PATH=/usr/bin:/bin:/Users/fly1800/var/megalib/bin
Start 2013-06-30T14:18:55
ActivePerl-1800 CPAN-2.00
Reading '/Users/fly1800/var/cpan/Metadata'
Database was generated on Sun, 30 Jun 2013 14:53:02 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
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
BioPerl-1.6.901/Bio/AnalysisResultI.pm
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BioPerl-1.6.901/Bio/DasI.pm
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BioPerl-1.6.901/Bio/UpdateableSeqI.pm
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BioPerl-1.6.901/Bio/Biblio/MedlineJournalArticle.pm
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BioPerl-1.6.901/Bio/Cluster
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BioPerl-1.6.901/Bio/Cluster/SequenceFamily.pm
BioPerl-1.6.901/Bio/Cluster/UniGene.pm
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BioPerl-1.6.901/Bio/ClusterIO
BioPerl-1.6.901/Bio/ClusterIO/dbsnp.pm
BioPerl-1.6.901/Bio/ClusterIO/unigene.pm
BioPerl-1.6.901/Bio/CodonUsage
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BioPerl-1.6.901/Bio/Coordinate
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BioPerl-1.6.901/Bio/Coordinate/Collection.pm
BioPerl-1.6.901/Bio/Coordinate/ExtrapolatingPair.pm
BioPerl-1.6.901/Bio/Coordinate/GeneMapper.pm
BioPerl-1.6.901/Bio/Coordinate/Graph.pm
BioPerl-1.6.901/Bio/Coordinate/MapperI.pm
BioPerl-1.6.901/Bio/Coordinate/Pair.pm
BioPerl-1.6.901/Bio/Coordinate/Result.pm
BioPerl-1.6.901/Bio/Coordinate/ResultI.pm
BioPerl-1.6.901/Bio/Coordinate/Utils.pm
BioPerl-1.6.901/Bio/Coordinate/Result
BioPerl-1.6.901/Bio/Coordinate/Result/Gap.pm
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BioPerl-1.6.901/Bio/Das
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BioPerl-1.6.901/Bio/Das/SegmentI.pm
BioPerl-1.6.901/Bio/DB
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BioPerl-1.6.901/Bio/DB/LocationI.pm
BioPerl-1.6.901/Bio/DB/MeSH.pm
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BioPerl-1.6.901/Bio/DB/QueryI.pm
BioPerl-1.6.901/Bio/DB/RandomAccessI.pm
BioPerl-1.6.901/Bio/DB/ReferenceI.pm
BioPerl-1.6.901/Bio/DB/RefSeq.pm
BioPerl-1.6.901/Bio/DB/Registry.pm
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BioPerl-1.6.901/Bio/DB/SeqHound.pm
BioPerl-1.6.901/Bio/DB/SeqI.pm
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BioPerl-1.6.901/Bio/DB/Universal.pm
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BioPerl-1.6.901/Bio/DB/Biblio
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BioPerl-1.6.901/Bio/DB/Expression
BioPerl-1.6.901/Bio/DB/Expression/geo.pm
BioPerl-1.6.901/Bio/DB/Flat
BioPerl-1.6.901/Bio/DB/Flat/BDB.pm
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BioPerl-1.6.901/Bio/DB/Flat/BDB
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BioPerl-1.6.901/Bio/DB/Flat/BDB/fasta.pm
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BioPerl-1.6.901/Bio/DB/GFF
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BioPerl-1.6.901/Bio/DB/GFF/Featname.pm
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BioPerl-1.6.901/Bio/DB/GFF/Homol.pm
BioPerl-1.6.901/Bio/DB/GFF/RelSegment.pm
BioPerl-1.6.901/Bio/DB/GFF/Segment.pm
BioPerl-1.6.901/Bio/DB/GFF/Typename.pm
BioPerl-1.6.901/Bio/DB/GFF/Adaptor
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BioPerl-1.6.901/Bio/DB/GFF/Adaptor/berkeleydb.pm
BioPerl-1.6.901/Bio/DB/GFF/Adaptor/biofetch.pm
BioPerl-1.6.901/Bio/DB/GFF/Adaptor/biofetch_oracle.pm
BioPerl-1.6.901/Bio/DB/GFF/Adaptor/dbi.pm
BioPerl-1.6.901/Bio/DB/GFF/Adaptor/memory.pm
BioPerl-1.6.901/Bio/DB/GFF/Adaptor/berkeleydb
BioPerl-1.6.901/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
BioPerl-1.6.901/Bio/DB/GFF/Adaptor/dbi
BioPerl-1.6.901/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
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BioPerl-1.6.901/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm
BioPerl-1.6.901/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm
BioPerl-1.6.901/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm
BioPerl-1.6.901/Bio/DB/GFF/Adaptor/dbi/oracle.pm
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BioPerl-1.6.901/Bio/DB/GFF/Aggregator
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BioPerl-1.6.901/Bio/DB/GFF/Aggregator/clone.pm
BioPerl-1.6.901/Bio/DB/GFF/Aggregator/coding.pm
BioPerl-1.6.901/Bio/DB/GFF/Aggregator/gene.pm
BioPerl-1.6.901/Bio/DB/GFF/Aggregator/match.pm
BioPerl-1.6.901/Bio/DB/GFF/Aggregator/none.pm
BioPerl-1.6.901/Bio/DB/GFF/Aggregator/orf.pm
BioPerl-1.6.901/Bio/DB/GFF/Aggregator/processed_transcript.pm
BioPerl-1.6.901/Bio/DB/GFF/Aggregator/so_transcript.pm
BioPerl-1.6.901/Bio/DB/GFF/Aggregator/transcript.pm
BioPerl-1.6.901/Bio/DB/GFF/Aggregator/ucsc_acembly.pm
BioPerl-1.6.901/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
BioPerl-1.6.901/Bio/DB/GFF/Aggregator/ucsc_genscan.pm
