok 37 # skip Network tests have not been requested ok 38 # skip Network tests have not been requested ok 39 # skip Network tests have not been requested ok 40 # skip Network tests have not been requested ok 41 # skip Network tests have not been requested ok t/RemoteDB/HIV/HIVQueryHelper.t .............. 1..40 ok 1 - use Bio::DB::HIV::HIVQueryHelper; ok 2 - The object isa HIVSchema ok 3 - The object isa QRY ok 4 - The object isa R ok 5 - The object isa Q ok 6 - schema load ok 7 - HIVSchema->can(...) ok 8 - fields complete ok 9 - tables complete ok 10 - aliases complete ok 11 ok 12 - test field syntax ok ok 13 - test field syntax ok ok 14 - test alias by field name ok 15 - correct primary key for SequenceEntry ok 16 - correct number of foreign keys for AUthor ok 17 - correct foreign table for au_pub_id ok 18 - correct annotation key hash ok 19 - QRY->can(...) ok 20 - R->can(...) ok 21 - Q->can(...) ok 22 - null QRY ok 23 - null R (request object) ok 24 - null Q (atomic query object) ok 25 - R obj create and init (1) ok 26 - R obj create and init (2) ok 27 - R::In ok 28 - !R::In ok 29 - R::Eq ok 30 - QRY obj create and init (1) ok 31 - QRY obj create and init (2) ok 32 - QRY obj create and init (3) ok 33 - QRY overload | ok 34 - QRY overload & ok 35 - QRY nontrivial & ok 36 - parse: ('odds bodkins', a)[X] m[Y] u[Z] OR 'b'[X] {A B [C] [D]} ok 37 - make: 2 queries returned ok 38 - {annotation fields} parsed correctly ok 39 - parse: ('odds bodkins', a)[X] m[Y] u[Z] AND b[X] {A B [C] [D]} ok 40 - above query is null ok t/RemoteDB/MeSH.t ............................ skipped: Network tests have not been requested t/RemoteDB/Query/GenBank.t ................... skipped: Network tests have not been requested t/RemoteDB/RefSeq.t .......................... 1..16 ok 1 - use Bio::DB::RefSeq; ok 2 - use Bio::DB::GenBank; ok 3 - use Bio::DB::EMBL; ok 4 ok 5 ok 6 ok 7 # skip Network tests have not been requested ok 8 # skip Network tests have not been requested ok 9 # skip Network tests have not been requested ok 10 # skip Network tests have not been requested ok 11 # skip Network tests have not been requested ok 12 # skip Network tests have not been requested ok 13 # skip Network tests have not been requested ok 14 # skip Network tests have not been requested ok 15 # skip Network tests have not been requested ok 16 # skip Network tests have not been requested ok t/RemoteDB/SeqHound.t ........................ skipped: Network tests have not been requested t/RemoteDB/SeqRead_fail.t .................... skipped: Network tests have not been requested t/RemoteDB/SeqVersion.t ...................... 1..10 ok 1 - use Bio::DB::SeqVersion; ok 2 ok 3 # skip Network tests have not been requested ok 4 # skip Network tests have not been requested ok 5 # skip Network tests have not been requested ok 6 # skip Network tests have not been requested ok 7 # skip Network tests have not been requested ok 8 # skip Network tests have not been requested ok 9 # skip Network tests have not been requested ok 10 # skip Network tests have not been requested ok t/RemoteDB/SwissProt.t ....................... skipped: Network tests have not been requested t/RemoteDB/Taxonomy.t ........................ 1..103 ok 1 - use Bio::DB::Taxonomy; ok 2 - use Bio::Tree::Tree; ok 3 ok 4 ok 5 # skip Network tests have not been requested ok 6 # skip Network tests have not been requested ok 7 # skip Network tests have not been requested ok 8 # skip Network tests have not been requested ok 9 # skip Network tests have not been requested ok 10 # skip Network tests have not been requested ok 11 # skip Network tests have not been requested ok 12 # skip Network tests have not been requested ok 13 # skip Network tests have not been requested ok 14 # skip Network tests have not been requested ok 15 # skip Network tests have not been requested ok 16 # skip Network tests have not been requested ok 17 # skip Network tests have not been