PATH=/opt/SUNWspro/bin:/usr/local/bin:/opt/csw/bin:/usr/ccs/bin:/usr/bin:/usr/sbin
Start 2011-05-23T08:55:46
ActivePerl-818 CPAN-1.9402
Going to read '/export/home/fly818/var/cpan/Metadata'
  Database was generated on Sun, 22 May 2011 20:33:56 GMT
Running make for C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz
Checksum for /net/nas/data/cpan/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz ok
Will not use Archive::Tar, need 1.00
BioPerl-1.6.901
BioPerl-1.6.901/AUTHORS
BioPerl-1.6.901/BioPerl.pm
BioPerl-1.6.901/BUGS
BioPerl-1.6.901/Build.PL
BioPerl-1.6.901/Changes
BioPerl-1.6.901/DEPENDENCIES
BioPerl-1.6.901/DEPRECATED
BioPerl-1.6.901/INSTALL
BioPerl-1.6.901/INSTALL.SKIP
BioPerl-1.6.901/INSTALL.WIN
BioPerl-1.6.901/LICENSE
BioPerl-1.6.901/MANIFEST
BioPerl-1.6.901/META.json
BioPerl-1.6.901/META.yml
BioPerl-1.6.901/README
BioPerl-1.6.901/Bio
BioPerl-1.6.901/Bio/AlignIO.pm
BioPerl-1.6.901/Bio/AnalysisI.pm
BioPerl-1.6.901/Bio/AnalysisParserI.pm
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BioPerl-1.6.901/Bio/Coordinate/Graph.pm
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BioPerl-1.6.901/doc
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BioPerl-1.6.901/doc/README
BioPerl-1.6.901/doc/Deobfuscator
BioPerl-1.6.901/doc/Deobfuscator/Build.PL
BioPerl-1.6.901/doc/Deobfuscator/Changes
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BioPerl-1.6.901/doc/Deobfuscator/LICENSE
BioPerl-1.6.901/doc/Deobfuscator/Makefile.PL
BioPerl-1.6.901/doc/Deobfuscator/MANIFEST
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BioPerl-1.6.901/doc/Deobfuscator/bin
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BioPerl-1.6.901/doc/Deobfuscator/cgi-bin/deob_interface.cgi
BioPerl-1.6.901/doc/Deobfuscator/lib
BioPerl-1.6.901/doc/Deobfuscator/lib/Deobfuscator.pm
BioPerl-1.6.901/doc/Deobfuscator/t
BioPerl-1.6.901/doc/Deobfuscator/t/00.load.t
BioPerl-1.6.901/doc/Deobfuscator/t/pod.t
BioPerl-1.6.901/examples
BioPerl-1.6.901/examples/bioperl.pl
BioPerl-1.6.901/examples/generate_random_seq.pl
BioPerl-1.6.901/examples/longorf.pl
BioPerl-1.6.901/examples/make_primers.pl
BioPerl-1.6.901/examples/rev_and_trans.pl
BioPerl-1.6.901/examples/revcom_dir.pl
BioPerl-1.6.901/examples/subsequence.cgi
BioPerl-1.6.901/examples/align
BioPerl-1.6.901/examples/align/align_on_codons.pl
BioPerl-1.6.901/examples/align/aligntutorial.pl
BioPerl-1.6.901/examples/align/clustalw.pl
BioPerl-1.6.901/examples/align/simplealign.pl
BioPerl-1.6.901/examples/biblio
BioPerl-1.6.901/examples/biblio/biblio-eutils-example.pl
BioPerl-1.6.901/examples/biblio/biblio-soap-example.pl
BioPerl-1.6.901/examples/biblio/biblio_soap.pl
BioPerl-1.6.901/examples/Bio-DB-GFF
BioPerl-1.6.901/examples/Bio-DB-GFF/load_ucsc.pl
BioPerl-1.6.901/examples/cluster
BioPerl-1.6.901/examples/cluster/dbsnp.pl
BioPerl-1.6.901/examples/contributed
BioPerl-1.6.901/examples/contributed/nmrpdb_parse.pl
BioPerl-1.6.901/examples/contributed/prosite2perl.pl
BioPerl-1.6.901/examples/contributed/rebase2list.pl
BioPerl-1.6.901/examples/db
BioPerl-1.6.901/examples/db/dbfetch
BioPerl-1.6.901/examples/db/est_tissue_query.pl
BioPerl-1.6.901/examples/db/gb2features.pl
BioPerl-1.6.901/examples/db/get_seqs.pl
BioPerl-1.6.901/examples/db/getGenBank.pl
BioPerl-1.6.901/examples/db/rfetch.pl
BioPerl-1.6.901/examples/db/use_registry.pl
BioPerl-1.6.901/examples/liveseq
BioPerl-1.6.901/examples/liveseq/change_gene.pl
BioPerl-1.6.901/examples/popgen
BioPerl-1.6.901/examples/popgen/parse_calc_stats.pl
BioPerl-1.6.901/examples/quality
BioPerl-1.6.901/examples/quality/svgtrace.pl
BioPerl-1.6.901/examples/root
BioPerl-1.6.901/examples/root/exceptions1.pl
BioPerl-1.6.901/examples/root/exceptions2.pl
BioPerl-1.6.901/examples/root/exceptions3.pl
BioPerl-1.6.901/examples/root/exceptions4.pl
BioPerl-1.6.901/examples/root/README
BioPerl-1.6.901/examples/root/lib
BioPerl-1.6.901/examples/root/lib/TestInterface.pm
BioPerl-1.6.901/examples/root/lib/TestObject.pm
BioPerl-1.6.901/examples/searchio
BioPerl-1.6.901/examples/searchio/blast_example.pl
BioPerl-1.6.901/examples/searchio/custom_writer.pl
BioPerl-1.6.901/examples/searchio/hitwriter.pl
BioPerl-1.6.901/examples/searchio/hspwriter.pl
BioPerl-1.6.901/examples/searchio/htmlwriter.pl
BioPerl-1.6.901/examples/searchio/psiblast_features.pl
BioPerl-1.6.901/examples/searchio/psiblast_iterations.pl
BioPerl-1.6.901/examples/searchio/rawwriter.pl
BioPerl-1.6.901/examples/searchio/resultwriter.pl
BioPerl-1.6.901/examples/searchio/waba2gff.pl
BioPerl-1.6.901/examples/searchio/waba2gff3.pl
BioPerl-1.6.901/examples/sirna
BioPerl-1.6.901/examples/sirna/rnai_finder.cgi
BioPerl-1.6.901/examples/sirna/TAG
BioPerl-1.6.901/examples/structure
BioPerl-1.6.901/examples/structure/structure-io.pl
BioPerl-1.6.901/examples/tk
BioPerl-1.6.901/examples/tk/gsequence.pl
BioPerl-1.6.901/examples/tk/hitdisplay.pl
BioPerl-1.6.901/examples/tools
BioPerl-1.6.901/examples/tools/extract_genes.pl
BioPerl-1.6.901/examples/tools/gb_to_gff.pl
BioPerl-1.6.901/examples/tools/gff2ps.pl
BioPerl-1.6.901/examples/tools/parse_codeml.pl
BioPerl-1.6.901/examples/tools/psw.pl
BioPerl-1.6.901/examples/tools/reverse-translate.pl
BioPerl-1.6.901/examples/tools/run_genscan.pl
BioPerl-1.6.901/examples/tools/run_primer3.pl
BioPerl-1.6.901/examples/tools/seq_pattern.pl
BioPerl-1.6.901/examples/tools/standaloneblast.pl
BioPerl-1.6.901/examples/tree
BioPerl-1.6.901/examples/tree/paup2phylip.pl
BioPerl-1.6.901/ide
BioPerl-1.6.901/ide/bioperl.komodo
BioPerl-1.6.901/ide/bioperl-mode
BioPerl-1.6.901/ide/bioperl-mode/README
BioPerl-1.6.901/ide/bioperl-mode/dist
BioPerl-1.6.901/ide/bioperl-mode/dist/bioperl-mode-xemacs.tar
BioPerl-1.6.901/ide/bioperl-mode/dist/bioperl-mode-xemacs.tar.md5
BioPerl-1.6.901/ide/bioperl-mode/dist/bioperl-mode.tar
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BioPerl-1.6.901/t/Ontology/OntologyEngine.t
BioPerl-1.6.901/t/Ontology/OntologyStore.t
BioPerl-1.6.901/t/Ontology/Relationship.t
BioPerl-1.6.901/t/Ontology/RelationshipType.t
BioPerl-1.6.901/t/Ontology/Term.t
BioPerl-1.6.901/t/Ontology/IO
BioPerl-1.6.901/t/Ontology/IO/go.t
BioPerl-1.6.901/t/Ontology/IO/interpro.t
BioPerl-1.6.901/t/Ontology/IO/obo.t
BioPerl-1.6.901/t/Phenotype
BioPerl-1.6.901/t/Phenotype/Correlate.t
BioPerl-1.6.901/t/Phenotype/Measure.t
BioPerl-1.6.901/t/Phenotype/MeSH.t
BioPerl-1.6.901/t/Phenotype/MiniMIMentry.t
BioPerl-1.6.901/t/Phenotype/OMIMentry.t
BioPerl-1.6.901/t/Phenotype/OMIMentryAllelicVariant.t
BioPerl-1.6.901/t/Phenotype/OMIMparser.t
BioPerl-1.6.901/t/Phenotype/Phenotype.t
BioPerl-1.6.901/t/PopGen
BioPerl-1.6.901/t/PopGen/Coalescent.t
BioPerl-1.6.901/t/PopGen/HtSNP.t
BioPerl-1.6.901/t/PopGen/MK.t
BioPerl-1.6.901/t/PopGen/PopGen.t
BioPerl-1.6.901/t/PopGen/PopGenSims.t
BioPerl-1.6.901/t/PopGen/TagHaplotype.t
BioPerl-1.6.901/t/RemoteDB
BioPerl-1.6.901/t/RemoteDB/BioFetch.t
BioPerl-1.6.901/t/RemoteDB/CUTG.t
BioPerl-1.6.901/t/RemoteDB/EMBL.t
BioPerl-1.6.901/t/RemoteDB/EntrezGene.t
BioPerl-1.6.901/t/RemoteDB/EUtilities.t
BioPerl-1.6.901/t/RemoteDB/GenBank.t
BioPerl-1.6.901/t/RemoteDB/GenPept.t
BioPerl-1.6.901/t/RemoteDB/MeSH.t
BioPerl-1.6.901/t/RemoteDB/RefSeq.t
BioPerl-1.6.901/t/RemoteDB/SeqHound.t
BioPerl-1.6.901/t/RemoteDB/SeqRead_fail.t
BioPerl-1.6.901/t/RemoteDB/SeqVersion.t
BioPerl-1.6.901/t/RemoteDB/SwissProt.t
BioPerl-1.6.901/t/RemoteDB/Taxonomy.t
BioPerl-1.6.901/t/RemoteDB/HIV
BioPerl-1.6.901/t/RemoteDB/HIV/HIV.t
BioPerl-1.6.901/t/RemoteDB/HIV/HIVAnnotProcessor.t
BioPerl-1.6.901/t/RemoteDB/HIV/HIVQuery.t
BioPerl-1.6.901/t/RemoteDB/HIV/HIVQueryHelper.t
BioPerl-1.6.901/t/RemoteDB/Query
BioPerl-1.6.901/t/RemoteDB/Query/GenBank.t
BioPerl-1.6.901/t/Restriction
BioPerl-1.6.901/t/Restriction/Analysis-refac.t
BioPerl-1.6.901/t/Restriction/Analysis.t
BioPerl-1.6.901/t/Restriction/Gel.t
BioPerl-1.6.901/t/Restriction/IO.t
BioPerl-1.6.901/t/Root
BioPerl-1.6.901/t/Root/Exception.t
BioPerl-1.6.901/t/Root/HTTPget.t
BioPerl-1.6.901/t/Root/RootI.t
BioPerl-1.6.901/t/Root/RootIO.t
BioPerl-1.6.901/t/Root/Storable.t
BioPerl-1.6.901/t/Root/Tempfile.t
BioPerl-1.6.901/t/Root/Utilities.t
BioPerl-1.6.901/t/SearchIO
BioPerl-1.6.901/t/SearchIO/axt.t
BioPerl-1.6.901/t/SearchIO/blast.t
BioPerl-1.6.901/t/SearchIO/blast_pull.t
BioPerl-1.6.901/t/SearchIO/blasttable.t
BioPerl-1.6.901/t/SearchIO/blastxml.t
BioPerl-1.6.901/t/SearchIO/CigarString.t
BioPerl-1.6.901/t/SearchIO/cross_match.t
BioPerl-1.6.901/t/SearchIO/erpin.t
BioPerl-1.6.901/t/SearchIO/exonerate.t
BioPerl-1.6.901/t/SearchIO/fasta.t
BioPerl-1.6.901/t/SearchIO/gmap_f9.t
BioPerl-1.6.901/t/SearchIO/hmmer.t