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BioPerl-1.6.901/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm
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BioPerl-1.6.901/Bio/DB/GFF/Aggregator/ucsc_softberry.pm
BioPerl-1.6.901/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
BioPerl-1.6.901/Bio/DB/GFF/Aggregator/ucsc_unigene.pm
BioPerl-1.6.901/Bio/DB/GFF/Util
BioPerl-1.6.901/Bio/DB/GFF/Util/Binning.pm
BioPerl-1.6.901/Bio/DB/GFF/Util/Rearrange.pm
BioPerl-1.6.901/Bio/DB/HIV
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BioPerl-1.6.901/Bio/DB/HIV/lanl-schema.xml
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BioPerl-1.6.901/Bio/DB/SeqFeature
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BioPerl-1.6.901/Bio/DB/SeqFeature/Store/GFF2Loader.pm
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BioPerl-1.6.901/Bio/Event
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BioPerl-1.6.901/Bio/Factory/ApplicationFactoryI.pm
BioPerl-1.6.901/Bio/Factory/DriverFactory.pm
BioPerl-1.6.901/Bio/Factory/FTLocationFactory.pm
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BioPerl-1.6.901/Bio/Factory/MapFactoryI.pm
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BioPerl-1.6.901/Bio/Factory/ObjectFactory.pm
BioPerl-1.6.901/Bio/Factory/ObjectFactoryI.pm
BioPerl-1.6.901/Bio/Factory/SeqAnalysisParserFactory.pm
BioPerl-1.6.901/Bio/Factory/SeqAnalysisParserFactoryI.pm
BioPerl-1.6.901/Bio/Factory/SequenceFactoryI.pm
BioPerl-1.6.901/Bio/Factory/SequenceProcessorI.pm
BioPerl-1.6.901/Bio/Factory/SequenceStreamI.pm
BioPerl-1.6.901/Bio/Factory/TreeFactoryI.pm
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BioPerl-1.6.901/Bio/Index/Blast.pm
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BioPerl-1.6.901/Bio/Index/EMBL.pm
BioPerl-1.6.901/Bio/Index/Fasta.pm
BioPerl-1.6.901/Bio/Index/Fastq.pm
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BioPerl-1.6.901/Bio/Index/SwissPfam.pm
BioPerl-1.6.901/Bio/Index/Swissprot.pm
BioPerl-1.6.901/Bio/LiveSeq
BioPerl-1.6.901/Bio/LiveSeq/AARange.pm
BioPerl-1.6.901/Bio/LiveSeq/Chain.pm
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BioPerl-1.6.901/doc
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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/cgi-bin/deob_interface.cgi
BioPerl-1.6.901/doc/Deobfuscator/lib
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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
BioPerl-1.6.901/ide/bioperl-mode/dist/bioperl-mode.tar.md5
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BioPerl-1.6.901/t/RemoteDB/Query
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BioPerl-1.6.901/t/Restriction
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BioPerl-1.6.901/t/SearchIO/fasta.t
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BioPerl-1.6.901/t/SearchIO/hmmer.t
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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
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BioPerl-1.6.901/t/Seq
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BioPerl-1.6.901/t/Seq/EncodedSeq.t
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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
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BioPerl-1.6.901/t/SeqIO/gbxml.t
BioPerl-1.6.901/t/SeqIO/gcg.t
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BioPerl-1.6.901/t/SeqIO/MultiFile.t
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BioPerl-1.6.901/t/SeqIO/pir.t
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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
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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
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BioPerl-1.6.901/t/SeqTools/SeqPattern.t
BioPerl-1.6.901/t/SeqTools/SeqStats.t
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BioPerl-1.6.901/t/SeqTools/SeqWords.t
BioPerl-1.6.901/t/Structure
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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
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BioPerl-1.6.901/t/Tools/Genomewise.t
BioPerl-1.6.901/t/Tools/Genpred.t
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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
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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
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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
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BioPerl-1.6.901/t/Tools/Phylo/Molphy.t
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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: Building C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz
>>> /Users/fly1800/ap1800-297214/bin/perl-dynamic Build.PL
could not find ParserDetails.ini in /Users/fly1800/var/megalib/XML/SAX
Checking prerequisites...
recommends:
* Convert::Binary::C is not installed
* GraphViz is not installed
* PostScript::TextBlock is not installed
* SOAP::Lite is not installed
* SVG::Graph is not installed
* XML::DOM::XPath is not installed
Checking optional features...
EntrezGene............disabled
requires:
! Bio::ASN1::EntrezGene 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 ----
Data::Stag [requires]
Running Build test
Delayed until after prerequisites
Running test for module 'Data::Stag'
Running make for C/CM/CMUNGALL/Data-Stag-0.11.tar.gz
Checksum for /net/nas/data/cpan/authors/id/C/CM/CMUNGALL/Data-Stag-0.11.tar.gz ok
Data-Stag-0.11/
Data-Stag-0.11/c-ext/
Data-Stag-0.11/c-ext/README.c-ext
Data-Stag-0.11/c-ext/staglib.c
Data-Stag-0.11/c-ext/staglib.h
Data-Stag-0.11/Changes
Data-Stag-0.11/Data/
Data-Stag-0.11/Data/Stag/
Data-Stag-0.11/Data/Stag/Arr2HTML.pm
Data-Stag-0.11/Data/Stag/Base.pm
Data-Stag-0.11/Data/Stag/BaseGenerator.pm
Data-Stag-0.11/Data/Stag/BaseHandler.pm
Data-Stag-0.11/Data/Stag/ChainHandler.pm
Data-Stag-0.11/Data/Stag/DTDWriter.pm
Data-Stag-0.11/Data/Stag/GraphHandler.pm
Data-Stag-0.11/Data/Stag/HashDB.pm
Data-Stag-0.11/Data/Stag/IndentParser.pm
Data-Stag-0.11/Data/Stag/IndentWriter.pm
Data-Stag-0.11/Data/Stag/ITextParser.pm
Data-Stag-0.11/Data/Stag/ITextWriter.pm
Data-Stag-0.11/Data/Stag/null.pm
Data-Stag-0.11/Data/Stag/PerlWriter.pm
Data-Stag-0.11/Data/Stag/PodParser.pm
Data-Stag-0.11/Data/Stag/SAX2Stag.pm
Data-Stag-0.11/Data/Stag/Simple.pm
Data-Stag-0.11/Data/Stag/StagDB.pm
Data-Stag-0.11/Data/Stag/StagI.pm
Data-Stag-0.11/Data/Stag/StagImpl.pm
Data-Stag-0.11/Data/Stag/SxprParser.pm
Data-Stag-0.11/Data/Stag/SxprWriter.pm
Data-Stag-0.11/Data/Stag/Util.pm
Data-Stag-0.11/Data/Stag/Writer.pm
Data-Stag-0.11/Data/Stag/XMLParser.pm
Data-Stag-0.11/Data/Stag/XMLWriter.pm
Data-Stag-0.11/Data/Stag/XSLHandler.pm
Data-Stag-0.11/Data/Stag/XSLTHandler.pm
Data-Stag-0.11/Data/Stag.pm
Data-Stag-0.11/dev/
Data-Stag-0.11/dev/create-manifest.sh
Data-Stag-0.11/dev/data-stag.spec
Data-Stag-0.11/dev/mkspec.pl
Data-Stag-0.11/elisp/
Data-Stag-0.11/elisp/itext-mode.el
Data-Stag-0.11/homepage/
Data-Stag-0.11/homepage/archBIG.png
Data-Stag-0.11/homepage/dbstag-tutorial.sgml
Data-Stag-0.11/homepage/images/
Data-Stag-0.11/homepage/images/k-schema-diagram.png
Data-Stag-0.11/homepage/images/rr-schema-diagram.png
Data-Stag-0.11/homepage/index.html
Data-Stag-0.11/homepage/makefile
Data-Stag-0.11/homepage/mk.sh
Data-Stag-0.11/homepage/mkpodhtml.pl
Data-Stag-0.11/homepage/mkscriptdoc.pl
Data-Stag-0.11/homepage/script-docs/
Data-Stag-0.11/homepage/script-docs/selectall_html.html
Data-Stag-0.11/homepage/script-docs/selectall_xml.html
Data-Stag-0.11/homepage/script-docs/stag-autoddl.html
Data-Stag-0.11/homepage/script-docs/stag-autoschema.html
Data-Stag-0.11/homepage/script-docs/stag-autotemplate.html
Data-Stag-0.11/homepage/script-docs/stag-bulkload.html
Data-Stag-0.11/homepage/script-docs/stag-db.html
Data-Stag-0.11/homepage/script-docs/stag-diff.html
Data-Stag-0.11/homepage/script-docs/stag-drawtree.html
Data-Stag-0.11/homepage/script-docs/stag-elcount.html
Data-Stag-0.11/homepage/script-docs/stag-eval.html
Data-Stag-0.11/homepage/script-docs/stag-filter.html
Data-Stag-0.11/homepage/script-docs/stag-findsubtree.html
Data-Stag-0.11/homepage/script-docs/stag-flatten.html
Data-Stag-0.11/homepage/script-docs/stag-grep.html
Data-Stag-0.11/homepage/script-docs/stag-handle.html
Data-Stag-0.11/homepage/script-docs/stag-ir.html
Data-Stag-0.11/homepage/script-docs/stag-itext2simple.html
Data-Stag-0.11/homepage/script-docs/stag-itext2sxpr.html
Data-Stag-0.11/homepage/script-docs/stag-itext2xml.html
Data-Stag-0.11/homepage/script-docs/stag-join.html
Data-Stag-0.11/homepage/script-docs/stag-merge.html
Data-Stag-0.11/homepage/script-docs/stag-mogrify.html
Data-Stag-0.11/homepage/script-docs/stag-parse.html
Data-Stag-0.11/homepage/script-docs/stag-pgslurp.html
Data-Stag-0.11/homepage/script-docs/stag-query.html
Data-Stag-0.11/homepage/script-docs/stag-show-template.html
Data-Stag-0.11/homepage/script-docs/stag-sl2sql.html
Data-Stag-0.11/homepage/script-docs/stag-splitter.html
Data-Stag-0.11/homepage/script-docs/stag-storenode.html
Data-Stag-0.11/homepage/script-docs/stag-template2bin.html
Data-Stag-0.11/homepage/script-docs/stag-template2pod.html
Data-Stag-0.11/homepage/script-docs/stag-templates2scripts.html
Data-Stag-0.11/homepage/script-docs/stag-view.html
Data-Stag-0.11/homepage/script-docs/stag-xml2itext.html
Data-Stag-0.11/homepage/script-docs/stag-xmlsplit.html
Data-Stag-0.11/homepage/script-list.html
Data-Stag-0.11/homepage/stag-db-tutorial.html
Data-Stag-0.11/homepage/stag-poster.html
Data-Stag-0.11/INSTALL
Data-Stag-0.11/Makefile.PL
Data-Stag-0.11/MANIFEST
Data-Stag-0.11/META.yml
Data-Stag-0.11/README
Data-Stag-0.11/scripts/
Data-Stag-0.11/scripts/stag-autoschema.pl
Data-Stag-0.11/scripts/stag-db.pl
Data-Stag-0.11/scripts/stag-diff.pl
Data-Stag-0.11/scripts/stag-drawtree.pl