requested ok 18 # skip Network tests have not been requested ok 19 # skip Network tests have not been requested ok 20 # skip Network tests have not been requested ok 21 # skip Network tests have not been requested ok 22 # skip Network tests have not been requested ok 23 # skip Network tests have not been requested ok 24 # skip Network tests have not been requested ok 25 # skip Network tests have not been requested ok 26 # skip Network tests have not been requested ok 27 # skip Network tests have not been requested ok 28 # skip Network tests have not been requested ok 29 # skip Network tests have not been requested ok 30 # skip Network tests have not been requested ok 31 # skip Network tests have not been requested ok 32 # skip Network tests have not been requested ok 33 # skip Network tests have not been requested ok 34 # skip Network tests have not been requested ok 35 # skip Network tests have not been requested ok 36 # skip Network tests have not been requested ok 37 # skip Network tests have not been requested ok 38 # skip Network tests have not been requested ok 39 # skip Network tests have not been requested ok 40 # skip Network tests have not been requested ok 41 # skip Network tests have not been requested ok 42 # skip Network tests have not been requested 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 # skip Network tests have not been requested ok 91 # skip Network tests have not been requested ok 92 # skip Network tests have not been requested ok 93 # skip Network tests have not been requested ok 94 # skip Network tests have not been requested ok 95 ok 96 ok 97 ok 98 # skip Network tests have not been requested ok 99 ok 100 ok 101 ok 102 ok 103 ok t/Restriction/Analysis-refac.t ............... 1..29 ok 1 - use Bio::Restriction::IO; ok 2 - use Bio::Restriction::Analysis; ok 3 - read withrefm file ok 4 - parse withrefm file ok 5 - HindIII: nonambiguous intrasite cutter ok 6 - AarI: nonambiguous extrasite cutter ok 7 - AasI: ambiguous intrasite cutter ok 8 - BceSI: ambiguous extrasite cutter ok 9 - AjuI: cutter with central recog site ok 10 - TaqII: multi-extrasite cutter ok 11 ok 12 - HindIII plus ok 13 - HindIII minus ok 14 - AasI plus ok 15 - AasI minus ok 16 - AarI plus ok 17 - AarI minus ok 18 - BceSI plus ok 19 - BceSI minus ok 20 - AjuI plus ok 21 - AjuI minus ok 22 - TaqII plus ok 23 - TaqII minus ok 24 - build real B:R::Analysis object ok 25 - 13 fragments ok 26 - circularize ok 27 - recut ok 28 - circ: AasI # site at origin ok 29 - circ: still 13 fragments (cut site at origin) ok t/Restriction/Analysis.t ..................... 1..177 ok 1 - use Bio::Restriction::Enzyme; ok 2 - use Bio::Restriction::Enzyme::MultiCut; ok 3 - use Bio::Restriction::Enzyme::MultiSite; ok 4 - use Bio::Restriction::EnzymeCollection; ok 5 - use Bio::Restriction::Analysis; ok 6 - use Bio::SeqIO; ok 7 ok 8 - The object isa Bio::Restriction::EnzymeI ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 - The object isa Bio::PrimarySeqI 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 - bug 2179 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 - The object isa Bio::Restriction::EnzymeI ok 77 - The object isa Bio::Restriction::EnzymeI ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 - The object isa Bio::Restriction::EnzymeI ok 88 - The object isa Bio::Restriction::EnzymeI ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 - The object isa Bio::Restriction::Enzyme ok 100 ok 101 ok 102 - The object isa Bio::Restriction::Enzyme 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 - number of unique cutters ok 119 - number of RsaI fragments ok 120 - number of maximum cutters ok 121 - number of zero cutters ok 122 - number of cutters ok 123 - number of 3x cutters ok 124 - 4 MseI fragments ok 125 - 3 MseI cut sites ok 126 - expected 2 PspEI fragments ok 127 ok 128 ok 129 - expected 2 sizes for PspEI ok 130 ok 131 - not circular expected 1 fragments for