BioPerl-1.6.901/t/SearchIO/hmmer_pull.t
BioPerl-1.6.901/t/SearchIO/infernal.t
BioPerl-1.6.901/t/SearchIO/megablast.t
BioPerl-1.6.901/t/SearchIO/psl.t
BioPerl-1.6.901/t/SearchIO/rnamotif.t
BioPerl-1.6.901/t/SearchIO/SearchIO.t
BioPerl-1.6.901/t/SearchIO/sim4.t
BioPerl-1.6.901/t/SearchIO/SimilarityPair.t
BioPerl-1.6.901/t/SearchIO/Tiling.t
BioPerl-1.6.901/t/SearchIO/waba.t
BioPerl-1.6.901/t/SearchIO/wise.t
BioPerl-1.6.901/t/SearchIO/Writer
BioPerl-1.6.901/t/SearchIO/Writer/GbrowseGFF.t
BioPerl-1.6.901/t/SearchIO/Writer/HitTableWriter.t
BioPerl-1.6.901/t/SearchIO/Writer/HSPTableWriter.t
BioPerl-1.6.901/t/SearchIO/Writer/HTMLWriter.t
BioPerl-1.6.901/t/SearchIO/Writer/TextWriter.t
BioPerl-1.6.901/t/Seq
BioPerl-1.6.901/t/Seq/DBLink.t
BioPerl-1.6.901/t/Seq/EncodedSeq.t
BioPerl-1.6.901/t/Seq/LargeLocatableSeq.t
BioPerl-1.6.901/t/Seq/LargePSeq.t
BioPerl-1.6.901/t/Seq/LocatableSeq.t
BioPerl-1.6.901/t/Seq/MetaSeq.t
BioPerl-1.6.901/t/Seq/PrimaryQual.t
BioPerl-1.6.901/t/Seq/PrimarySeq.t
BioPerl-1.6.901/t/Seq/PrimedSeq.t
BioPerl-1.6.901/t/Seq/Quality.t
BioPerl-1.6.901/t/Seq/Seq.t
BioPerl-1.6.901/t/Seq/WithQuality.t
BioPerl-1.6.901/t/SeqFeature
BioPerl-1.6.901/t/SeqFeature/Clone.t
BioPerl-1.6.901/t/SeqFeature/FeatureIO.t
BioPerl-1.6.901/t/SeqFeature/Location.t
BioPerl-1.6.901/t/SeqFeature/LocationFactory.t
BioPerl-1.6.901/t/SeqFeature/Primer.t
BioPerl-1.6.901/t/SeqFeature/Range.t
BioPerl-1.6.901/t/SeqFeature/RangeI.t
BioPerl-1.6.901/t/SeqFeature/SeqAnalysisParser.t
BioPerl-1.6.901/t/SeqFeature/SeqFeatAnnotated.t
BioPerl-1.6.901/t/SeqFeature/SeqFeatCollection.t
BioPerl-1.6.901/t/SeqFeature/SeqFeature.t
BioPerl-1.6.901/t/SeqFeature/SeqFeaturePrimer.t
BioPerl-1.6.901/t/SeqFeature/Unflattener.t
BioPerl-1.6.901/t/SeqFeature/Unflattener2.t
BioPerl-1.6.901/t/SeqIO
BioPerl-1.6.901/t/SeqIO/abi.t
BioPerl-1.6.901/t/SeqIO/ace.t
BioPerl-1.6.901/t/SeqIO/agave.t
BioPerl-1.6.901/t/SeqIO/alf.t
BioPerl-1.6.901/t/SeqIO/asciitree.t
BioPerl-1.6.901/t/SeqIO/bsml.t
BioPerl-1.6.901/t/SeqIO/bsml_sax.t
BioPerl-1.6.901/t/SeqIO/chadoxml.t
BioPerl-1.6.901/t/SeqIO/chaos.t
BioPerl-1.6.901/t/SeqIO/chaosxml.t
BioPerl-1.6.901/t/SeqIO/ctf.t
BioPerl-1.6.901/t/SeqIO/embl.t
BioPerl-1.6.901/t/SeqIO/entrezgene.t
BioPerl-1.6.901/t/SeqIO/excel.t
BioPerl-1.6.901/t/SeqIO/exp.t
BioPerl-1.6.901/t/SeqIO/fasta.t
BioPerl-1.6.901/t/SeqIO/fastq.t
BioPerl-1.6.901/t/SeqIO/flybase_chadoxml.t
BioPerl-1.6.901/t/SeqIO/game.t
BioPerl-1.6.901/t/SeqIO/gbxml.t
BioPerl-1.6.901/t/SeqIO/gcg.t
BioPerl-1.6.901/t/SeqIO/genbank.t
BioPerl-1.6.901/t/SeqIO/Handler.t
BioPerl-1.6.901/t/SeqIO/interpro.t
BioPerl-1.6.901/t/SeqIO/kegg.t
BioPerl-1.6.901/t/SeqIO/largefasta.t
BioPerl-1.6.901/t/SeqIO/lasergene.t
BioPerl-1.6.901/t/SeqIO/locuslink.t
BioPerl-1.6.901/t/SeqIO/mbsout.t
BioPerl-1.6.901/t/SeqIO/metafasta.t
BioPerl-1.6.901/t/SeqIO/msout.t
BioPerl-1.6.901/t/SeqIO/MultiFile.t
BioPerl-1.6.901/t/SeqIO/Multiple_fasta.t
BioPerl-1.6.901/t/SeqIO/nexml.t
BioPerl-1.6.901/t/SeqIO/phd.t
BioPerl-1.6.901/t/SeqIO/pir.t
BioPerl-1.6.901/t/SeqIO/pln.t
BioPerl-1.6.901/t/SeqIO/qual.t
BioPerl-1.6.901/t/SeqIO/raw.t
BioPerl-1.6.901/t/SeqIO/scf.t
BioPerl-1.6.901/t/SeqIO/SeqBuilder.t
BioPerl-1.6.901/t/SeqIO/SeqIO.t
BioPerl-1.6.901/t/SeqIO/seqxml.t
BioPerl-1.6.901/t/SeqIO/Splicedseq.t
BioPerl-1.6.901/t/SeqIO/strider.t
BioPerl-1.6.901/t/SeqIO/swiss.t
BioPerl-1.6.901/t/SeqIO/tab.t
BioPerl-1.6.901/t/SeqIO/table.t
BioPerl-1.6.901/t/SeqIO/tigr.t
BioPerl-1.6.901/t/SeqIO/tigrxml.t
BioPerl-1.6.901/t/SeqIO/tinyseq.t
BioPerl-1.6.901/t/SeqIO/ztr.t
BioPerl-1.6.901/t/SeqTools
BioPerl-1.6.901/t/SeqTools/Backtranslate.t
BioPerl-1.6.901/t/SeqTools/CodonTable.t
BioPerl-1.6.901/t/SeqTools/ECnumber.t
BioPerl-1.6.901/t/SeqTools/GuessSeqFormat.t
BioPerl-1.6.901/t/SeqTools/OddCodes.t
BioPerl-1.6.901/t/SeqTools/SeqPattern.t
BioPerl-1.6.901/t/SeqTools/SeqStats.t
BioPerl-1.6.901/t/SeqTools/SeqUtils.t
BioPerl-1.6.901/t/SeqTools/SeqWords.t
BioPerl-1.6.901/t/Structure
BioPerl-1.6.901/t/Structure/IO.t
BioPerl-1.6.901/t/Structure/Structure.t
BioPerl-1.6.901/t/Tools
BioPerl-1.6.901/t/Tools/ePCR.t
BioPerl-1.6.901/t/Tools/Est2Genome.t
BioPerl-1.6.901/t/Tools/FootPrinter.t
BioPerl-1.6.901/t/Tools/Geneid.t
BioPerl-1.6.901/t/Tools/Genewise.t
BioPerl-1.6.901/t/Tools/Genomewise.t
BioPerl-1.6.901/t/Tools/Genpred.t
BioPerl-1.6.901/t/Tools/GFF.t
BioPerl-1.6.901/t/Tools/GuessSeqFormat.t
BioPerl-1.6.901/t/Tools/Hmmer.t
BioPerl-1.6.901/t/Tools/IUPAC.t
BioPerl-1.6.901/t/Tools/Lucy.t
BioPerl-1.6.901/t/Tools/Match.t
BioPerl-1.6.901/t/Tools/pICalculator.t
BioPerl-1.6.901/t/Tools/Primer3.t
BioPerl-1.6.901/t/Tools/Promoterwise.t
BioPerl-1.6.901/t/Tools/Pseudowise.t
BioPerl-1.6.901/t/Tools/QRNA.t
BioPerl-1.6.901/t/Tools/RandDistFunctions.t
BioPerl-1.6.901/t/Tools/RepeatMasker.t
BioPerl-1.6.901/t/Tools/rnamotif.t
BioPerl-1.6.901/t/Tools/Seg.t
BioPerl-1.6.901/t/Tools/Sigcleave.t
BioPerl-1.6.901/t/Tools/Signalp.t
BioPerl-1.6.901/t/Tools/Sim4.t
BioPerl-1.6.901/t/Tools/SiRNA.t
BioPerl-1.6.901/t/Tools/TandemRepeatsFinder.t
BioPerl-1.6.901/t/Tools/TargetP.t
BioPerl-1.6.901/t/Tools/Tmhmm.t
BioPerl-1.6.901/t/Tools/tRNAscanSE.t
BioPerl-1.6.901/t/Tools/Alignment
BioPerl-1.6.901/t/Tools/Alignment/Consed.t
BioPerl-1.6.901/t/Tools/Analysis
BioPerl-1.6.901/t/Tools/Analysis/DNA
BioPerl-1.6.901/t/Tools/Analysis/DNA/ESEfinder.t
BioPerl-1.6.901/t/Tools/Analysis/Protein
BioPerl-1.6.901/t/Tools/Analysis/Protein/Domcut.t
BioPerl-1.6.901/t/Tools/Analysis/Protein/ELM.t
BioPerl-1.6.901/t/Tools/Analysis/Protein/GOR4.t
BioPerl-1.6.901/t/Tools/Analysis/Protein/HNN.t
BioPerl-1.6.901/t/Tools/Analysis/Protein/Mitoprot.t
BioPerl-1.6.901/t/Tools/Analysis/Protein/NetPhos.t
BioPerl-1.6.901/t/Tools/Analysis/Protein/Scansite.t
BioPerl-1.6.901/t/Tools/Analysis/Protein/Sopma.t
BioPerl-1.6.901/t/Tools/EMBOSS
BioPerl-1.6.901/t/Tools/EMBOSS/Palindrome.t
BioPerl-1.6.901/t/Tools/EUtilities
BioPerl-1.6.901/t/Tools/EUtilities/egquery.t
BioPerl-1.6.901/t/Tools/EUtilities/einfo.t
BioPerl-1.6.901/t/Tools/EUtilities/elink_acheck.t
BioPerl-1.6.901/t/Tools/EUtilities/elink_lcheck.t
BioPerl-1.6.901/t/Tools/EUtilities/elink_llinks.t
BioPerl-1.6.901/t/Tools/EUtilities/elink_ncheck.t
BioPerl-1.6.901/t/Tools/EUtilities/elink_neighbor.t
BioPerl-1.6.901/t/Tools/EUtilities/elink_neighbor_history.t
BioPerl-1.6.901/t/Tools/EUtilities/elink_scores.t
BioPerl-1.6.901/t/Tools/EUtilities/epost.t
BioPerl-1.6.901/t/Tools/EUtilities/esearch.t
BioPerl-1.6.901/t/Tools/EUtilities/espell.t
BioPerl-1.6.901/t/Tools/EUtilities/esummary.t
BioPerl-1.6.901/t/Tools/EUtilities/EUtilParameters.t
BioPerl-1.6.901/t/Tools/Phylo
BioPerl-1.6.901/t/Tools/Phylo/Gerp.t
BioPerl-1.6.901/t/Tools/Phylo/Molphy.t
BioPerl-1.6.901/t/Tools/Phylo/PAML.t
BioPerl-1.6.901/t/Tools/Phylo/Phylip
BioPerl-1.6.901/t/Tools/Phylo/Phylip/ProtDist.t
BioPerl-1.6.901/t/Tools/Run
BioPerl-1.6.901/t/Tools/Run/Dummy.pm
BioPerl-1.6.901/t/Tools/Run/RemoteBlast.t
BioPerl-1.6.901/t/Tools/Run/RemoteBlast_rpsblast.t
BioPerl-1.6.901/t/Tools/Run/StandAloneBlast.t
BioPerl-1.6.901/t/Tools/Run/WBCommandExts.t
BioPerl-1.6.901/t/Tools/Run/WrapperBase.t
BioPerl-1.6.901/t/Tools/Run/Dummy
BioPerl-1.6.901/t/Tools/Run/Dummy/Config.pm
BioPerl-1.6.901/t/Tools/Signalp
BioPerl-1.6.901/t/Tools/Signalp/ExtendedSignalp.t
BioPerl-1.6.901/t/Tools/Spidey
BioPerl-1.6.901/t/Tools/Spidey/Spidey.t
BioPerl-1.6.901/t/Tree
BioPerl-1.6.901/t/Tree/Compatible.t
BioPerl-1.6.901/t/Tree/Node.t
BioPerl-1.6.901/t/Tree/RandomTreeFactory.t
BioPerl-1.6.901/t/Tree/Tree.t
BioPerl-1.6.901/t/Tree/TreeIO.t
BioPerl-1.6.901/t/Tree/TreeStatistics.t
BioPerl-1.6.901/t/Tree/PhyloNetwork
BioPerl-1.6.901/t/Tree/PhyloNetwork/Factory.t
BioPerl-1.6.901/t/Tree/PhyloNetwork/GraphViz.t
BioPerl-1.6.901/t/Tree/PhyloNetwork/MuVector.t
BioPerl-1.6.901/t/Tree/PhyloNetwork/PhyloNetwork.t
BioPerl-1.6.901/t/Tree/PhyloNetwork/RandomFactory.t
BioPerl-1.6.901/t/Tree/PhyloNetwork/TreeFactory.t
BioPerl-1.6.901/t/Tree/TreeIO
BioPerl-1.6.901/t/Tree/TreeIO/lintree.t
BioPerl-1.6.901/t/Tree/TreeIO/newick.t
BioPerl-1.6.901/t/Tree/TreeIO/nexml.t
BioPerl-1.6.901/t/Tree/TreeIO/nexus.t
BioPerl-1.6.901/t/Tree/TreeIO/nhx.t
BioPerl-1.6.901/t/Tree/TreeIO/phyloxml.t
BioPerl-1.6.901/t/Tree/TreeIO/svggraph.t
BioPerl-1.6.901/t/Tree/TreeIO/tabtree.t
BioPerl-1.6.901/t/Variation
BioPerl-1.6.901/t/Variation/AAChange.t
BioPerl-1.6.901/t/Variation/AAReverseMutate.t
BioPerl-1.6.901/t/Variation/Allele.t
BioPerl-1.6.901/t/Variation/DNAMutation.t
BioPerl-1.6.901/t/Variation/RNAChange.t
BioPerl-1.6.901/t/Variation/SeqDiff.t
BioPerl-1.6.901/t/Variation/SNP.t
BioPerl-1.6.901/t/Variation/Variation_IO.t