Data-Stag-0.11/scripts/stag-elcount.pl
Data-Stag-0.11/scripts/stag-eval.pl
Data-Stag-0.11/scripts/stag-filter.pl
Data-Stag-0.11/scripts/stag-findsubtree.pl
Data-Stag-0.11/scripts/stag-flatten.pl
Data-Stag-0.11/scripts/stag-grep.pl
Data-Stag-0.11/scripts/stag-handle.pl
Data-Stag-0.11/scripts/stag-itext2simple.pl
Data-Stag-0.11/scripts/stag-itext2sxpr.pl
Data-Stag-0.11/scripts/stag-itext2xml.pl
Data-Stag-0.11/scripts/stag-join.pl
Data-Stag-0.11/scripts/stag-merge.pl
Data-Stag-0.11/scripts/stag-mogrify.pl
Data-Stag-0.11/scripts/stag-parse.pl
Data-Stag-0.11/scripts/stag-query.pl
Data-Stag-0.11/scripts/stag-splitter.pl
Data-Stag-0.11/scripts/stag-view.pl
Data-Stag-0.11/scripts/stag-xml2itext.pl
Data-Stag-0.11/scripts/stag-xmlsplit.pl
Data-Stag-0.11/t/
Data-Stag-0.11/t/animal.x
Data-Stag-0.11/t/autoschema.t
Data-Stag-0.11/t/barfly.x
Data-Stag-0.11/t/bio.x
Data-Stag-0.11/t/chainhandler.t
Data-Stag-0.11/t/collapse.x
Data-Stag-0.11/t/data/
Data-Stag-0.11/t/data/attrs.xml
Data-Stag-0.11/t/data/bf.txt
Data-Stag-0.11/t/data/eco.el
Data-Stag-0.11/t/data/eco.itext
Data-Stag-0.11/t/data/homol.itext
Data-Stag-0.11/t/data/persons.el
Data-Stag-0.11/t/db.t
Data-Stag-0.11/t/emptytag.t
Data-Stag-0.11/t/get.t
Data-Stag-0.11/t/graph.x
Data-Stag-0.11/t/handlers.t
Data-Stag-0.11/t/handlers2.t
Data-Stag-0.11/t/handlers2.x
Data-Stag-0.11/t/hashdb.t
Data-Stag-0.11/t/hashdb.x
Data-Stag-0.11/t/homol.t
Data-Stag-0.11/t/lisp.x
Data-Stag-0.11/t/parsestr.t
Data-Stag-0.11/t/path.x
Data-Stag-0.11/t/path2.x
Data-Stag-0.11/t/qmatch.t
Data-Stag-0.11/t/roundtrip-attrs.t
Data-Stag-0.11/t/set-attrs.t
Data-Stag-0.11/t/set.t
Data-Stag-0.11/t/sxpr.t
Data-Stag-0.11/t/unhash.t
Data-Stag-0.11/t/unset.t
Data-Stag-0.11/t/write.t
Data-Stag-0.11/t/xml1.t
Data-Stag-0.11/t/xml2.t
CPAN.pm: Building C/CM/CMUNGALL/Data-Stag-0.11.tar.gz
>>> /Users/fly1800/ap1800-297214/bin/perl-dynamic Makefile.PL
External Module XML::LibXSLT, XSLT,
is not installed on this computer.
Data::Stag::XSLTHandler in Data::Stag needs it for XSLT Transformations
Information:
There are some external packages and perl modules, listed above, which
stag uses. This only effects the functionality which is listed above:
the rest of stag will work fine, which includes nearly all of the
core functionality.
Enjoy the rest of stag, which you can use after going 'make install'
Checking if your kit is complete...
Looks good
Writing Makefile for Data
Writing MYMETA.yml and MYMETA.json
>>> make
cp Data/Stag/DTDWriter.pm blib/lib/Data/Stag/DTDWriter.pm
cp Data/Stag/Util.pm blib/lib/Data/Stag/Util.pm
cp Data/Stag/StagImpl.pm blib/lib/Data/Stag/StagImpl.pm
cp Data/Stag/BaseGenerator.pm blib/lib/Data/Stag/BaseGenerator.pm
cp Data/Stag/SAX2Stag.pm blib/lib/Data/Stag/SAX2Stag.pm
cp Data/Stag.pm blib/lib/Data/Stag.pm
cp Data/Stag/Arr2HTML.pm blib/lib/Data/Stag/Arr2HTML.pm
cp Data/Stag/Base.pm blib/lib/Data/Stag/Base.pm
cp Data/Stag/XSLTHandler.pm blib/lib/Data/Stag/XSLTHandler.pm
cp Data/Stag/IndentParser.pm blib/lib/Data/Stag/IndentParser.pm
cp Data/Stag/PodParser.pm blib/lib/Data/Stag/PodParser.pm
cp Data/Stag/SxprParser.pm blib/lib/Data/Stag/SxprParser.pm
cp Data/Stag/Writer.pm blib/lib/Data/Stag/Writer.pm
cp Data/Stag/null.pm blib/lib/Data/Stag/null.pm
cp Data/Stag/PerlWriter.pm blib/lib/Data/Stag/PerlWriter.pm
cp Data/Stag/ITextParser.pm blib/lib/Data/Stag/ITextParser.pm
cp Data/Stag/ChainHandler.pm blib/lib/Data/Stag/ChainHandler.pm
cp Data/Stag/XMLParser.pm blib/lib/Data/Stag/XMLParser.pm
cp Data/Stag/GraphHandler.pm blib/lib/Data/Stag/GraphHandler.pm
cp Data/Stag/XSLHandler.pm blib/lib/Data/Stag/XSLHandler.pm
cp Data/Stag/StagDB.pm blib/lib/Data/Stag/StagDB.pm
cp Data/Stag/HashDB.pm blib/lib/Data/Stag/HashDB.pm
cp Data/Stag/IndentWriter.pm blib/lib/Data/Stag/IndentWriter.pm
cp Data/Stag/XMLWriter.pm blib/lib/Data/Stag/XMLWriter.pm
cp Data/Stag/ITextWriter.pm blib/lib/Data/Stag/ITextWriter.pm
cp Data/Stag/StagI.pm blib/lib/Data/Stag/StagI.pm
cp Data/Stag/BaseHandler.pm blib/lib/Data/Stag/BaseHandler.pm
cp Data/Stag/SxprWriter.pm blib/lib/Data/Stag/SxprWriter.pm
cp Data/Stag/Simple.pm blib/lib/Data/Stag/Simple.pm
cp scripts/stag-merge.pl blib/script/stag-merge.pl
/Users/fly1800/ap1800-297214/bin/perl-dynamic -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-merge.pl
cp scripts/stag-drawtree.pl blib/script/stag-drawtree.pl
/Users/fly1800/ap1800-297214/bin/perl-dynamic -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-drawtree.pl
cp scripts/stag-xml2itext.pl blib/script/stag-xml2itext.pl
/Users/fly1800/ap1800-297214/bin/perl-dynamic -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-xml2itext.pl
cp scripts/stag-join.pl blib/script/stag-join.pl
/Users/fly1800/ap1800-297214/bin/perl-dynamic -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-join.pl
cp scripts/stag-itext2simple.pl blib/script/stag-itext2simple.pl
/Users/fly1800/ap1800-297214/bin/perl-dynamic -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-itext2simple.pl