MwoI as it doesnt cut ok 132 ok 133 ok 134 - number of RsaI fragments ok 135 - 3 circular MseI fragments ok 136 - 3 circular MseI cut sites ok 137 - number for AciI a non-palindromic enzyme ok 138 - 1 fragment for MwoI as it cuts across the circ point ok 139 ok 140 ok 141 ok 142 ok 143 - 7 fragments in the multiple digest ok 144 - 7 positions in the multiple digest ok 145 - 7 sizes in the multiple digest ok 146 ok 147 - expected 9 cuts for HindI ok 148 - expect 9 fragment maps for HindI ok 149 - sequence for GT ok 150 - start at 40 ok 151 - end at 41 ok 152 - sequence for GGATTAAAAAAAGAGT ok 153 - start at 42 ok 154 - end at 57 ok 155 - sequence for GTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGT ok 156 - start at 58 ok 157 - end at 92 ok 158 - sequence for GAGTAAATTAAAATTTTATTGACTTAGGTCA ok 159 - start at 93 ok 160 - end at 123 ok 161 - sequence for CTAAATACTTTAACCAATATAGGCATAGCGCA ok 162 - start at 124 ok 163 - end at 155 ok 164 - sequence for CAGACAGATAAAAATTACAGAGTACA ok 165 - start at 156 ok 166 - end at 181 ok 167 - sequence for CAACATCCATGAAACGCATTAGCA ok 168 - start at 182 ok 169 - end at 205 ok 170 - sequence for CCA ok 171 - start at 206 ok 172 - end at 208 ok 173 - sequence for CCAGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGT ok 174 - start at 209 ok 175 - end at 39 ok 176 ok 177 - bug 2139 ok t/Restriction/Gel.t .......................... 1..9 ok 1 - use Bio::PrimarySeq; ok 2 - use Bio::Restriction::Analysis; ok 3 - use Bio::Tools::Gel; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok t/Restriction/IO.t ........................... 1..18 ok 1 - use Bio::Restriction::IO; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 not ok 8 # TODO writing to a file doesn't seem to work? prints to STDOUT! # Failed (TODO) test at t/Restriction/IO.t line 31. ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 # skip Network tests have not been requested ok 17 # skip Network tests have not been requested ok 18 # skip Network tests have not been requested ok t/Root/Exception.t ........................... 1..8 ok 1 - use TestObject; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok t/Root/RootI.t ............................... 1..56 ok 1 - use Bio::Root::Root; ok 2 - use Bio::Seq; ok 3 ok 4 - The object isa Bio::Root::RootI ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 - simple ok 16 - simple ok 17 - warns for versions below current version 1.006001 ok 18 - warns for versions below current version 1.006001 ok 19 - throws for versions above 1.006001 ok 20 - throws for versions above 1.006001 ok 21 - throws for versions equal to 1.006001 ok 22 - simple ok 23 - simple ok 24 - warns for versions below current version 1.006001 ok 25 - warns for versions below current version 1.006001 ok 26 - throws for versions above 1.006001 ok 27 - throws for versions above 1.006001 ok 28 - arg callable since method was created ok 29 - mal-formed arg callable since method was created with good name ok 30 - Bio::Foo2->can('t3') ok 31 - Methods don't pollute original Bio::Root::Root namespace ok 32 - Bio::Foo2->can('test_4') ok 33 - Methods don't pollute original Bio::Root::Root namespace ok 34 - Bio::Foo3->can('t5') ok 35 - arg not in method list not created ok 36 - Bio::Foo3->can('t5') ok 37 - Methods don't pollute original Bio::Root::Root namespace ok 38 - verbose was set correctly ok 39 - synonym was set correctly ok 40 - real method of synonym was set correctly ok 41 - mal-formed arg correctly resolved to created method ok 42 - synonym of set method was set correctly ok 43 - Bio::Foo4->can('t7') ok 44 - Methods don't pollute original Bio::Root::Root namespace ok 45 - Bio::Foo4->can('test7') ok 46 - Methods don't pollute original Bio::Root::Root namespace ok 47 - Bio::Foo4->can('test_8') ok 48 - Methods don't pollute original Bio::Root::Root namespace ok 49 - Bio::Foo4->can('t8') ok 50 - Methods don't pollute original Bio::Root::Root namespace ok 51 - must use proper versioning scheme ok 52 - warns for versions >= 1.006001 ok 53 - warns for versions >= 1.006001 ok 54 - throws for versions >= 1.006001 ok 55 - throws for versions >= 1.006001 ok 56 - No warnings/exceptions below 1.006001 ok t/Root/RootIO.t .............................. 