  CPAN.pm: Going to build C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz

>>> /export/home/fly818/bin/perl Build.PL 
could not find ParserDetails.ini in /export/home/fly818/var/megalib/XML/SAX
Checking prerequisites...
  requires:
    !  DB_File is not installed
  recommends:
    *  GD is not installed
    *  GraphViz is not installed

Checking optional features...
DB_File Tests.........disabled
  requires:
    ! DB_File is not installed
EntrezGene............disabled
  requires:
    ! Bio::ASN1::EntrezGene is not installed
Pg Tests..............disabled
  requires:
    ! DBD::Pg is not installed

ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the versions
of the modules indicated above before proceeding with this installation

############################# WARNING #############################

Bio::ASN1::EntrezGene not found. This is an *optional* module;
however, because it has a circular dependency with BioPerl we do not
include it on our list of recommended modules.

If you require EntrezGene functionality, you can install
Bio::ASN1::EntrezGene after BioPerl has finished installing.  

############################# WARNING #############################

Do you want to run the Bio::DB::GFF or Bio::DB::SeqFeature::Store live database tests? y/n [n]   - will not run the BioDBGFF or BioDBSeqFeature live database tests

Install [a]ll BioPerl scripts, [n]one, or choose groups [i]nteractively? [a]   - will install all scripts

Do you want to run tests that require connection to servers across the internet
(likely to cause some failures)? y/n [n]   - will not run internet-requiring tests
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'BioPerl' version '1.006901'
---- Unsatisfied dependencies detected during ----
----      CJFIELDS/BioPerl-1.6.901.tar.gz     ----
    DB_File [requires]
Running Build test
  Delayed until after prerequisites
Running test for module 'DB_File'

______________________ D i s t r o P r e f s ______________________
                           DB_File.yml[0]                           
Running make for P/PM/PMQS/DB_File-1.822.tar.gz
Disabled via prefs file '/export/home/fly818/etc/distroprefs/DB_File.yml' doc 0
  PMQS/DB_File-1.822.tar.gz
  [disabled] -- NA Disabled via prefs file '/export/home/fly818/etc/distroprefs/DB_File.yml' doc 0
Running Build for C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz
  Has already been unwrapped into directory /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE

  CPAN.pm: Going to build C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz

Warning: Prerequisite 'DB_File => 0' for 'CJFIELDS/BioPerl-1.6.901.tar.gz' failed when processing 'PMQS/DB_File-1.822.tar.gz' with 'unwrapped => NO Disabled via prefs file '/export/home/fly818/etc/distroprefs/DB_File.yml' doc 0'. Continuing, but chances to succeed are limited.
>>> ./Build
Building BioPerl
  CJFIELDS/BioPerl-1.6.901.tar.gz
  ./Build -- OK
Running Build test
>>> ./Build test verbose=1
Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS
Changing sharpbang in blib/script/bp_sreformat.PLS to /export/home/fly818/bin/perl
Deleting blib/script/bp_sreformat.PLS.bak
Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS
Changing sharpbang in blib/script/tree2pag.PLS to /export/home/fly818/bin/perl
Deleting blib/script/tree2pag.PLS.bak
Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS
Changing sharpbang in blib/script/meta_gff.PLS to /export/home/fly818/bin/perl
Deleting blib/script/meta_gff.PLS.bak
Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS
Changing sharpbang in blib/script/heterogeneity_test.PLS to /export/home/fly818/bin/perl
Deleting blib/script/heterogeneity_test.PLS.bak
Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS
Changing sharpbang in blib/script/flanks.PLS to /export/home/fly818/bin/perl
Deleting blib/script/flanks.PLS.bak
Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS
Changing sharpbang in blib/script/biogetseq.PLS to /export/home/fly818/bin/perl
Deleting blib/script/biogetseq.PLS.bak
Copying scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS
Changing sharpbang in blib/script/bp_seqfeature_delete.PLS to /export/home/fly818/bin/perl
Deleting blib/script/bp_seqfeature_delete.PLS.bak
Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS
Changing sharpbang in blib/script/fastam9_to_table.PLS to /export/home/fly818/bin/perl
Deleting blib/script/fastam9_to_table.PLS.bak
Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS
Changing sharpbang in blib/script/seq_length.PLS to /export/home/fly818/bin/perl
Deleting blib/script/seq_length.PLS.bak
Copying scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS
Changing sharpbang in blib/script/bp_seqfeature_load.PLS to /export/home/fly818/bin/perl
Deleting blib/script/bp_seqfeature_load.PLS.bak
Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS
Changing sharpbang in blib/script/genbank2gff.PLS to /export/home/fly818/bin/perl
Deleting blib/script/genbank2gff.PLS.bak
Copying scripts/das/das_server.pl -> blib/script/das_server.pl
Changing sharpbang in blib/script/das_server.pl to /export/home/fly818/bin/perl
Deleting blib/script/das_server.pl.bak
Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS
Changing sharpbang in blib/script/taxid4species.PLS to /export/home/fly818/bin/perl
Deleting blib/script/taxid4species.PLS.bak
Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS
Changing sharpbang in blib/script/blast2tree.PLS to /export/home/fly818/bin/perl
Deleting blib/script/blast2tree.PLS.bak
Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS
Changing sharpbang in blib/script/query_entrez_taxa.PLS to /export/home/fly818/bin/perl
Deleting blib/script/query_entrez_taxa.PLS.bak
Copying scripts/utilities/bp_netinstall.PLS -> blib/script/bp_netinstall.PLS
Changing sharpbang in blib/script/bp_netinstall.PLS to /export/home/fly818/bin/perl
Deleting blib/script/bp_netinstall.PLS.bak
Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS
Changing sharpbang in blib/script/search2alnblocks.PLS to /export/home/fly818/bin/perl
Deleting blib/script/search2alnblocks.PLS.bak
Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS
Changing sharpbang in blib/script/taxonomy2tree.PLS to /export/home/fly818/bin/perl
Deleting blib/script/taxonomy2tree.PLS.bak
Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS
Changing sharpbang in blib/script/download_query_genbank.PLS to /export/home/fly818/bin/perl
Deleting blib/script/download_query_genbank.PLS.bak
Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS
Changing sharpbang in blib/script/mask_by_search.PLS to /export/home/fly818/bin/perl
Deleting blib/script/mask_by_search.PLS.bak
Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS
Changing sharpbang in blib/script/gccalc.PLS to /export/home/fly818/bin/perl
Deleting blib/script/gccalc.PLS.bak
Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS
Changing sharpbang in blib/script/composite_LD.PLS to /export/home/fly818/bin/perl
Deleting blib/script/composite_LD.PLS.bak
Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS
Changing sharpbang in blib/script/aacomp.PLS to /export/home/fly818/bin/perl
Deleting blib/script/aacomp.PLS.bak
Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS
Changing sharpbang in blib/script/process_wormbase.PLS to /export/home/fly818/bin/perl
Deleting blib/script/process_wormbase.PLS.bak
Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS
Changing sharpbang in blib/script/local_taxonomydb_query.PLS to /export/home/fly818/bin/perl
Deleting blib/script/local_taxonomydb_query.PLS.bak
Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS
Changing sharpbang in blib/script/biblio.PLS to /export/home/fly818/bin/perl
Deleting blib/script/biblio.PLS.bak
Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS
Changing sharpbang in blib/script/seqretsplit.PLS to /export/home/fly818/bin/perl
Deleting blib/script/seqretsplit.PLS.bak
Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS
Changing sharpbang in blib/script/genbank2gff3.PLS to /export/home/fly818/bin/perl
Deleting blib/script/genbank2gff3.PLS.bak
Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS
Changing sharpbang in blib/script/search2BSML.PLS to /export/home/fly818/bin/perl
Deleting blib/script/search2BSML.PLS.bak
Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS
Changing sharpbang in blib/script/seqconvert.PLS to /export/home/fly818/bin/perl
Deleting blib/script/seqconvert.PLS.bak
Copying scripts/DB-HIV/hivq.PLS -> blib/script/hivq.PLS
Changing sharpbang in blib/script/hivq.PLS to /export/home/fly818/bin/perl
Deleting blib/script/hivq.PLS.bak
Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS
Changing sharpbang in blib/script/parse_hmmsearch.PLS to /export/home/fly818/bin/perl
Deleting blib/script/parse_hmmsearch.PLS.bak
Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS
Changing sharpbang in blib/script/bp_seqret.PLS to /export/home/fly818/bin/perl
Deleting blib/script/bp_seqret.PLS.bak
Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS
Changing sharpbang in blib/script/filter_search.PLS to /export/home/fly818/bin/perl
Deleting blib/script/filter_search.PLS.bak
Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS
Changing sharpbang in blib/script/nexus2nh.PLS to /export/home/fly818/bin/perl
Deleting blib/script/nexus2nh.PLS.bak
Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS
Changing sharpbang in blib/script/generate_histogram.PLS to /export/home/fly818/bin/perl
Deleting blib/script/generate_histogram.PLS.bak
Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS
Changing sharpbang in blib/script/load_gff.PLS to /export/home/fly818/bin/perl
Deleting blib/script/load_gff.PLS.bak
Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS
Changing sharpbang in blib/script/split_seq.PLS to /export/home/fly818/bin/perl
Deleting blib/script/split_seq.PLS.bak
Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS
Changing sharpbang in blib/script/bp_fetch.PLS to /export/home/fly818/bin/perl
Deleting blib/script/bp_fetch.PLS.bak
Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS
Changing sharpbang in blib/script/mutate.PLS to /export/home/fly818/bin/perl
Deleting blib/script/mutate.PLS.bak
Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS
Changing sharpbang in blib/script/process_sgd.PLS to /export/home/fly818/bin/perl
Deleting blib/script/process_sgd.PLS.bak
Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS
Changing sharpbang in blib/script/bp_index.PLS to /export/home/fly818/bin/perl
Deleting blib/script/bp_index.PLS.bak
Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS
Changing sharpbang in blib/script/dbsplit.PLS to /export/home/fly818/bin/perl
Deleting blib/script/dbsplit.PLS.bak
Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS
Changing sharpbang in blib/script/oligo_count.PLS to /export/home/fly818/bin/perl
Deleting blib/script/oligo_count.PLS.bak
Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS
Changing sharpbang in blib/script/process_gadfly.PLS to /export/home/fly818/bin/perl
Deleting blib/script/process_gadfly.PLS.bak
Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS
Changing sharpbang in blib/script/hmmer_to_table.PLS to /export/home/fly818/bin/perl
Deleting blib/script/hmmer_to_table.PLS.bak
Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS
Changing sharpbang in blib/script/biofetch_genbank_proxy.PLS to /export/home/fly818/bin/perl
Deleting blib/script/biofetch_genbank_proxy.PLS.bak
Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS
Changing sharpbang in blib/script/extract_feature_seq.PLS to /export/home/fly818/bin/perl
Deleting blib/script/extract_feature_seq.PLS.bak
Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS
Changing sharpbang in blib/script/bulk_load_gff.PLS to /export/home/fly818/bin/perl
Deleting blib/script/bulk_load_gff.PLS.bak
Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS
Changing sharpbang in blib/script/search2gff.PLS to /export/home/fly818/bin/perl
Deleting blib/script/search2gff.PLS.bak
Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS
Changing sharpbang in blib/script/make_mrna_protein.PLS to /export/home/fly818/bin/perl
Deleting blib/script/make_mrna_protein.PLS.bak
Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS
Changing sharpbang in blib/script/unflatten_seq.PLS to /export/home/fly818/bin/perl
Deleting blib/script/unflatten_seq.PLS.bak
Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS
Changing sharpbang in blib/script/search2tribe.PLS to /export/home/fly818/bin/perl
Deleting blib/script/search2tribe.PLS.bak
Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS
Changing sharpbang in blib/script/bioflat_index.PLS to /export/home/fly818/bin/perl
Deleting blib/script/bioflat_index.PLS.bak
Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS
Changing sharpbang in blib/script/pairwise_kaks.PLS to /export/home/fly818/bin/perl
Deleting blib/script/pairwise_kaks.PLS.bak
Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS
Changing sharpbang in blib/script/fast_load_gff.PLS to /export/home/fly818/bin/perl
Deleting blib/script/fast_load_gff.PLS.bak
Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS
Changing sharpbang in blib/script/chaos_plot.PLS to /export/home/fly818/bin/perl
Deleting blib/script/chaos_plot.PLS.bak
Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS
Changing sharpbang in blib/script/bp_mrtrans.PLS to /export/home/fly818/bin/perl
Deleting blib/script/bp_mrtrans.PLS.bak
Copying scripts/Bio-DB-EUtilities/einfo.PLS -> blib/script/einfo.PLS
Changing sharpbang in blib/script/einfo.PLS to /export/home/fly818/bin/perl
Deleting blib/script/einfo.PLS.bak
Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS
Changing sharpbang in blib/script/bp_nrdb.PLS to /export/home/fly818/bin/perl
Deleting blib/script/bp_nrdb.PLS.bak
Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS
Changing sharpbang in blib/script/classify_hits_kingdom.PLS to /export/home/fly818/bin/perl
Deleting blib/script/classify_hits_kingdom.PLS.bak
Copying scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS
Copying scripts/utilities/revtrans-motif.PLS -> blib/script/revtrans-motif.PLS
Changing sharpbang in blib/script/revtrans-motif.PLS to /export/home/fly818/bin/perl
Deleting blib/script/revtrans-motif.PLS.bak
Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS
Changing sharpbang in blib/script/remote_blast.PLS to /export/home/fly818/bin/perl
Deleting blib/script/remote_blast.PLS.bak
Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS
Changing sharpbang in blib/script/search2table.PLS to /export/home/fly818/bin/perl
Deleting blib/script/search2table.PLS.bak
Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS
Changing sharpbang in blib/script/translate_seq.PLS to /export/home/fly818/bin/perl
Deleting blib/script/translate_seq.PLS.bak
t/Align/AlignStats.t ......................... 
1..45
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 44 - Warn if seqs don't overlap
ok 45
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/Graphics.t ........................... skipped: The optional module GD (or dependencies thereof) was not installed
t/Align/SimpleAlign.t ........................ 
1..199
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 (align)
ok 37 - overall_percentage_identity (short)
ok 38 - overall_percentage_identity (long)
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:472
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:195
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1146
# STACK: try{} block t/Align/SimpleAlign.t:421
# STACK: Sub::Uplevel::uplevel /export/home/fly818/var/megalib/Sub/Uplevel.pm:150
# STACK: Test::Exception::_try_as_caller /export/home/fly818/var/megalib/Test/Exception.pm:136
# STACK: Test::Exception::lives_ok /export/home/fly818/var/megalib/Test/Exception.pm:297
# 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:472
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:195
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1146
# STACK: try{} block t/Align/SimpleAlign.t:421
# STACK: Sub::Uplevel::uplevel /export/home/fly818/var/megalib/Sub/Uplevel.pm:150
# STACK: Test::Exception::_try_as_caller /export/home/fly818/var/megalib/Test/Exception.pm:136
# STACK: Test::Exception::lives_ok /export/home/fly818/var/megalib/Test/Exception.pm:297
# 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:472
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:195
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1146
# STACK: try{} block t/Align/SimpleAlign.t:421
# STACK: Sub::Uplevel::uplevel /export/home/fly818/var/megalib/Sub/Uplevel.pm:150
# STACK: Test::Exception::_try_as_caller /export/home/fly818/var/megalib/Test/Exception.pm:136
# STACK: Test::Exception::lives_ok /export/home/fly818/var/megalib/Test/Exception.pm:297
# 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:472
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:195
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1146
# STACK: try{} block t/Align/SimpleAlign.t:421
# STACK: Sub::Uplevel::uplevel /export/home/fly818/var/megalib/Sub/Uplevel.pm:150
# STACK: Test::Exception::_try_as_caller /export/home/fly818/var/megalib/Test/Exception.pm:136
# STACK: Test::Exception::lives_ok /export/home/fly818/var/megalib/Test/Exception.pm:297
# 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
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 - The object isa Bio::SimpleAlign
ok 195 - consensus string looks ok
ok 196 - looks like correct unmasked alignment (from clustalw)
ok 197 - looks like correct masked alignment (from clustalw)
ok 198
ok 199 - 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