cp scripts/stag-diff.pl blib/script/stag-diff.pl
/Users/fly1800/ap1800-297214/bin/perl-dynamic -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-diff.pl
cp scripts/stag-findsubtree.pl blib/script/stag-findsubtree.pl
/Users/fly1800/ap1800-297214/bin/perl-dynamic -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-findsubtree.pl
cp scripts/stag-query.pl blib/script/stag-query.pl
/Users/fly1800/ap1800-297214/bin/perl-dynamic -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-query.pl
cp scripts/stag-parse.pl blib/script/stag-parse.pl
/Users/fly1800/ap1800-297214/bin/perl-dynamic -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-parse.pl
cp scripts/stag-flatten.pl blib/script/stag-flatten.pl
/Users/fly1800/ap1800-297214/bin/perl-dynamic -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-flatten.pl
cp scripts/stag-filter.pl blib/script/stag-filter.pl
/Users/fly1800/ap1800-297214/bin/perl-dynamic -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-filter.pl
cp scripts/stag-grep.pl blib/script/stag-grep.pl
/Users/fly1800/ap1800-297214/bin/perl-dynamic -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-grep.pl
cp scripts/stag-mogrify.pl blib/script/stag-mogrify.pl
/Users/fly1800/ap1800-297214/bin/perl-dynamic -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-mogrify.pl
cp scripts/stag-itext2xml.pl blib/script/stag-itext2xml.pl
/Users/fly1800/ap1800-297214/bin/perl-dynamic -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-itext2xml.pl
cp scripts/stag-view.pl blib/script/stag-view.pl
/Users/fly1800/ap1800-297214/bin/perl-dynamic -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-view.pl
cp scripts/stag-handle.pl blib/script/stag-handle.pl
/Users/fly1800/ap1800-297214/bin/perl-dynamic -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-handle.pl
cp scripts/stag-db.pl blib/script/stag-db.pl
/Users/fly1800/ap1800-297214/bin/perl-dynamic -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-db.pl
cp scripts/stag-splitter.pl blib/script/stag-splitter.pl
/Users/fly1800/ap1800-297214/bin/perl-dynamic -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-splitter.pl
cp scripts/stag-itext2sxpr.pl blib/script/stag-itext2sxpr.pl
/Users/fly1800/ap1800-297214/bin/perl-dynamic -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-itext2sxpr.pl
cp scripts/stag-autoschema.pl blib/script/stag-autoschema.pl
/Users/fly1800/ap1800-297214/bin/perl-dynamic -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-autoschema.pl
Manifying blib/man1/stag-findsubtree.pl.1
Manifying blib/man1/stag-query.pl.1
Manifying blib/man1/stag-drawtree.pl.1
Manifying blib/man1/stag-merge.pl.1
Manifying blib/man1/stag-diff.pl.1
Manifying blib/man1/stag-join.pl.1
Manifying blib/man1/stag-handle.pl.1
Manifying blib/man1/stag-db.pl.1
Manifying blib/man1/stag-view.pl.1
Manifying blib/man1/stag-autoschema.pl.1
Manifying blib/man1/stag-splitter.pl.1
Manifying blib/man1/stag-flatten.pl.1
Manifying blib/man1/stag-filter.pl.1
Manifying blib/man1/stag-parse.pl.1
Manifying blib/man1/stag-grep.pl.1
Manifying blib/man1/stag-mogrify.pl.1
Manifying blib/man3/Data::Stag::StagDB.3
Manifying blib/man3/Data::Stag.3
Manifying blib/man3/Data::Stag::XSLHandler.3
Manifying blib/man3/Data::Stag::HashDB.3
Manifying blib/man3/Data::Stag::XMLWriter.3
Manifying blib/man3/Data::Stag::BaseGenerator.3
Manifying blib/man3/Data::Stag::ITextWriter.3
Manifying blib/man3/Data::Stag::ITextParser.3
Manifying blib/man3/Data::Stag::BaseHandler.3
Manifying blib/man3/Data::Stag::Simple.3
Manifying blib/man3/Data::Stag::PerlWriter.3
Manifying blib/man3/Data::Stag::IndentParser.3
Manifying blib/man3/Data::Stag::SAX2Stag.3
Manifying blib/man3/Data::Stag::null.3
Manifying blib/man3/Data::Stag::SxprWriter.3
Manifying blib/man3/Data::Stag::SxprParser.3
Manifying blib/man3/Data::Stag::ChainHandler.3
Manifying blib/man3/Data::Stag::StagImpl.3
Manifying blib/man3/Data::Stag::XMLParser.3
Manifying blib/man3/Data::Stag::Arr2HTML.3
Manifying blib/man3/Data::Stag::XSLTHandler.3
Manifying blib/man3/Data::Stag::Writer.3
Manifying blib/man3/Data::Stag::GraphHandler.3
Manifying blib/man3/Data::Stag::PodParser.3
Manifying blib/man3/Data::Stag::DTDWriter.3
Manifying blib/man3/Data::Stag::IndentWriter.3
CMUNGALL/Data-Stag-0.11.tar.gz
make -- OK
Running make test
>>> make test TEST_VERBOSE=1
PERL_DL_NONLAZY=1 /Users/fly1800/ap1800-297214/bin/perl-dynamic "-MExtUtils::Command::MM" "-e" "test_harness(1, 'blib/lib', 'blib/arch')" t/*.t
t/autoschema.t .......
1..3
# Running under perl version 5.018000 for darwin
# Current time local: Sun Jun 30 14:19:35 2013
# Current time GMT: Sun Jun 30 21:19:35 2013
# Using Test.pm version 1.26
'(db
(species_set
(species+
(common_name "VARCHAR\(31\)")
(binomial "VARCHAR\(31\)")
(tax_id "INT")))
(gene_set
(gene+
(symbol "VARCHAR\(15\)")
(tax_id "INT")
(phenotype* "VARCHAR\(31\)")
(GO_term "VARCHAR\(63\)")
(map?