1..31 ok 1 - use Bio::Root::IO; ok 2 ok 3 - throw() ok 4 - throw() verbose(-1) ok 5 - warn() ok 6 - throw() verbose(1) ok 7 - stack_trace() ok 8 - set verbosity to 1 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - filename, read ok 15 ok 16 - filename, write ok 17 ok 18 ok 19 ok 20 - handle, read ok 21 ok 22 - handle, write ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 # skip Network tests have not been requested ok 31 # skip Network tests have not been requested ok t/Root/Storable.t ............................ 1..35 ok 1 - use Bio::Root::Storable; 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/Root/Tempfile.t ............................ 1..18 ok 1 - use Bio::Root::IO; ok 2 ok 3 - The object isa Bio::Root::IO ok 4 ok 5 ok 6 - auto UNLINK => 1 ok 7 ok 8 ok 9 - tempfile deleted ok 10 ok 11 - UNLINK => 0 ok 12 ok 13 ok 14 ok 15 - tempfile suffix ok 16 ok 17 - tempfile() in scalar context ok 18 ok --------------------- WARNING --------------------- MSG: find_exe: Multiple paths to 'gzip' found. Using /bin/gzip. --------------------------------------------------- --------------------- WARNING --------------------- MSG: find_exe: Multiple paths to 'gzip' found. Using /bin/gzip. --------------------------------------------------- --------------------- WARNING --------------------- MSG: find_exe: Multiple paths to 'gunzip' found. Using /bin/gunzip. --------------------------------------------------- --------------------- WARNING --------------------- MSG: find_exe: Multiple paths to 'gzip' found. Using /bin/gzip. --------------------------------------------------- --------------------- WARNING --------------------- MSG: find_exe: Multiple paths to 'gunzip' found. Using /bin/gunzip. --------------------------------------------------- t/Root/Utilities.t ........................... 1..56 ok 1 - use Bio::Root::Utilities; ok 2 - The object isa Bio::Root::Utilities 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 - file_date() ok 38 - unix (\n or 012 or ^J) ok 39 - date format ok 40 - date format ok 41 - date format ok 42 - date format ok 43 - date format 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 t/SearchDist.t ............................... skipped: The optional module Bio::Ext::Align (or dependencies thereof) was not installed t/SearchIO/CigarString.t ..................... 1..4 ok 1 - use Bio::SearchIO; ok 2 ok 3 ok 4 ok t/SearchIO/SearchIO.t ........................ 1..19 ok 1 - use Bio::SearchIO; ok 2 - blastxml for f.blastxml ok 3 - fasta for f.fy ok 4 - exonerate for f.exonerate ok 5 - blast for f.tblx ok 6 - fasta for f.fx ok 7 - fasta for f.osearch ok 8 - blast for filename.bls ok 9 - exonerate for f.exon ok 10 - fasta for f.SSEARCH.m9 ok 11 - blast for filename.blast ok 12 - fasta for f.m9 ok 13 - blast for f.blx ok 14 - blastxml for f.xml ok 15 - fasta for f.fasta ok 16 - fasta for f.fa ok 17 - blast for fast.bls ok 18 - fasta for f.ssearch ok 19 - fasta for f.psearch ok t/SearchIO/SimilarityPair.t .................. 1..12 ok 1 - use Bio::SearchIO; ok 2 - use Bio::SeqIO; ok 3 ok 4 - The object isa Bio::SeqI ok 5 ok 6 - The object isa Bio::SearchIO ok 7 ok 8 - The object isa Bio::Search::Hit::HitI ok 9 ok 10 - The object isa Bio::SeqFeatureI ok 11 ok 12 ok Use of qw(...) as parentheses is deprecated at t/SearchIO/Tiling.t line 301. Use of qw(...) as parentheses is deprecated at Bio/Search/Tiling/MapTiling.pm line 191. make: *** wait: No child processes. Stop. make: *** Waiting for unfinished jobs.... make: *** wait: No child processes. Stop. Timeout (max run time is 300s) /home/fly1600/ap1600/bin/perl-static killed by signal 15.