#   Failed test 'use Bio::AlignIO::nexml;'
#   at t/AlignIO/nexml.t line 7.
#     Tried to use 'Bio::AlignIO::nexml'.
#     Error:  Can't locate Bio/Phylo/Factory.pm in @INC (@INC contains: ../.. /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE/blib/lib /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE/blib/arch /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE /export/home/fly818/var/megalib /export/home/fly818/ap818/site/lib /export/home/fly818/ap818/lib .) at /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE/blib/lib/Bio/Nexml/Factory.pm line 90.
# BEGIN failed--compilation aborted at /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE/blib/lib/Bio/Nexml/Factory.pm line 90.
# Compilation failed in require at /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE/blib/lib/Bio/AlignIO/nexml.pm line 65.
# BEGIN failed--compilation aborted at /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE/blib/lib/Bio/AlignIO/nexml.pm line 65.
# Compilation failed in require at (eval 35) line 2.
# BEGIN failed--compilation aborted at (eval 35) line 2.
# WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support
# Looks like you failed 1 test of 125.
t/AlignIO/nexml.t ............................ 
1..125
not ok 1 - use Bio::AlignIO::nexml;
ok 2 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 3 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 4 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 5 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 6 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 7 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 8 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 9 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 10 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 11 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 12 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 13 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 14 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 15 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 16 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 17 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 18 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 19 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 20 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 21 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 22 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 23 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 24 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 25 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 26 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 27 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 28 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 29 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 30 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 31 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 32 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 33 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 34 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 35 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 36 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 37 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 38 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 39 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 40 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 41 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 42 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 43 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 44 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 45 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 46 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 47 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 48 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 49 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 50 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 51 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 52 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 53 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 54 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 55 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 56 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 57 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 58 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 59 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 60 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 61 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 62 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 63 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 64 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 65 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 66 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 67 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 68 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 69 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 70 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 71 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 72 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 73 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 74 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 75 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 76 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 77 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 78 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 79 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 80 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 81 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 82 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 83 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 84 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 85 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 86 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 87 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 88 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 89 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 90 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 91 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 92 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 93 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 94 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 95 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 96 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 97 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 98 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 99 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 100 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 101 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 102 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 103 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 104 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 105 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 106 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 107 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 108 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 109 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 110 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 111 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 112 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 113 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 114 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 115 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 116 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 117 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 118 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 119 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 120 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 121 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 122 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 123 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 124 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 125 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/125 subtests 
	(less 124 skipped subtests: 0 okay)
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..16
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
ok 7
ok 8
not ok 9 # TODO problems with default strand, length?

#   Failed (TODO) test at t/AlignIO/phylip.t line 44.
#          got: undef
#     expected: '0'
not ok 10 # TODO problems with default strand, length?

#   Failed (TODO) test at t/AlignIO/phylip.t line 45.
#          got: '50'
#     expected: '47'
ok 11 - The object isa Bio::Align::AlignI
ok 12
ok 13 - The object isa Bio::AlignIO
ok 14 - The object isa Bio::Align::AlignI
ok 15
ok 16
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..84
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
ok 35 - The object isa Bio::Seq::MetaI
ok 36 - Rfam meta data
ok 37 - Rfam meta data
ok 38 - The object isa Bio::AlignIO
ok 39
ok 40 - The object isa Bio::Align::AlignI
ok 41
ok 42
ok 43
ok 44
ok 45 - The object isa Bio::Annotation::SimpleValue
ok 46 - Pfam annotation
ok 47
ok 48 - The object isa Bio::Align::AlignI
ok 49
ok 50
ok 51
ok 52
ok 53 - The object isa Bio::Align::AlignI
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59 - The object isa Bio::Seq::MetaI
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 aln meta data
ok 66 - Pfam seq meta data
ok 67 - Pfam seq meta data
ok 68 - Pfam seq meta data
ok 69 - Pfam seq meta data
ok 70
ok 71 - The object isa Bio::SeqFeatureI
ok 72 - The object isa Bio::Seq::Meta
ok 73 - The object isa Bio::AnnotationI
ok 74 - The object isa Bio::Annotation::DBLink
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok
t/AlignIO/xmfa.t ............................. 
1..30
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 start
ok 5 - xmfa input test for end
ok 6 - xmfa strand test
ok 7 - xmfa input test for id
ok 8 - xmfa input test for id
ok 9 - xmfa input test 
ok 10 - xmfa input test for start
ok 11 - xmfa input test for end
ok 12 - xmfa strand test
ok 13 - xmfa input test for id
ok 14 - xmfa input test for id
ok 15 - xmfa input test 
ok 16 - xmfa input test for start
ok 17 - xmfa input test for end
ok 18 - xmfa strand test
ok 19 - xmfa input test for id
ok 20 - xmfa input test for id
ok 21 - xmfa alignment score
ok 22 - The object isa Bio::Align::AlignI
ok 23 - xmfa input test 
ok 24 - xmfa strand
ok 25 - xmfa input test for description
ok 26 - xmfa input test for id
ok 27 - xmfa input test for end
ok 28 - xmfa input test for end
ok 29 - xmfa alignment score
ok 30 - 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..159
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
ok 112 - add tree to AlignI
ok 113 - get seq from node id
ok 114
ok 115 - The object isa Bio::Annotation::Tree
ok 116 - The object isa Bio::AnnotationI
ok 117 - default itext
ok 118 - roundtrip
ok 119 - itext
ok 120 - spxr
ok 121 - indent
ok 122 - xml
ok 123 - The object isa Data::Stag::StagI
ok 124
ok 125 - child changes
ok 126 - The object isa Data::Stag::StagI
ok 127
ok 128 - child changes
ok 129 - The object isa Data::Stag::StagI
ok 130
ok 131 - child changes
ok 132 - child changes in parent node
ok 133 - no tags
ok 134 - before Stag node
ok 135 - after Stag node
ok 136 - both stag nodes
ok 137 - different instances
ok 138 - before TagTree
ok 139 - after TagTree
ok 140 - both stag nodes
ok 141 - different instances
ok 142 - before TagTree
ok 143 - after TagTree
ok 144 - stag nodes
ok 145 - same instance
ok 146 - before TagTree
ok 147 - after TagTree
ok 148 - stag nodes
ok 149 - different instance
ok 150 - The object isa Bio::AnnotationI
ok 151 - The object isa Data::Stag::StagI
ok 152 - child changes
ok 153 - The object isa Data::Stag::StagI
ok 154 - child changes
ok 155 - The object isa Data::Stag::StagI
ok 156 - child changes
ok 157
ok 158
ok 159 - 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
Bio::Assembly::IO: could not load tigr - for more details on supported formats please see the Assembly::IO docs
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::Assembly::IO::tigr. Can't locate DB_File.pm in @INC (@INC contains: . /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE/blib/lib /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE/blib/arch /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE /export/home/fly818/var/megalib /export/home/fly818/ap818/site/lib /export/home/fly818/ap818/lib) at Bio/SeqFeature/Collection.pm line 146.
BEGIN failed--compilation aborted at Bio/SeqFeature/Collection.pm line 146.
Compilation failed in require at Bio/Assembly/Singlet.pm line 91.
BEGIN failed--compilation aborted at Bio/Assembly/Singlet.pm line 91.
Compilation failed in require at Bio/Assembly/IO/tigr.pm line 237.
BEGIN failed--compilation aborted at Bio/Assembly/IO/tigr.pm line 237.
Compilation failed in require at Bio/Root/Root.pm line 543.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545
STACK: Bio::Assembly::IO::_load_format_module Bio/Assembly/IO.pm:296
STACK: Bio::Assembly::IO::new Bio/Assembly/IO.pm:138
STACK: t/Assembly/ContigSpectrum.t:12
-----------------------------------------------------------


#   Failed test 'The thing isa Bio::Assembly::IO'
#   at t/Assembly/ContigSpectrum.t line 16.
#     The thing isn't defined
Can't call method "next_assembly" on an undefined value at t/Assembly/ContigSpectrum.t line 17.
# Looks like you planned 236 tests but ran 3.
# Looks like you failed 1 test of 3 run.
# Looks like your test exited with 2 just after 3.
t/Assembly/ContigSpectrum.t .................. 
1..236
ok 1 - use Bio::Assembly::IO;
ok 2 - use Bio::Assembly::Tools::ContigSpectrum;
not ok 3 - The thing isa Bio::Assembly::IO
Dubious, test returned 2 (wstat 512, 0x200)
Failed 234/236 subtests 
t/Assembly/IO/bowtie.t ....................... skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Assembly/IO/sam.t .......................... skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Assembly/core.t ............................ skipped: The optional module DB_File (or dependencies thereof) was not installed
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/CoordinateBoundaryTest.t ........ 
1..174
ok 1 - use Bio::Location::Simple;
ok 2 - use Bio::Coordinate::Pair;
ok 3
ok 4 - The object isa Bio::Location::Simple
ok 5
ok 6 - The object isa Bio::Location::Simple
ok 7
ok 8 - The object isa Bio::Location::Simple
ok 9
ok 10 - The object isa Bio::Coordinate::Pair
ok 11
ok 12 - The object isa Bio::Coordinate::Pair
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 - The object isa Bio::LocationI
ok 33
ok 34 - The object isa Bio::Coordinate::Result
ok 35
ok 36 - The object isa Bio::Coordinate::Result
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 - The object isa Bio::LocationI
ok 51
ok 52 - The object isa Bio::Coordinate::Result
ok 53
ok 54 - The object isa Bio::Coordinate::Result
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::LocationI
ok 69
ok 70 - The object isa Bio::Coordinate::Result
ok 71
ok 72 - The object isa Bio::Coordinate::Result
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 - The object isa Bio::LocationI
ok 89
ok 90 - The object isa Bio::Coordinate::Result
ok 91
ok 92 - The object isa Bio::Coordinate::Result
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 - The object isa Bio::Location::Simple
ok 109
ok 110 - The object isa Bio::Location::Simple
ok 111
ok 112 - The object isa Bio::Location::Simple
ok 113
ok 114 - The object isa Bio::Coordinate::Pair
ok 115
ok 116 - The object isa Bio::Coordinate::Pair
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 - The object isa Bio::Coordinate::Result
ok 133
ok 134 - The object isa Bio::Coordinate::Result
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142 - The object isa Bio::Coordinate::Result
ok 143
ok 144 - The object isa Bio::Coordinate::Result
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152 - The object isa Bio::Coordinate::Result
ok 153
ok 154 - The object isa Bio::Coordinate::Result
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164 - The object isa Bio::Coordinate::Result
ok 165
ok 166 - The object isa Bio::Coordinate::Result
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
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/Draw/Pictogram.t ........................... 
1..6
ok 1 - use Bio::Draw::Pictogram;
ok 2 - use Bio::SeqIO;
ok 3 - use Bio::Matrix::PSM::IO;
ok 4 - The object isa Bio::Draw::Pictogram
ok 5
ok 6
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

You are loading a Bio::DB::GFF database with GFF3 formatted data.
While this will likely work fine, the Bio::DB::GFF schema does not
always faithfully capture the complexity represented in GFF3 files.
Unless you have a specific reason for using Bio::DB::GFF, we suggest
that you use a Bio::DB::SeqFeature::Store database and its corresponding
loader, bp_seqfeature_load.pl.

t/LocalDB/BioDBGFF.t ......................... 
1..275
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 # skip fetch_feature_by_gid() not implemented by this adaptor
ok 102 # skip fetch_feature_by_gid() not implemented by this adaptor
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 # skip delete_groups() not implemented by this adaptor
ok 133 # skip delete_groups() not implemented by this adaptor
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok 176
ok 177
ok 178
ok 179
ok 180
ok 181
ok 182
ok 183
ok 184
ok 185
ok 186
ok 187
ok 188
ok 189
ok 190
ok 191
ok 192
ok 193
ok 194
ok 195
ok 196
ok 197
ok 198
ok 199
ok 200
ok 201
ok 202
ok 203
ok 204
ok 205
ok 206
ok 207
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 # skip fetch_feature_by_gid() not implemented by this adaptor
ok 239 # skip fetch_feature_by_gid() not implemented by this adaptor
ok 240
ok 241
ok 242
ok 243
ok 244
ok 245
ok 246 # skip preferred groups are not supported by gff3
ok 247 # skip preferred groups are not supported by gff3
ok 248 # skip preferred groups are not supported by gff3
ok 249
ok 250
ok 251
ok 252
ok 253
ok 254
ok 255
ok 256
ok 257
ok 258
ok 259
ok 260
ok 261
ok 262
ok 263
ok 264
ok 265
ok 266
ok 267
ok 268
ok 269 # skip delete_groups() not implemented by this adaptor
ok 270 # skip delete_groups() not implemented by this adaptor
ok 271
ok 272
ok 273
ok 274
ok 275
ok
AnyDBM_File doesn't define an EXISTS method at Bio/DB/Fasta.pm line 617
# Looks like you planned 17 tests but ran 4.
# Looks like your test exited with 255 just after 4.
t/LocalDB/DBFasta.t .......................... 
1..17
ok 1
ok 2
ok 3
ok 4
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 13/17 subtests 
AnyDBM_File doesn't define an EXISTS method at Bio/DB/Qual.pm line 584
# Looks like you planned 38 tests but ran 11.
# Looks like your test exited with 255 just after 11.
t/LocalDB/DBQual.t ........................... 
1..38
ok 1 - use Bio::Root::IO;
ok 2 - use File::Copy;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 27/38 subtests 
t/LocalDB/Flat.t ............................. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/LocalDB/Index/Blast.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/Index/BlastTable.t ................. 
1..27
ok 1 - use Cwd;
ok 2 - use Bio::SearchIO;
ok 3 - use Bio::Index::BlastTable;
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/LocalDB/Index/Index.t ...................... skipped: The optional module DB_File (or dependencies thereof) was not installed
t/LocalDB/Registry.t ......................... 
1..14
ok 1 - use Bio::DB::Registry;
ok 2 - use Bio::DB::Flat;
ok 3
ok 4 # skip The optional module DB_File (or dependencies thereof) was not installed
ok 5 # skip The optional module DB_File (or dependencies thereof) was not installed
ok 6 # skip Network tests have not been requested
ok 7 # skip Network tests have not been requested
ok 8 # skip Network tests have not been requested
ok 9 # skip Network tests have not been requested
ok 10 # skip Network tests have not been requested
ok 11 # skip Network tests have not been requested
ok 12 # skip Network tests have not been requested
ok 13 # skip Network tests have not been requested
ok 14 # skip Network tests have not been requested
ok