(cytological
(chromosome "INT")
(band "VARCHAR\(15\)")))
(synonym "VARCHAR\(7\)")))
(similarity_set
(pair+
(symbol+ "VARCHAR\(15\)"))))
ok 1
ok 2
ok 3
ok
t/chainhandler.t .....
1..2
# Running under perl version 5.018000 for darwin
# Current time local: Sun Jun 30 14:19:35 2013
# Current time GMT: Sun Jun 30 21:19:35 2013
# Using Test.pm version 1.26
chainhandler...
checking..
ok 1
ok 2
ok
t/db.t ...............
1..1
# Running under perl version 5.018000 for darwin
# Current time local: Sun Jun 30 14:19:35 2013
# Current time GMT: Sun Jun 30 21:19:35 2013
# Using Test.pm version 1.26
lucas
george
star wars
sci-fi
ford
harrison
han solo
fisher
carrie
princess leia
hamill
mark
luke skywalker
earl-jones
james
darth vader
prowse
david
darth vader
guiness
alec
obi-wan kenobi
attack of the clones
sci-fi
mcgregor
ewan
obi-wan kenobi
portman
natalie
princess amigdala
jackson
peter
braindead
horror
-
-
-
lord of the rings
fantasy
lee
christopher
saruman
kellan
ian
gandalf
kurosawa
akira
seven samurai
samurai
mifune
toshiro
Kikuchiyo
cameron
john
terminator
sci-fi
schwarzenegger
arnold
terminator
terminator2
sci-fi
schwarzenegger
arnold
terminator
coen
joel
barton fink
odd
turturro
john
barton fink
goodman
john
charlie meadows
coen
ethan
barton fink
odd
turturro
john
barton fink
goodman
john
charlie meadows
star wars
sci-fi
lucas
george
US
han solo
ford
harrison
princess leia
fisher
carrie
luke skywalker
hamill
mark
darth vader
earl-jones
james
prowse
david
obi-wan kenobi
guiness
alec
attack of the clones
sci-fi
lucas
george
US
obi-wan kenobi
mcgregor
ewan
princess amigdala
portman
natalie
braindead
horror
jackson
peter
new zealand
-
-
-
lord of the rings
fantasy
jackson
peter
new zealand
saruman
lee
christopher
gandalf
kellan
ian
seven samurai
samurai
kurosawa
akira
japan
Kikuchiyo
mifune
toshiro
terminator
sci-fi
cameron
john
US
terminator
schwarzenegger
arnold
terminator2
sci-fi
cameron
john
US
terminator
schwarzenegger
arnold
barton fink
odd
coen
joel
US
coen
ethan
US
barton fink
turturro
john
charlie meadows
goodman
john
isa
dog
mammal
isa
cat
mammal
isa
mammal
animal
isa
zebra
horse
isa
horse
mammal
isa
unicorn
horse
isa
unicorn
imaginary-animal
instance-of
rover
dog
instance-of
whiskers
cat
instance-of
spot
dog
parent-of
spot
rover
ok 1
ok
t/emptytag.t .........
1..3
# Running under perl version 5.018000 for darwin
# Current time local: Sun Jun 30 14:19:35 2013
# Current time GMT: Sun Jun 30 21:19:35 2013
# Using Test.pm version 1.26
foo
0
0
'(a
(b "foo")
(c "")
(d "0")
(e "0")
(f ""))
ok 1
ok 2
4
1
1
4
ok 3
ok
t/get.t ..............
1..17
# Running under perl version 5.018000 for darwin
# Current time local: Sun Jun 30 14:19:35 2013
# Current time GMT: Sun Jun 30 21:19:35 2013
# Using Test.pm version 1.26
ok 1
ok 2
house mouse
Mus musculus
10090
fruitfly
Drosophila melanogaster
7227
human
Homo sapiens
9606
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
HGNC
9606
Hemochromatosis
Porphyria variegata
iron homeostasis
Hfe
MR2
10090
integral membrane protein
S:HGNC Hfe HGNC Hfe WNT3A Wnt3a
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok
t/handlers.t .........
1..9
# Running under perl version 5.018000 for darwin
# Current time local: Sun Jun 30 14:19:35 2013
# Current time GMT: Sun Jun 30 21:19:35 2013
# Using Test.pm version 1.26
CACHING HGNC
CACHING Hfe
house mouse
Mus musculus
10090
fruitfly
Drosophila melanogaster
7227
human
Homo sapiens
9606
HGNC
9606
Hemochromatosis
Porphyria variegata
iron homeostasis
human
Homo sapiens
9606
Hfe
MR2
10090
integral membrane protein
house mouse
Mus musculus
10090
HGNC
Hfe
HGNC
9606
Hemochromatosis
Porphyria variegata
iron homeostasis
human
Homo sapiens
9606
Hfe
MR2
10090
integral membrane protein
house mouse
Mus musculus
10090
WNT3A
Wnt3a
Dunno what symbol WNT3A is
Dunno what symbol Wnt3a is
remaining tree:
'(db
(species_set
(species
(common_name "house mouse")
(binomial "Mus musculus")
(tax_id "10090"))
(species
(common_name "fruitfly")
(binomial "Drosophila melanogaster")
(tax_id "7227"))
(species
(common_name "human")
(binomial "Homo sapiens")
(tax_id "9606")))
(gene_set
(gene
(symbol "HGNC")
(tax_id "9606")
(phenotype "Hemochromatosis")
(phenotype "Porphyria variegata")
(GO_term "iron homeostasis")
(map
(cytological
(chromosome "6")
(band "p21.3"))
(foo "1"))
(species
(common_name "human")
(binomial "Homo sapiens")
(tax_id "9606")))
(gene
(symbol "Hfe")
(synonym "MR2")
(tax_id "10090")
(GO_term "integral membrane protein")
(species
(common_name "house mouse")
(binomial "Mus musculus")
(tax_id "10090"))))
(similarity_set
(pair
(symbol "HGNC")
(symbol "Hfe")
(gene
(symbol "HGNC")
(tax_id "9606")
(phenotype "Hemochromatosis")
(phenotype "Porphyria variegata")
(GO_term "iron homeostasis")
(map
(cytological
(chromosome "6")
(band "p21.3"))
(foo "1"))
(species
(common_name "human")
(binomial "Homo sapiens")
(tax_id "9606")))