#   Failed test 'use Bio::DB::SeqFeature::Store::GFF3Loader;'
#   in t/LocalDB/SeqFeature.t at line 16.
#     Tried to use 'Bio::DB::SeqFeature::Store::GFF3Loader'.
#     Error:  Can't locate DB_File.pm in @INC (@INC contains: . .. ./t/lib /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE/blib/lib /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE/blib/arch /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE /export/home/fly818/var/megalib /export/home/fly818/ap818/site/lib /export/home/fly818/ap818/lib) at Bio/DB/SeqFeature/Store/LoadHelper.pm line 38.
# BEGIN failed--compilation aborted at t/LocalDB/SeqFeature.t line 16.
# Compilation failed in require at Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72.
# Compilation failed in require at (eval 57) line 2.
# BEGIN failed--compilation aborted at (eval 57) line 2.
# Looks like you planned 116 tests but ran 2 extra.
# Looks like you failed 1 test of 118 run.
t/LocalDB/SeqFeature.t ....................... 
1..116
ok 1 - use Bio::SeqFeature::Generic;
ok 2 - use Bio::DB::SeqFeature::Store;
not ok 3 - use Bio::DB::SeqFeature::Store::GFF3Loader;
ok 4 - use Bio::Root::IO;
ok 5 - use Bio::DB::Fasta;
ok 6 - use File::Copy;
ok 7
ok 8
ok 9 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 10 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 11 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 12 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 13 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 14 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 15 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 16 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 17 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 18 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 19 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 20 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 21 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 22 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 23 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 24 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 25 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 26 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 27 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 28 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 29 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 30 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 31 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 32 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 33 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 34 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 35 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 36 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 37 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 38 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 39 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 40 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 41 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 42 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 43 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 44 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 45 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 46 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 47 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 48 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 49 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 50 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 51 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 52 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 53 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 54 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 55 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 56 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 57 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 58 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 59 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 60 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 61 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 62 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 63 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 64 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 65 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 66 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 67 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 68 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 69 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 70 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 71 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 72 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 73 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 74 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 75 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 76 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 77 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 78 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 79 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 80 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 81 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 82 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 83 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 84 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 85 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 86 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 87 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 88 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 89 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 90 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 91 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 92 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 93 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 94 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 95 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 96 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 97 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 98 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 99 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 100 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 101 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 102 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 103 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 104 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 105 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 106 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 107 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 108 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 109 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 110 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 111 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 112 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 113 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 114 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 115 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 116 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 117 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
ok 118 # skip GFF3 loader failed? Skipping all! Can't locate object method "new" via package "Bio::DB::SeqFeature::Store::GFF3Loader" at t/LocalDB/SeqFeature.t line 38.
# 
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/116 subtests 
	(less 110 skipped subtests: 5 okay)

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't locate DB_File.pm in @INC (@INC contains: . /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE/blib/lib /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE/blib/arch /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE /export/home/fly818/var/megalib /export/home/fly818/ap818/site/lib /export/home/fly818/ap818/lib) at Bio/DB/Taxonomy/flatfile.pm line 89.
BEGIN failed--compilation aborted at Bio/DB/Taxonomy/flatfile.pm line 89.
Compilation failed in require at Bio/Root/Root.pm line 543.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545
STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:263
STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:114
STACK: t/LocalDB/transfac_pro.t:18
-----------------------------------------------------------
Bio::DB::Taxonomy: flatfile cannot be found
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't locate DB_File.pm in @INC (@INC contains: . /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE/blib/lib /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE/blib/arch /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE /export/home/fly818/var/megalib /export/home/fly818/ap818/site/lib /export/home/fly818/ap818/lib) at Bio/DB/Taxonomy/flatfile.pm line 89.
BEGIN failed--compilation aborted at Bio/DB/Taxonomy/flatfile.pm line 89.
Compilation failed in require at Bio/Root/Root.pm line 543.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545
STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:263
STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:114
STACK: t/LocalDB/transfac_pro.t:18
-----------------------------------------------------------

For more information about the Bio::DB::Taxonomy system please see
the Bio::DB::Taxonomy docs.  This includes ways of checking for 
formats at compile time, not run time.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::TFBS::transfac_pro. Can't locate DB_File.pm in @INC (@INC contains: . /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE/blib/lib /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE/blib/arch /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE /export/home/fly818/var/megalib /export/home/fly818/ap818/site/lib /export/home/fly818/ap818/lib) at Bio/DB/TFBS/transfac_pro.pm line 118.
BEGIN failed--compilation aborted at Bio/DB/TFBS/transfac_pro.pm line 118.
Compilation failed in require at Bio/Root/Root.pm line 543.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545
STACK: Bio::DB::TFBS::_load_tax_module Bio/DB/TFBS.pm:151
STACK: Bio::DB::TFBS::new Bio/DB/TFBS.pm:130
STACK: t/LocalDB/transfac_pro.t:25
-----------------------------------------------------------
Bio::DB::TFBS: transfac_pro cannot be found
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::TFBS::transfac_pro. Can't locate DB_File.pm in @INC (@INC contains: . /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE/blib/lib /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE/blib/arch /export/home/fly818/var/cpan/build/BioPerl-1.6.901-dXkHQE /export/home/fly818/var/megalib /export/home/fly818/ap818/site/lib /export/home/fly818/ap818/lib) at Bio/DB/TFBS/transfac_pro.pm line 118.
BEGIN failed--compilation aborted at Bio/DB/TFBS/transfac_pro.pm line 118.
Compilation failed in require at Bio/Root/Root.pm line 543.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545
STACK: Bio::DB::TFBS::_load_tax_module Bio/DB/TFBS.pm:151
STACK: Bio::DB::TFBS::new Bio/DB/TFBS.pm:130
STACK: t/LocalDB/transfac_pro.t:25
-----------------------------------------------------------

For more information about the Bio::DB::TFBS system please see
the Bio::DB::TFBS docs.  This includes ways of checking for 
formats at compile time, not run time.

#   Failed test at t/LocalDB/transfac_pro.t line 25.
Can't call method "get_reference_ids" on an undefined value at t/LocalDB/transfac_pro.t line 33.
# Looks like you planned 115 tests but ran 4.
# Looks like you failed 1 test of 4 run.
# Looks like your test exited with 2 just after 4.
t/LocalDB/transfac_pro.t ..................... 
1..115
ok 1 - use Bio::Matrix::PSM::IO;
ok 2 - use Bio::DB::TFBS;
ok 3 - use Bio::DB::Taxonomy;
not ok 4
Dubious, test returned 2 (wstat 512, 0x200)
Failed 112/115 subtests 
t/Map/Cyto.t ................................. 
1..110
ok 1 - use Bio::Map::CytoMap;
ok 2 - use Bio::Map::CytoPosition;
ok 3 - use Bio::Map::CytoMarker;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14 - The object isa Bio::Map::CytoPosition
ok 15
ok 16
ok 17
ok 18 - The object isa Bio::Range
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok
t/Map/Linkage.t .............................. 
1..18
ok 1 - use Bio::Map::LinkagePosition;
ok 2 - use Bio::Map::Microsatellite;
ok 3 - use Bio::Map::LinkageMap;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok
t/Map/Map.t .................................. 
1..267
ok 1 - use Bio::Map::SimpleMap;
ok 2 - use Bio::Map::Marker;
ok 3 - use Bio::Map::Position;
ok 4 - use Bio::Map::Relative;
ok 5 - use Bio::Map::Mappable;
ok 6
ok 7
ok 8
ok 9
ok 10 - Length is 0
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151 - use Bio::Map::Gene;
ok 152 - use Bio::Map::GeneMap;
ok 153 - use Bio::Map::TranscriptionFactor;
ok 154 - use Bio::Map::GeneRelative;
ok 155 - use Bio::Map::GenePosition;
ok 156 - use Bio::Map::Prediction;
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok 176
ok 177
ok 178
ok 179
ok 180
ok 181
ok 182
ok 183
ok 184
ok 185
ok 186
ok 187
ok 188
ok 189
ok 190
ok 191
ok 192
ok 193
ok 194
ok 195
ok 196
ok 197
ok 198
ok 199
ok 200
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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
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ok 48
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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
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ok 31
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ok 37
ok 38
ok 39
ok
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
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
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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
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ok 54
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ok 56
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ok 69
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ok 71
ok 72
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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
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
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
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ok 51
ok 52
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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
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ok 11
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ok 13
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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
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ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok
t/Ontology/IO/interpro.t ..................... 
1..69
ok 1 - use Bio::OntologyIO;
ok 2 - The object isa Bio::OntologyIO::InterProParser
ok 3
ok 4 - get_dbxrefs on leaf terms is non-empty
ok 5 - get_dbxrefs(member_list) on leaf terms is non-empty
ok 6 - get_dbxrefs(sec_list) on leaf terms is non-empty
ok 7 - get_dbxrefs(class_list) on leaf terms is non-empty
ok 8 - get_dbxrefs(pub_list) on leaf terms is non-empty
ok 9 - get_dbxrefs(example_list) on leaf terms is non-empty
ok 10 - get_dbxrefs(external_doc_list) on leaf terms is non-empty
ok 11 - get_members on leaf terms is non-empty
ok 12 - class_list on leaf terms is non-empty
ok 13 - get_examples on leaf terms is non-empty
ok 14 - get_external_documents on leaf terms is non-empty
ok 15 - get_references on leaf terms is non-empty
ok 16 - protein_count on leaf terms is non-empty
ok 17 - to_string looks reasonable
ok 18 - There are 8 root InterPro terms
ok 19 - The object isa Bio::Ontology::Ontology
ok 20 - term Integrins alpha chain in ontology InterPro
ok 21 - The object isa Bio::Ontology::Ontology
ok 22 - term post-translational modification in ontology InterPro
ok 23 - The object isa Bio::Ontology::Ontology
ok 24 - term Repeat in ontology InterPro
ok 25 - The object isa Bio::Ontology::Ontology
ok 26 - term Binding Site in ontology InterPro
ok 27 - The object isa Bio::Ontology::Ontology
ok 28 - term Cdc20/Fizzy in ontology InterPro
ok 29 - The object isa Bio::Ontology::Ontology
ok 30 - term Conserved Site in ontology InterPro
ok 31 - The object isa Bio::Ontology::Ontology
ok 32 - term Region in ontology InterPro
ok 33 - The object isa Bio::Ontology::Ontology
ok 34 - term Kringle in ontology InterPro
ok 35 - The object isa Bio::Ontology::Ontology
ok 36 - term Helix-turn-helix, AraC type  in ontology InterPro
ok 37 - The object isa Bio::Ontology::Ontology
ok 38 - term Active Site in ontology InterPro
ok 39 - The object isa Bio::Ontology::Ontology
ok 40 - term Active Site in ontology InterPro
ok 41 - The object isa Bio::Ontology::Ontology
ok 42 - term Binding Site in ontology InterPro
ok 43 - The object isa Bio::Ontology::Ontology
ok 44 - term Conserved Site in ontology InterPro
ok 45 - The object isa Bio::Ontology::Ontology
ok 46 - term Domain in ontology InterPro
ok 47 - The object isa Bio::Ontology::Ontology
ok 48 - term Family in ontology InterPro
ok 49 - The object isa Bio::Ontology::Ontology
ok 50 - term Region in ontology InterPro
ok 51 - The object isa Bio::Ontology::Ontology
ok 52 - term Repeat in ontology InterPro
ok 53 - The object isa Bio::Ontology::Ontology
ok 54 - term post-translational modification in ontology InterPro
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61 - Integrins alpha chain term has one parent
ok 62 - Integrins alpha chain term has one ancestor
ok 63 - Cdc20/Fizzy term has one parent
ok 64 - Cdc20/Fizzy term has one ancestor
ok 65 - Kringle term has one parent
ok 66 - Kringle term has one ancestor
ok 67 - Helix-turn-helix, AraC type  term has one parent
ok 68 - Helix-turn-helix, AraC type  term has one ancestor
ok 69 - secondary accession map has 2 keys
ok
t/Ontology/IO/obo.t .......................... 
1..92
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 84 - got a ontology IO handler isa Bio::OntologyIO
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok
t/Ontology/Ontology.t ........................ 
1..55
ok 1 - use Bio::OntologyIO;
ok 2 - use Bio::Ontology::RelationshipType;
ok 3 - The object isa Bio::Ontology::Ontology
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 - Interpro XML file interpro.xml can be parsed
ok 54 - Interpro XML file interpro_sample.xml can be parsed
ok 55 - Interpro XML file interpro_relationship.xml can be parsed
ok
t/Ontology/OntologyEngine.t .................. 
1..31
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 - adding a relationship with an undef object term fails
ok 9 - adding a relationship with an undef object term fails
ok 10 - adding a relationship with an undef subject term fails
ok 11 - adding a relationship with an undef subject term fails
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok
t/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..31
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 30 # skip Network tests have not been requested
ok 31 # 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
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t/Phenotype/OMIMparser.t ..................... 
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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
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ok 105 - The object isa Bio::Phenotype::OMIM::MiniMIMentry
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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
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ok 41
ok 42 - operator overloading in AnnotationI is deprecated
ok 43 - operator overloading in AnnotationI is deprecated
ok 44
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ok 46 - operator overloading in AnnotationI is deprecated
ok 47 - operator overloading in AnnotationI is deprecated
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ok 99 - operator overloading in AnnotationI is deprecated
ok 100 - operator overloading in AnnotationI is deprecated
ok 101
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ok 103 - operator overloading in AnnotationI is deprecated
ok 104 - operator overloading in AnnotationI is deprecated
ok 105
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ok
t/PodSyntax.t ................................ 
1..1011
ok 1 - POD test for Bio/AlignIO.pm
ok 2 - POD test for Bio/AnalysisI.pm
ok 3 - POD test for Bio/AnalysisParserI.pm
ok 4 - POD test for Bio/AnalysisResultI.pm
ok 5 - POD test for Bio/AnnotatableI.pm
ok 6 - POD test for Bio/AnnotationCollectionI.pm
ok 7 - POD test for Bio/AnnotationI.pm
ok 8 - POD test for Bio/Biblio.pm
ok 9 - POD test for Bio/ClusterI.pm
ok 10 - POD test for Bio/ClusterIO.pm
ok 11 - POD test for Bio/DasI.pm
ok 12 - POD test for Bio/DBLinkContainerI.pm
ok 13 - POD test for Bio/DescribableI.pm
ok 14 - POD test for Bio/FeatureHolderI.pm
ok 15 - POD test for Bio/FeatureIO.pm
ok 16 - POD test for Bio/HandlerBaseI.pm
ok 17 - POD test for Bio/IdCollectionI.pm
ok 18 - POD test for Bio/IdentifiableI.pm
ok 19 - POD test for Bio/LocatableSeq.pm
ok 20 - POD test for Bio/Perl.pm
ok 21 - POD test for Bio/LocationI.pm
ok 22 - POD test for Bio/MapIO.pm
ok 23 - POD test for Bio/NexmlIO.pm
ok 24 - POD test for Bio/OntologyIO.pm
ok 25 - POD test for Bio/ParameterBaseI.pm
ok 26 - POD test for Bio/PhyloNetwork.pm
ok 27 - POD test for Bio/PrimarySeq.pm
ok 28 - POD test for Bio/PrimarySeqI.pm
ok 29 - POD test for Bio/PullParserI.pm
ok 30 - POD test for Bio/Range.pm
ok 31 - POD test for Bio/RangeI.pm
ok 32 - POD test for Bio/SearchDist.pm
ok 33 - POD test for Bio/SearchIO.pm
ok 34 - POD test for Bio/Seq.pm
ok 35 - POD test for Bio/SeqAnalysisParserI.pm
ok 36 - POD test for Bio/SeqFeatureI.pm
ok 37 - POD test for Bio/SeqI.pm
ok 38 - POD test for Bio/SeqIO.pm
ok 39 - POD test for Bio/SeqUtils.pm
ok 40 - POD test for Bio/SimpleAlign.pm
ok 41 - POD test for Bio/SimpleAnalysisI.pm
ok 42 - POD test for Bio/Species.pm
ok 43 - POD test for Bio/Taxon.pm
ok 44 - POD test for Bio/Taxonomy.pm
ok 45 - POD test for Bio/TreeIO.pm
ok 46 - POD test for Bio/UpdateableSeqI.pm
ok 47 - POD test for Bio/WebAgent.pm
ok 48 - POD test for examples/bioperl.pl (no pod)
ok 49 - POD test for examples/generate_random_seq.pl (no pod)
ok 50 - POD test for examples/longorf.pl
ok 51 - POD test for examples/make_primers.pl (no pod)
ok 52 - POD test for examples/rev_and_trans.pl (no pod)
ok 53 - POD test for examples/revcom_dir.pl (no pod)
ok 54 - POD test for examples/subsequence.cgi (no pod)
ok 55 - POD test for maintenance/authors.pl
ok 56 - POD test for maintenance/check_NAME.pl
ok 57 - POD test for maintenance/check_URLs.pl
ok 58 - POD test for maintenance/cvs2cl_by_file.pl
ok 59 - POD test for maintenance/dependencies.pl
ok 60 - POD test for maintenance/deprecated.pl
ok 61 - POD test for maintenance/find_mod_deps.pl
ok 62 - POD test for maintenance/module_usage.pl (no pod)
ok 63 - POD test for maintenance/modules.pl
ok 64 - POD test for maintenance/ncbi_blast_switches.pl (no pod)
ok 65 - POD test for maintenance/pod.pl
ok 66 - POD test for maintenance/symlink_script.pl
ok 67 - POD test for maintenance/version.pl
ok 68 - POD test for Bio/Align/AlignI.pm
ok 69 - POD test for Bio/Align/DNAStatistics.pm
ok 70 - POD test for Bio/Align/Graphics.pm
ok 71 - POD test for Bio/Align/PairwiseStatistics.pm
ok 72 - POD test for Bio/Align/ProteinStatistics.pm
ok 73 - POD test for Bio/Align/StatisticsI.pm
ok 74 - POD test for Bio/Align/Utilities.pm
ok 75 - POD test for Bio/AlignIO/arp.pm
ok 76 - POD test for Bio/AlignIO/bl2seq.pm
ok 77 - POD test for Bio/AlignIO/clustalw.pm
ok 78 - POD test for Bio/AlignIO/emboss.pm
ok 79 - POD test for Bio/AlignIO/fasta.pm
ok 80 - POD test for Bio/AlignIO/largemultifasta.pm
ok 81 - POD test for Bio/AlignIO/maf.pm
ok 82 - POD test for Bio/AlignIO/mase.pm
ok 83 - POD test for Bio/AlignIO/mega.pm
ok 84 - POD test for Bio/AlignIO/meme.pm
ok 85 - POD test for Bio/AlignIO/metafasta.pm
ok 86 - POD test for Bio/AlignIO/msf.pm
ok 87 - POD test for Bio/AlignIO/nexml.pm
ok 88 - POD test for Bio/AlignIO/nexus.pm
ok 89 - POD test for Bio/AlignIO/pfam.pm
ok 90 - POD test for Bio/AlignIO/phylip.pm
ok 91 - POD test for Bio/AlignIO/po.pm
ok 92 - POD test for Bio/AlignIO/proda.pm
ok 93 - POD test for Bio/AlignIO/prodom.pm
ok 94 - POD test for Bio/AlignIO/psi.pm