(gene
(symbol "Hfe")
(synonym "MR2")
(tax_id "10090")
(GO_term "integral membrane protein")
(species
(common_name "house mouse")
(binomial "Mus musculus")
(tax_id "10090"))))
(pair
(symbol "WNT3A")
(symbol "Wnt3a")
(comment "Dunno what symbol WNT3A is")
(comment "Dunno what symbol Wnt3a is"))))
HGNC
Hfe
HGNC
9606
Hemochromatosis
Porphyria variegata
iron homeostasis
human
Homo sapiens
9606
Hfe
MR2
10090
integral membrane protein
house mouse
Mus musculus
10090
WNT3A
Wnt3a
Dunno what symbol WNT3A is
Dunno what symbol Wnt3a is
HGNC
9606
Hemochromatosis
Porphyria variegata
iron homeostasis
human
Homo sapiens
9606
Hfe
MR2
10090
integral membrane protein
house mouse
Mus musculus
10090
ok 1
ok 2
ok 3
ok 4
'(gene
(symbol "Hfe")
(synonym "MR2")
(tax_id "10090")
(GO_term "integral membrane protein")
(species
(common_name "house mouse")
(binomial "Mus musculus")
(tax_id "10090")))
ok 5
ok 6
ok 7
ok 8
ok 9
names=gene_set gene symbol tax_id phenotype phenotype GO_term map cytological chromosome band foo species common_name binomial tax_id gene symbol synonym tax_id GO_term species common_name binomial tax_id
=>gene_set
gene_set=>gene
gene=>symbol
gene=>tax_id
gene=>phenotype
gene=>phenotype
gene=>GO_term
gene=>map
map=>cytological
cytological=>chromosome
cytological=>band
map=>foo
gene=>species
species=>common_name
species=>binomial
species=>tax_id
gene_set=>gene
gene=>symbol
gene=>synonym
gene=>tax_id
gene=>GO_term
gene=>species
species=>common_name
species=>binomial
species=>tax_id
ok
t/handlers2.t ........
1..9
# Running under perl version 5.018000 for darwin
# Current time local: Sun Jun 30 14:19:35 2013
# Current time GMT: Sun Jun 30 21:19:35 2013
# Using Test.pm version 1.26
original:
house mouse
Mus musculus
10090
house mouse
Mus musculus
10090
fruitfly
Drosophila melanogaster
7227
fruitfly
Drosophila melanogaster
7227
human
Homo sapiens
9606
human
Homo sapiens
9606
remaining tree:
'(db
(species_set
(species
(common_name "house mouse")
(binomial "Mus musculus")
(tax_id "10090"))
(species
(common_name "house mouse")
(binomial "Mus musculus")
(tax_id "10090"))
(species
(common_name "fruitfly")
(binomial "Drosophila melanogaster")
(tax_id "7227"))
(species
(common_name "fruitfly")
(binomial "Drosophila melanogaster")
(tax_id "7227"))
(species
(common_name "human")
(binomial "Homo sapiens")
(tax_id "9606"))
(species
(common_name "human")
(binomial "Homo sapiens")
(tax_id "9606"))))
ok 1
ok 2
ok 3
'( "")
'( "")
ok 4
ok 5
ok 6
ok 7
ok 8
'(set)
ok 9
ok
t/hashdb.t ...........
1..2
# Running under perl version 5.018000 for darwin
# Current time local: Sun Jun 30 14:19:36 2013
# Current time GMT: Sun Jun 30 21:19:36 2013
# Using Test.pm version 1.26
'(species
(common_name "fruitfly")
(binomial "Drosophila melanogaster")
(tax_id "7227"))
ok 1
HASHING
HASHED
gene:
symbol: HGNC
tax_id: 9606
phenotype: Hemochromatosis
phenotype: Porphyria variegata
GO_term: iron homeostasis
map:
cytological:
chromosome: 6
band: p21.3
ok 2
ok
t/homol.t ............
1..9
# Running under perl version 5.018000 for darwin
# Current time local: Sun Jun 30 14:19:36 2013
# Current time GMT: Sun Jun 30 21:19:36 2013
# Using Test.pm version 1.26
HGNC
human
Homo sapiens
9606
Hemochromatosis
Porphyria variegata
iron homeostasis
Hfe
MR2
house mouse
Mus musculus
10090
integral membrane protein
ok 1
ok 2
ok 3
ok 4
ok 5
HGNC
human
Homo sapiens
9606
Hemochromatosis
Porphyria variegata
iron homeostasis
Hfe
MR2
house mouse
Mus musculus
10090
integral membrane protein
ok 6
ok 7
ok 8
ok 9
names=gene_set gene symbol species common_name binomial tax_id phenotype phenotype GO_term map cytological chromosome band gene symbol synonym species common_name binomial tax_id GO_term
=>gene_set
gene_set=>gene
gene=>symbol
gene=>species
species=>common_name
species=>binomial
species=>tax_id
gene=>phenotype
gene=>phenotype
gene=>GO_term
gene=>map
map=>cytological
cytological=>chromosome
cytological=>band
gene_set=>gene
gene=>symbol
gene=>synonym
gene=>species
species=>common_name
species=>binomial
species=>tax_id
gene=>GO_term
ok
t/parsestr.t .........
1..6
# Running under perl version 5.018000 for darwin
# Current time local: Sun Jun 30 14:19:36 2013
# Current time GMT: Sun Jun 30 21:19:36 2013
# Using Test.pm version 1.26
bar
y
ok 1
example of mixedcontent
'(yo
(paragraph
(@
(id "1"))
(. "example of")
(bold "mixed")
(. "content")))
ok 2
ok 3
ok 4
'(yo
(paragraph
(@
(id "1"))
(. "example of")
(bold "mixed")
(. "content")))
TEXT
'(yo
(paragraph
(@
(id "1"))
(. "TEXT")))
ok 5
ok 6
ok
t/qmatch.t ...........
1..9
# Running under perl version 5.018000 for darwin
# Current time local: Sun Jun 30 14:19:36 2013
# Current time GMT: Sun Jun 30 21:19:36 2013
# Using Test.pm version 1.26
big dave
methyl
foo
shuggy
bar
auchtermuchty
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
2
1
2
ok 7
ok 8
2
ok 9
2
1
ok
t/roundtrip-attrs.t ..