ok 95 - POD test for Bio/AlignIO/selex.pm
ok 96 - POD test for Bio/AlignIO/stockholm.pm
ok 97 - POD test for Bio/AlignIO/xmfa.pm
ok 98 - POD test for Bio/Annotation/AnnotationFactory.pm
ok 99 - POD test for Bio/Annotation/Collection.pm
ok 100 - POD test for Bio/Annotation/Comment.pm
ok 101 - POD test for Bio/Annotation/DBLink.pm
ok 102 - POD test for Bio/Annotation/OntologyTerm.pm
ok 103 - POD test for Bio/Annotation/Reference.pm
ok 104 - POD test for Bio/Annotation/Relation.pm
ok 105 - POD test for Bio/Annotation/SimpleValue.pm
ok 106 - POD test for Bio/Annotation/StructuredValue.pm
ok 107 - POD test for Bio/Annotation/TagTree.pm
ok 108 - POD test for Bio/Annotation/Target.pm
ok 109 - POD test for Bio/Annotation/Tree.pm
ok 110 - POD test for Bio/Annotation/TypeManager.pm
ok 111 - POD test for Bio/Assembly/Contig.pm
ok 112 - POD test for Bio/Assembly/ContigAnalysis.pm
ok 113 - POD test for Bio/Assembly/IO.pm
ok 114 - POD test for Bio/Assembly/Scaffold.pm
ok 115 - POD test for Bio/Assembly/ScaffoldI.pm
ok 116 - POD test for Bio/Assembly/Singlet.pm
ok 117 - POD test for Bio/Biblio/Article.pm
ok 118 - POD test for Bio/Biblio/BiblioBase.pm
ok 119 - POD test for Bio/Biblio/Book.pm
ok 120 - POD test for Bio/Biblio/BookArticle.pm
ok 121 - POD test for Bio/Biblio/IO.pm
ok 122 - POD test for Bio/Biblio/Journal.pm
ok 123 - POD test for Bio/Biblio/JournalArticle.pm
ok 124 - POD test for Bio/Biblio/MedlineArticle.pm
ok 125 - POD test for Bio/Biblio/MedlineBook.pm
ok 126 - POD test for Bio/Biblio/MedlineBookArticle.pm
ok 127 - POD test for Bio/Biblio/MedlineJournal.pm
ok 128 - POD test for Bio/Biblio/MedlineJournalArticle.pm
ok 129 - POD test for Bio/Biblio/Organisation.pm
ok 130 - POD test for Bio/Biblio/Patent.pm
ok 131 - POD test for Bio/Biblio/Person.pm
ok 132 - POD test for Bio/Biblio/Proceeding.pm
ok 133 - POD test for Bio/Biblio/Provider.pm
ok 134 - POD test for Bio/Biblio/PubmedArticle.pm
ok 135 - POD test for Bio/Biblio/PubmedBookArticle.pm
ok 136 - POD test for Bio/Biblio/Ref.pm
ok 137 - POD test for Bio/Biblio/PubmedJournalArticle.pm
ok 138 - POD test for Bio/Biblio/Service.pm
ok 139 - POD test for Bio/Biblio/TechReport.pm
ok 140 - POD test for Bio/Biblio/Thesis.pm
ok 141 - POD test for Bio/Biblio/WebResource.pm
ok 142 - POD test for Bio/Cluster/ClusterFactory.pm
ok 143 - POD test for Bio/Cluster/FamilyI.pm
ok 144 - POD test for Bio/Cluster/SequenceFamily.pm
ok 145 - POD test for Bio/Cluster/UniGene.pm
ok 146 - POD test for Bio/Cluster/UniGeneI.pm
ok 147 - POD test for Bio/ClusterIO/dbsnp.pm
ok 148 - POD test for Bio/ClusterIO/unigene.pm
ok 149 - POD test for Bio/CodonUsage/IO.pm
ok 150 - POD test for Bio/CodonUsage/Table.pm
ok 151 - POD test for Bio/Coordinate/Chain.pm
ok 152 - POD test for Bio/Coordinate/Collection.pm
ok 153 - POD test for Bio/Coordinate/ExtrapolatingPair.pm
ok 154 - POD test for Bio/Coordinate/GeneMapper.pm
ok 155 - POD test for Bio/Coordinate/Graph.pm
ok 156 - POD test for Bio/Coordinate/MapperI.pm
ok 157 - POD test for Bio/Coordinate/Pair.pm
ok 158 - POD test for Bio/Coordinate/Result.pm
ok 159 - POD test for Bio/Coordinate/ResultI.pm
ok 160 - POD test for Bio/Coordinate/Utils.pm
ok 161 - POD test for Bio/Das/FeatureTypeI.pm
ok 162 - POD test for Bio/Das/SegmentI.pm
ok 163 - POD test for Bio/DB/Ace.pm
ok 164 - POD test for Bio/DB/BiblioI.pm
ok 165 - POD test for Bio/DB/BioFetch.pm
ok 166 - POD test for Bio/DB/CUTG.pm
ok 167 - POD test for Bio/DB/DBFetch.pm
ok 168 - POD test for Bio/DB/EMBL.pm
ok 169 - POD test for Bio/DB/EntrezGene.pm
ok 170 - POD test for Bio/DB/EUtilities.pm
ok 171 - POD test for Bio/DB/Expression.pm
ok 172 - POD test for Bio/DB/Failover.pm
ok 173 - POD test for Bio/DB/Fasta.pm
ok 174 - POD test for Bio/DB/FileCache.pm
ok 175 - POD test for Bio/DB/Flat.pm
ok 176 - POD test for Bio/DB/GenBank.pm
ok 177 - POD test for Bio/DB/GenericWebAgent.pm
ok 178 - POD test for Bio/DB/GenPept.pm
ok 179 - POD test for Bio/DB/GFF.pm
ok 180 - POD test for Bio/DB/HIV.pm
ok 181 - POD test for Bio/DB/InMemoryCache.pm
ok 182 - POD test for Bio/DB/LocationI.pm
ok 183 - POD test for Bio/DB/MeSH.pm
ok 184 - POD test for Bio/DB/NCBIHelper.pm
ok 185 - POD test for Bio/DB/Qual.pm
ok 186 - POD test for Bio/DB/QueryI.pm
ok 187 - POD test for Bio/DB/RandomAccessI.pm
ok 188 - POD test for Bio/DB/ReferenceI.pm
ok 189 - POD test for Bio/DB/RefSeq.pm
ok 190 - POD test for Bio/DB/Registry.pm
ok 191 - POD test for Bio/DB/SeqFeature.pm
ok 192 - POD test for Bio/DB/SeqHound.pm
ok 193 - POD test for Bio/DB/SeqI.pm
ok 194 - POD test for Bio/DB/SeqVersion.pm
ok 195 - POD test for Bio/DB/SwissProt.pm
ok 196 - POD test for Bio/DB/Taxonomy.pm
ok 197 - POD test for Bio/DB/TFBS.pm
ok 198 - POD test for Bio/DB/Universal.pm
ok 199 - POD test for Bio/DB/UpdateableSeqI.pm
ok 200 - POD test for Bio/DB/WebDBSeqI.pm
ok 201 - POD test for Bio/Draw/Pictogram.pm
ok 202 - POD test for Bio/Event/EventGeneratorI.pm
ok 203 - POD test for Bio/Event/EventHandlerI.pm
ok 204 - POD test for Bio/Factory/AnalysisI.pm
ok 205 - POD test for Bio/Factory/ApplicationFactoryI.pm
ok 206 - POD test for Bio/Factory/DriverFactory.pm
ok 207 - POD test for Bio/Factory/FTLocationFactory.pm
ok 208 - POD test for Bio/Factory/LocationFactoryI.pm
ok 209 - POD test for Bio/Factory/MapFactoryI.pm
ok 210 - POD test for Bio/Factory/ObjectBuilderI.pm
ok 211 - POD test for Bio/Factory/ObjectFactory.pm
ok 212 - POD test for Bio/Factory/ObjectFactoryI.pm
ok 213 - POD test for Bio/Factory/SeqAnalysisParserFactory.pm
ok 214 - POD test for Bio/Factory/SeqAnalysisParserFactoryI.pm
ok 215 - POD test for Bio/Factory/SequenceFactoryI.pm
ok 216 - POD test for Bio/Factory/SequenceProcessorI.pm
ok 217 - POD test for Bio/Factory/SequenceStreamI.pm
ok 218 - POD test for Bio/Factory/TreeFactoryI.pm
ok 219 - POD test for Bio/FeatureIO/bed.pm
ok 220 - POD test for Bio/FeatureIO/gff.pm
ok 221 - POD test for Bio/FeatureIO/gtf.pm
ok 222 - POD test for Bio/FeatureIO/interpro.pm
ok 223 - POD test for Bio/FeatureIO/ptt.pm
ok 224 - POD test for Bio/FeatureIO/vecscreen_simple.pm
ok 225 - POD test for Bio/Index/Abstract.pm
ok 226 - POD test for Bio/Index/AbstractSeq.pm
ok 227 - POD test for Bio/Index/Blast.pm
ok 228 - POD test for Bio/Index/BlastTable.pm
ok 229 - POD test for Bio/Index/EMBL.pm
ok 230 - POD test for Bio/Index/Fasta.pm
ok 231 - POD test for Bio/Index/Fastq.pm
ok 232 - POD test for Bio/Index/GenBank.pm
ok 233 - POD test for Bio/Index/Hmmer.pm
ok 234 - POD test for Bio/Index/Qual.pm
ok 235 - POD test for Bio/Index/Stockholm.pm
ok 236 - POD test for Bio/Index/SwissPfam.pm
ok 237 - POD test for Bio/Index/Swissprot.pm
ok 238 - POD test for Bio/LiveSeq/AARange.pm
ok 239 - POD test for Bio/LiveSeq/Chain.pm
ok 240 - POD test for Bio/LiveSeq/ChainI.pm
ok 241 - POD test for Bio/LiveSeq/DNA.pm
ok 242 - POD test for Bio/LiveSeq/Exon.pm
ok 243 - POD test for Bio/LiveSeq/Gene.pm
ok 244 - POD test for Bio/LiveSeq/Intron.pm
ok 245 - POD test for Bio/LiveSeq/Mutation.pm
ok 246 - POD test for Bio/LiveSeq/Mutator.pm
ok 247 - POD test for Bio/LiveSeq/Prim_Transcript.pm
ok 248 - POD test for Bio/LiveSeq/Range.pm
ok 249 - POD test for Bio/LiveSeq/Repeat_Region.pm
ok 250 - POD test for Bio/LiveSeq/Repeat_Unit.pm
ok 251 - POD test for Bio/LiveSeq/SeqI.pm
ok 252 - POD test for Bio/LiveSeq/Transcript.pm
ok 253 - POD test for Bio/LiveSeq/Translation.pm
ok 254 - POD test for Bio/Location/Atomic.pm
ok 255 - POD test for Bio/Location/AvWithinCoordPolicy.pm
ok 256 - POD test for Bio/Location/CoordinatePolicyI.pm
ok 257 - POD test for Bio/Location/Fuzzy.pm
ok 258 - POD test for Bio/Location/FuzzyLocationI.pm
ok 259 - POD test for Bio/Location/NarrowestCoordPolicy.pm
ok 260 - POD test for Bio/Location/Simple.pm
ok 261 - POD test for Bio/Location/Split.pm
ok 262 - POD test for Bio/Location/SplitLocationI.pm
ok 263 - POD test for Bio/Location/WidestCoordPolicy.pm
ok 264 - POD test for Bio/Map/Clone.pm
ok 265 - POD test for Bio/Map/Contig.pm
ok 266 - POD test for Bio/Map/CytoMap.pm
ok 267 - POD test for Bio/Map/CytoMarker.pm
ok 268 - POD test for Bio/Map/CytoPosition.pm
ok 269 - POD test for Bio/Map/EntityI.pm
ok 270 - POD test for Bio/Map/FPCMarker.pm
ok 271 - POD test for Bio/Map/Gene.pm
ok 272 - POD test for Bio/Map/GeneMap.pm
ok 273 - POD test for Bio/Map/GenePosition.pm
ok 274 - POD test for Bio/Map/GeneRelative.pm
ok 275 - POD test for Bio/Map/LinkageMap.pm
ok 276 - POD test for Bio/Map/LinkagePosition.pm
ok 277 - POD test for Bio/Map/MapI.pm
ok 278 - POD test for Bio/Map/Mappable.pm
ok 279 - POD test for Bio/Map/MappableI.pm
ok 280 - POD test for Bio/Map/Marker.pm
ok 281 - POD test for Bio/Map/MarkerI.pm
ok 282 - POD test for Bio/Map/Microsatellite.pm
ok 283 - POD test for Bio/Map/OrderedPosition.pm
ok 284 - POD test for Bio/Map/OrderedPositionWithDistance.pm
ok 285 - POD test for Bio/Map/Physical.pm
ok 286 - POD test for Bio/Map/Position.pm
ok 287 - POD test for Bio/Map/PositionHandler.pm
ok 288 - POD test for Bio/Map/PositionHandlerI.pm
ok 289 - POD test for Bio/Map/PositionI.pm
ok 290 - POD test for Bio/Map/PositionWithSequence.pm
ok 291 - POD test for Bio/Map/Prediction.pm
ok 292 - POD test for Bio/Map/Relative.pm
ok 293 - POD test for Bio/Map/RelativeI.pm
ok 294 - POD test for Bio/Map/SimpleMap.pm
ok 295 - POD test for Bio/Map/TranscriptionFactor.pm
ok 296 - POD test for Bio/MapIO/fpc.pm
ok 297 - POD test for Bio/MapIO/mapmaker.pm
ok 298 - POD test for Bio/Matrix/Generic.pm
ok 299 - POD test for Bio/Matrix/IO.pm
ok 300 - POD test for Bio/Matrix/MatrixI.pm
ok 301 - POD test for Bio/Matrix/Mlagan.pm
ok 302 - POD test for Bio/Matrix/PhylipDist.pm
ok 303 - POD test for Bio/Matrix/Scoring.pm
ok 304 - POD test for Bio/MolEvol/CodonModel.pm
ok 305 - POD test for Bio/Nexml/Factory.pm
ok 306 - POD test for Bio/Ontology/DocumentRegistry.pm
ok 307 - POD test for Bio/Ontology/GOterm.pm
ok 308 - POD test for Bio/Ontology/InterProTerm.pm
ok 309 - POD test for Bio/Ontology/OBOEngine.pm
ok 310 - POD test for Bio/Ontology/OBOterm.pm
ok 311 - POD test for Bio/Ontology/Ontology.pm
ok 312 - POD test for Bio/Ontology/OntologyEngineI.pm
ok 313 - POD test for Bio/Ontology/OntologyI.pm
ok 314 - POD test for Bio/Ontology/OntologyStore.pm
ok 315 - POD test for Bio/Ontology/Path.pm
ok 316 - POD test for Bio/Ontology/PathI.pm
ok 317 - POD test for Bio/Ontology/Relationship.pm
ok 318 - POD test for Bio/Ontology/RelationshipFactory.pm
ok 319 - POD test for Bio/Ontology/RelationshipI.pm
ok 320 - POD test for Bio/Ontology/RelationshipType.pm
ok 321 - POD test for Bio/Ontology/SimpleOntologyEngine.pm
ok 322 - POD test for Bio/Ontology/Term.pm
ok 323 - POD test for Bio/Ontology/TermFactory.pm
ok 324 - POD test for Bio/Ontology/TermI.pm
ok 325 - POD test for Bio/PopGen/Genotype.pm
ok 326 - POD test for Bio/PopGen/GenotypeI.pm
ok 327 - POD test for Bio/PopGen/HtSNP.pm
ok 328 - POD test for Bio/PopGen/Individual.pm
ok 329 - POD test for Bio/PopGen/IndividualI.pm
ok 330 - POD test for Bio/PopGen/IO.pm
ok 331 - POD test for Bio/PopGen/Marker.pm
ok 332 - POD test for Bio/PopGen/MarkerI.pm
ok 333 - POD test for Bio/PopGen/PopStats.pm
ok 334 - POD test for Bio/PopGen/Population.pm
ok 335 - POD test for Bio/PopGen/PopulationI.pm
ok 336 - POD test for Bio/PopGen/Statistics.pm
ok 337 - POD test for Bio/PopGen/TagHaplotype.pm
ok 338 - POD test for Bio/PopGen/Utilities.pm
ok 339 - POD test for Bio/OntologyIO/dagflat.pm
ok 340 - POD test for Bio/OntologyIO/goflat.pm
ok 341 - POD test for Bio/OntologyIO/InterProParser.pm
ok 342 - POD test for Bio/OntologyIO/obo.pm
ok 343 - POD test for Bio/OntologyIO/simplehierarchy.pm
ok 344 - POD test for Bio/OntologyIO/soflat.pm
ok 345 - POD test for Bio/Phenotype/Correlate.pm
ok 346 - POD test for Bio/Phenotype/Measure.pm
ok 347 - POD test for Bio/Phenotype/Phenotype.pm
ok 348 - POD test for Bio/Phenotype/PhenotypeI.pm
ok 349 - POD test for Bio/PhyloNetwork/Factory.pm
ok 350 - POD test for Bio/PhyloNetwork/FactoryX.pm
ok 351 - POD test for Bio/PhyloNetwork/GraphViz.pm
ok 352 - POD test for Bio/PhyloNetwork/muVector.pm
ok 353 - POD test for Bio/PhyloNetwork/RandomFactory.pm
ok 354 - POD test for Bio/PhyloNetwork/TreeFactory.pm
ok 355 - POD test for Bio/PhyloNetwork/TreeFactoryMulti.pm
ok 356 - POD test for Bio/PhyloNetwork/TreeFactoryX.pm
ok 357 - POD test for Bio/Restriction/Analysis.pm
ok 358 - POD test for Bio/Restriction/Enzyme.pm
ok 359 - POD test for Bio/Restriction/EnzymeCollection.pm
ok 360 - POD test for Bio/Restriction/EnzymeI.pm
ok 361 - POD test for Bio/Restriction/IO.pm
ok 362 - POD test for Bio/Root/Build.pm
ok 363 - POD test for Bio/Root/Exception.pm
ok 364 - POD test for Bio/Root/HTTPget.pm
ok 365 - POD test for Bio/Root/IO.pm
ok 366 - POD test for Bio/Root/Root.pm
ok 367 - POD test for Bio/Root/RootI.pm
ok 368 - POD test for Bio/Root/Storable.pm
ok 369 - POD test for Bio/Root/Test.pm
ok 370 - POD test for Bio/Root/Utilities.pm
ok 371 - POD test for Bio/Root/Version.pm
ok 372 - POD test for Bio/Search/BlastStatistics.pm
ok 373 - POD test for Bio/Search/BlastUtils.pm
ok 374 - POD test for Bio/Search/DatabaseI.pm
ok 375 - POD test for Bio/Search/GenericDatabase.pm
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ok 782 - POD test for Bio/PopGen/IO/prettybase.pm
ok 783 - POD test for Bio/PopGen/Simulation/Coalescent.pm
ok 784 - POD test for Bio/PopGen/Simulation/GeneticDrift.pm
ok 785 - POD test for Bio/OntologyIO/Handlers/BaseSAXHandler.pm
ok 786 - POD test for Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
ok 787 - POD test for Bio/OntologyIO/Handlers/InterProHandler.pm
ok 788 - POD test for Bio/Phenotype/MeSH/Term.pm
ok 789 - POD test for Bio/Phenotype/MeSH/Twig.pm
ok 790 - POD test for Bio/Phenotype/OMIM/MiniMIMentry.pm
ok 791 - POD test for Bio/Phenotype/OMIM/OMIMentry.pm
ok 792 - POD test for Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm
ok 793 - POD test for Bio/Phenotype/OMIM/OMIMparser.pm
ok 794 - POD test for Bio/Restriction/Enzyme/MultiCut.pm
ok 795 - POD test for Bio/Restriction/Enzyme/MultiSite.pm
ok 796 - POD test for Bio/Restriction/IO/bairoch.pm
ok 797 - POD test for Bio/Restriction/IO/base.pm
ok 798 - POD test for Bio/Restriction/IO/itype2.pm
ok 799 - POD test for Bio/Restriction/IO/prototype.pm
ok 800 - POD test for Bio/Restriction/IO/withrefm.pm
ok 801 - POD test for Bio/Root/Test/Warn.pm
ok 802 - POD test for Bio/Search/Hit/BlastHit.pm
ok 803 - POD test for Bio/Search/Hit/BlastPullHit.pm
ok 804 - POD test for Bio/Search/Hit/Fasta.pm
ok 805 - POD test for Bio/Search/Hit/GenericHit.pm
ok 806 - POD test for Bio/Search/Hit/HitFactory.pm
ok 807 - POD test for Bio/Search/Hit/HitI.pm
ok 808 - POD test for Bio/Search/Hit/hmmer3Hit.pm
ok 809 - POD test for Bio/Search/Hit/HMMERHit.pm
ok 810 - POD test for Bio/Search/Hit/HmmpfamHit.pm
ok 811 - POD test for Bio/Search/Hit/ModelHit.pm
ok 812 - POD test for Bio/Search/Hit/PsiBlastHit.pm
ok 813 - POD test for Bio/Search/Hit/PullHitI.pm
ok 814 - POD test for Bio/Search/HSP/BlastHSP.pm
ok 815 - POD test for Bio/Search/HSP/BlastPullHSP.pm
ok 816 - POD test for Bio/Search/HSP/FastaHSP.pm
ok 817 - POD test for Bio/Search/HSP/GenericHSP.pm
ok 818 - POD test for Bio/Search/HSP/hmmer3HSP.pm
ok 819 - POD test for Bio/Search/HSP/HMMERHSP.pm
ok 820 - POD test for Bio/Search/HSP/HmmpfamHSP.pm
ok 821 - POD test for Bio/Search/HSP/HSPFactory.pm
ok 822 - POD test for Bio/Search/HSP/HSPI.pm
ok 823 - POD test for Bio/Search/HSP/ModelHSP.pm
ok 824 - POD test for Bio/Search/HSP/PsiBlastHSP.pm
ok 825 - POD test for Bio/Search/HSP/PSLHSP.pm
ok 826 - POD test for Bio/Search/HSP/PullHSPI.pm
ok 827 - POD test for Bio/Search/HSP/WABAHSP.pm
ok 828 - POD test for Bio/Search/Iteration/GenericIteration.pm
ok 829 - POD test for Bio/Search/Iteration/IterationI.pm
ok 830 - POD test for Bio/Search/Result/BlastPullResult.pm
ok 831 - POD test for Bio/Search/Result/BlastResult.pm
ok 832 - POD test for Bio/Search/Result/CrossMatchResult.pm
ok 833 - POD test for Bio/Search/Result/GenericResult.pm
ok 834 - POD test for Bio/Search/Result/hmmer3Result.pm
ok 835 - POD test for Bio/Search/Result/HMMERResult.pm
ok 836 - POD test for Bio/Search/Result/HmmpfamResult.pm
ok 837 - POD test for Bio/Search/Result/PullResultI.pm
ok 838 - POD test for Bio/Search/Result/ResultFactory.pm
ok 839 - POD test for Bio/Search/Result/ResultI.pm
ok 840 - POD test for Bio/Search/Result/WABAResult.pm
ok 841 - POD test for Bio/Search/Tiling/MapTileUtils.pm
ok 842 - POD test for Bio/Search/Tiling/MapTiling.pm
ok 843 - POD test for Bio/Search/Tiling/TilingI.pm
ok 844 - POD test for Bio/SearchIO/Writer/BSMLResultWriter.pm
ok 845 - POD test for Bio/SearchIO/Writer/GbrowseGFF.pm
ok 846 - POD test for Bio/SearchIO/Writer/HitTableWriter.pm
ok 847 - POD test for Bio/SearchIO/Writer/HSPTableWriter.pm
ok 848 - POD test for Bio/SearchIO/Writer/HTMLResultWriter.pm
ok 849 - POD test for Bio/SearchIO/Writer/ResultTableWriter.pm
ok 850 - POD test for Bio/SearchIO/Writer/TextResultWriter.pm
ok 851 - POD test for Bio/SearchIO/XML/BlastHandler.pm
ok 852 - POD test for Bio/SearchIO/XML/PsiBlastHandler.pm
ok 853 - POD test for Bio/Seq/Meta/Array.pm
ok 854 - POD test for Bio/SeqFeature/Gene/Exon.pm
ok 855 - POD test for Bio/SeqFeature/Gene/ExonI.pm
ok 856 - POD test for Bio/SeqFeature/Gene/GeneStructure.pm
ok 857 - POD test for Bio/SeqFeature/Gene/GeneStructureI.pm
ok 858 - POD test for Bio/SeqFeature/Gene/Intron.pm
ok 859 - POD test for Bio/SeqFeature/Gene/NC_Feature.pm
ok 860 - POD test for Bio/SeqFeature/Gene/Poly_A_site.pm
ok 861 - POD test for Bio/SeqFeature/Gene/Promoter.pm
ok 862 - POD test for Bio/SeqFeature/Gene/Transcript.pm
ok 863 - POD test for Bio/SeqFeature/Gene/TranscriptI.pm
ok 864 - POD test for Bio/SeqFeature/Gene/UTR.pm
ok 865 - POD test for Bio/SeqFeature/SiRNA/Oligo.pm
ok 866 - POD test for Bio/SeqFeature/SiRNA/Pair.pm
ok 867 - POD test for Bio/SeqFeature/Tools/FeatureNamer.pm
ok 868 - POD test for Bio/SeqFeature/Tools/IDHandler.pm
ok 869 - POD test for Bio/SeqFeature/Tools/TypeMapper.pm
ok 870 - POD test for Bio/SeqFeature/Tools/Unflattener.pm
ok 871 - POD test for Bio/SeqIO/game/featHandler.pm
ok 872 - POD test for Bio/SeqIO/game/gameHandler.pm
ok 873 - POD test for Bio/SeqIO/game/gameSubs.pm
ok 874 - POD test for Bio/SeqIO/game/gameWriter.pm
ok 875 - POD test for Bio/SeqIO/game/seqHandler.pm
ok 876 - POD test for Bio/SeqIO/Handler/GenericRichSeqHandler.pm
ok 877 - POD test for Bio/SeqIO/tinyseq/tinyseqHandler.pm
ok 878 - POD test for Bio/Structure/IO/pdb.pm
ok 879 - POD test for Bio/Tools/Alignment/Consed.pm
ok 880 - POD test for Bio/Tools/Alignment/Trim.pm
ok 881 - POD test for Bio/Tools/Analysis/SimpleAnalysisBase.pm
ok 882 - POD test for Bio/Tools/EMBOSS/Palindrome.pm
ok 883 - POD test for Bio/Tools/EUtilities/EUtilDataI.pm
ok 884 - POD test for Bio/Tools/EUtilities/EUtilParameters.pm
ok 885 - POD test for Bio/Tools/EUtilities/History.pm
ok 886 - POD test for Bio/Tools/EUtilities/HistoryI.pm
ok 887 - POD test for Bio/Tools/EUtilities/Info.pm
ok 888 - POD test for Bio/Tools/EUtilities/Link.pm
ok 889 - POD test for Bio/Tools/EUtilities/Query.pm
ok 890 - POD test for Bio/Tools/EUtilities/Summary.pm
ok 891 - POD test for Bio/Tools/HMMER/Domain.pm
ok 892 - POD test for Bio/Tools/HMMER/Results.pm
ok 893 - POD test for Bio/Tools/HMMER/Set.pm
ok 894 - POD test for Bio/Tools/Phylo/Gerp.pm
ok 895 - POD test for Bio/Tools/Phylo/Gumby.pm
ok 896 - POD test for Bio/Tools/Phylo/Molphy.pm
ok 897 - POD test for Bio/Tools/Phylo/PAML.pm
ok 898 - POD test for Bio/Tools/Prediction/Exon.pm
ok 899 - POD test for Bio/Tools/Prediction/Gene.pm
ok 900 - POD test for Bio/Tools/Primer/AssessorI.pm
ok 901 - POD test for Bio/Tools/Primer/Feature.pm
ok 902 - POD test for Bio/Tools/Primer/Pair.pm
ok 903 - POD test for Bio/Tools/Run/GenericParameters.pm
ok 904 - POD test for Bio/Tools/Run/hmmer3.pm (no pod)
ok 905 - POD test for Bio/Tools/Run/ParametersI.pm
ok 906 - POD test for Bio/Tools/Run/RemoteBlast.pm
ok 907 - POD test for Bio/Tools/Run/StandAloneBlast.pm
ok 908 - POD test for Bio/Tools/Run/StandAloneNCBIBlast.pm
ok 909 - POD test for Bio/Tools/Run/StandAloneWUBlast.pm
ok 910 - POD test for Bio/Tools/Run/WrapperBase.pm
ok 911 - POD test for Bio/Tools/SeqPattern/Backtranslate.pm
ok 912 - POD test for Bio/Tools/Signalp/ExtendedSignalp.pm
ok 913 - POD test for Bio/Tools/Sim4/Exon.pm
ok 914 - POD test for Bio/Tools/Sim4/Results.pm
ok 915 - POD test for Bio/Tools/Spidey/Exon.pm
ok 916 - POD test for Bio/Tools/Spidey/Results.pm
ok 917 - POD test for Bio/Tree/Draw/Cladogram.pm
ok 918 - POD test for Bio/Variation/IO/flat.pm
ok 919 - POD test for Bio/Variation/IO/xml.pm
ok 920 - POD test for examples/root/lib/TestInterface.pm
ok 921 - POD test for examples/root/lib/TestObject.pm
ok 922 - POD test for Bio/DB/Flat/BDB/embl.pm
ok 923 - POD test for Bio/DB/Flat/BDB/fasta.pm
ok 924 - POD test for Bio/DB/Flat/BDB/genbank.pm
ok 925 - POD test for Bio/DB/Flat/BDB/swiss.pm
ok 926 - POD test for Bio/DB/GFF/Adaptor/ace.pm
ok 927 - POD test for Bio/DB/GFF/Adaptor/berkeleydb.pm
ok 928 - POD test for Bio/DB/GFF/Adaptor/biofetch.pm
ok 929 - POD test for Bio/DB/GFF/Adaptor/biofetch_oracle.pm
ok 930 - POD test for Bio/DB/GFF/Adaptor/dbi.pm
ok 931 - POD test for Bio/DB/GFF/Adaptor/memory.pm
ok 932 - POD test for Bio/DB/GFF/Aggregator/alignment.pm
ok 933 - POD test for Bio/DB/GFF/Aggregator/clone.pm
ok 934 - POD test for Bio/DB/GFF/Aggregator/coding.pm
ok 935 - POD test for Bio/DB/GFF/Aggregator/gene.pm
ok 936 - POD test for Bio/DB/GFF/Aggregator/match.pm
ok 937 - POD test for Bio/DB/GFF/Aggregator/none.pm
ok 938 - POD test for Bio/DB/GFF/Aggregator/orf.pm
ok 939 - POD test for Bio/DB/GFF/Aggregator/processed_transcript.pm
ok 940 - POD test for Bio/DB/GFF/Aggregator/so_transcript.pm
ok 941 - POD test for Bio/DB/GFF/Aggregator/transcript.pm
ok 942 - POD test for Bio/DB/GFF/Aggregator/ucsc_acembly.pm
ok 943 - POD test for Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
ok 944 - POD test for Bio/DB/GFF/Aggregator/ucsc_genscan.pm
ok 945 - POD test for Bio/DB/GFF/Aggregator/ucsc_refgene.pm
ok 946 - POD test for Bio/DB/GFF/Aggregator/ucsc_sanger22.pm
ok 947 - POD test for Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm
ok 948 - POD test for Bio/DB/GFF/Aggregator/ucsc_softberry.pm
ok 949 - POD test for Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
ok 950 - POD test for Bio/DB/GFF/Aggregator/ucsc_unigene.pm
ok 951 - POD test for Bio/DB/GFF/Util/Binning.pm
ok 952 - POD test for Bio/DB/GFF/Util/Rearrange.pm
ok 953 - POD test for Bio/DB/SeqFeature/Store/bdb.pm
ok 954 - POD test for Bio/DB/SeqFeature/Store/berkeleydb.pm
ok 955 - POD test for Bio/DB/SeqFeature/Store/berkeleydb3.pm
ok 956 - POD test for Bio/DB/SeqFeature/Store/FeatureFileLoader.pm
ok 957 - POD test for Bio/DB/SeqFeature/Store/GFF2Loader.pm
ok 958 - POD test for Bio/DB/SeqFeature/Store/GFF3Loader.pm
ok 959 - POD test for Bio/DB/SeqFeature/Store/Loader.pm
ok 960 - POD test for Bio/DB/SeqFeature/Store/LoadHelper.pm
ok 961 - POD test for Bio/DB/SeqFeature/Store/memory.pm
ok 962 - POD test for Bio/Matrix/PSM/IO/mast.pm
ok 963 - POD test for Bio/Matrix/PSM/IO/masta.pm
ok 964 - POD test for Bio/Matrix/PSM/IO/meme.pm
ok 965 - POD test for Bio/Matrix/PSM/IO/psiblast.pm
ok 966 - POD test for Bio/Matrix/PSM/IO/transfac.pm
ok 967 - POD test for Bio/Structure/SecStr/DSSP/Res.pm
ok 968 - POD test for Bio/Structure/SecStr/STRIDE/Res.pm
ok 969 - POD test for Bio/Tools/Analysis/DNA/ESEfinder.pm
ok 970 - POD test for Bio/Tools/Analysis/Protein/Domcut.pm
ok 971 - POD test for Bio/Tools/Analysis/Protein/ELM.pm
ok 972 - POD test for Bio/Tools/Analysis/Protein/GOR4.pm
ok 973 - POD test for Bio/Tools/Analysis/Protein/HNN.pm
ok 974 - POD test for Bio/Tools/Analysis/Protein/Mitoprot.pm
ok 975 - POD test for Bio/Tools/Analysis/Protein/NetPhos.pm
ok 976 - POD test for Bio/Tools/Analysis/Protein/Scansite.pm
ok 977 - POD test for Bio/Tools/Analysis/Protein/Sopma.pm
ok 978 - POD test for Bio/Tools/EUtilities/Info/FieldInfo.pm
ok 979 - POD test for Bio/Tools/EUtilities/Info/LinkInfo.pm
ok 980 - POD test for Bio/Tools/EUtilities/Link/LinkSet.pm
ok 981 - POD test for Bio/Tools/EUtilities/Link/UrlLink.pm
ok 982 - POD test for Bio/Tools/EUtilities/Query/GlobalQuery.pm
ok 983 - POD test for Bio/Tools/EUtilities/Summary/DocSum.pm
ok 984 - POD test for Bio/Tools/EUtilities/Summary/Item.pm
ok 985 - POD test for Bio/Tools/EUtilities/Summary/ItemContainerI.pm
ok 986 - POD test for Bio/Tools/Phylo/Molphy/Result.pm
ok 987 - POD test for Bio/Tools/Phylo/PAML/Codeml.pm
ok 988 - POD test for Bio/Tools/Phylo/PAML/ModelResult.pm
ok 989 - POD test for Bio/Tools/Phylo/PAML/Result.pm
ok 990 - POD test for Bio/Tools/Phylo/Phylip/ProtDist.pm
ok 991 - POD test for Bio/Tools/Primer/Assessor/Base.pm
ok 992 - POD test for Bio/Tools/Run/WrapperBase/CommandExts.pm
ok 993 - POD test for Bio/Tools/SiRNA/Ruleset/saigo.pm
ok 994 - POD test for Bio/Tools/SiRNA/Ruleset/tuschl.pm
ok 995 - POD test for Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
ok 996 - POD test for Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
ok 997 - POD test for Bio/DB/GFF/Adaptor/dbi/iterator.pm
ok 998 - POD test for Bio/DB/GFF/Adaptor/dbi/mysql.pm
ok 999 - POD test for Bio/DB/GFF/Adaptor/dbi/mysqlace.pm
ok 1000 - POD test for Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm
ok 1001 - POD test for Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm
ok 1002 - POD test for Bio/DB/GFF/Adaptor/dbi/oracle.pm
ok 1003 - POD test for Bio/DB/GFF/Adaptor/dbi/oracleace.pm
ok 1004 - POD test for Bio/DB/GFF/Adaptor/dbi/pg.pm
ok 1005 - POD test for Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
ok 1006 - POD test for Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
ok 1007 - POD test for Bio/DB/GFF/Adaptor/memory/iterator.pm
ok 1008 - POD test for Bio/DB/SeqFeature/Store/DBI/Iterator.pm
ok 1009 - POD test for Bio/DB/SeqFeature/Store/DBI/mysql.pm
ok 1010 - POD test for Bio/DB/SeqFeature/Store/DBI/Pg.pm
ok 1011 - POD test for Bio/DB/SeqFeature/Store/DBI/SQLite.pm
ok
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

Timeout (max run time is 300s)
/export/home/fly818/bin/perl killed by signal 15