1..5
# Running under perl version 5.018000 for darwin
# Current time local: Sun Jun 30 14:19:36 2013
# Current time GMT: Sun Jun 30 21:19:36 2013
# Using Test.pm version 1.26
ok 1
ok 2
ok 3
'(address
(a
(@
(href "mailto:cjm@fruitfly.org"))
(. "fred")))
ok 4
Stag - Structured Tag Library
Stag - Structured Tag Library
top
#000000
images/celtic-stag.gif
|
The Stag project currently consists of two perl modules,
both of which are available from
http://www.cpan.orgCPANor
http://sourceforge.net/projects/stagsourceforge:
Data::StagThis module is for manipulating data as recursively
nested tag/value pairs (
Structured
tags or
Simple
Tree
aggreggates). At this time there is only a perl
implementation,
http://search.cpan.org/perldoc?Data::StagData::Stag, but C and Lisp implementations
are planned.
Stags can easily be represented as XML or as lisp-style
S-expressions, or using the Stag native indented text
format. They can also be represented in perl using nested
arrays.
DBIx::DBStagThis module is for conversion between relational
representations and hierarchical (Stag)
representations. SQL query results are automatically
decomposed into the relations and a hierarchical structure
is inferred. This modules also allows you to create SQL
templates - a powerful way of reusing SQL statements
joining multiple tables.
http://search.cpan.org/perldoc?DBIx::DBStagDBIx::DBStag
|
http://sourceforge.net
31
http://sourceforge.net/sflogo.php?group_id=68482&type=1
SourceForge.net Logo
88
0
mailto:cjm@fruitfly.orgfred
Last modified: Mon Apr 12 11:33:36 PDT 2004
mailto:cjm@fruitfly.org
ok 5
ok
t/set-attrs.t ........
1..3
# Running under perl version 5.018000 for darwin
# Current time local: Sun Jun 30 14:19:37 2013
# Current time GMT: Sun Jun 30 21:19:37 2013
# Using Test.pm version 1.26
'(person
(name "jim")
(phone_no "555-1111")
(phone_no "555-2222"))
'(person
(name "jim")
(phone_no "555-1111")
(phone_no "555-2222")
(phone_no "555-3333")
(phone_no "555-4444"))
'(dataset
(person
(name "jim")
(phone_no "555-1111")
(phone_no "555-2222")
(phone_no "555-3333")
(phone_no "555-4444"))
(person
(name "fred")
(phone_no "555-5555")))
'(dataset
(person
(name "jim")
(phone_no "555-1111")
(phone_no "555-2222")
(phone_no "555-3333")
(phone_no "555-4444"))
(person
(name "fred")
(phone_no "555-5555"))
(person
(name "fred")
(phone_no "555-5555")))
jim
555-1111
555-2222
555-3333
555-4444
jim
555-1111
555-2222
555-3333
555-4444
ok 1
ok 2
ok 3
ok
t/set.t ..............
1..2
# Running under perl version 5.018000 for darwin
# Current time local: Sun Jun 30 14:19:37 2013
# Current time GMT: Sun Jun 30 21:19:37 2013
# Using Test.pm version 1.26
detective
Sherlock Holmes
James Bond
secret agent
detective
Sherlock Holmes
London
221B Baker Street
Great Britain
James Bond
secret agent
ok 1
detective
Sherlock Holmes
London
221B Baker Street
Great Britain
James Bond
secret agent
ok 2
ok
t/sxpr.t .............
1..2
# Running under perl version 5.018000 for darwin
# Current time local: Sun Jun 30 14:19:37 2013
# Current time GMT: Sun Jun 30 21:19:37 2013
# Using Test.pm version 1.26
ok 1
ok 2
ok
t/unhash.t ...........
1..4
# Running under perl version 5.018000 for darwin
# Current time local: Sun Jun 30 14:19:37 2013
# Current time GMT: Sun Jun 30 21:19:37 2013
# Using Test.pm version 1.26
NY
Katonah
Hickory Street
10578
Sarah
James
30
34
Hill
James
Garden City
NY
The Manse
19 Chestnut Ln
11291
Sarah
James
30
Hickory Street
NY
Katonah
10578
11291
NY
Garden City
The Manse
19 Chestnut Ln
James
Hill
34
The Manse 19 Chestnut Ln
ok 1
blonde
blue
Fred
Jill
John
Gerald
Jill
John
Gerald
Fred
blue
blonde
Jill John Gerald
ok 2
ok 3
ok 4
ok
t/unset.t ............
1..4
# Running under perl version 5.018000 for darwin
# Current time local: Sun Jun 30 14:19:37 2013
# Current time GMT: Sun Jun 30 21:19:37 2013
# Using Test.pm version 1.26
ok 1
ok 2
ok 3
ok 4
ok
t/write.t ............
1..1
# Running under perl version 5.018000 for darwin
# Current time local: Sun Jun 30 14:19:37 2013
# Current time GMT: Sun Jun 30 21:19:37 2013
# Using Test.pm version 1.26
about to write to t/data/test.sxpr
written!!
'(db
(species_set
(species
(common_name "house mouse")
(binomial "Mus musculus")
(tax_id "10090"))
(species
(common_name "fruitfly")
(binomial "Drosophila melanogaster")
(tax_id "7227"))
(species
(common_name "human")
(binomial "Homo sapiens")
(tax_id "9606")))
(gene_set
(gene
(symbol "HGNC")
(tax_id "9606")
(phenotype "Hemochromatosis")
(phenotype "Porphyria variegata")
(GO_term "iron homeostasis")
(map
(cytological
(chromosome "6")
(band "p21.3"))))
(gene
(symbol "Hfe")
(synonym "MR2")
(tax_id "10090")
(GO_term "integral membrane protein")))
(similarity_set
(pair
(symbol "HGNC")
(symbol "Hfe"))
(pair
(symbol "WNT3A")
(symbol "Wnt3a"))))
ok 1
ok
t/xml1.t .............
1..7
# Running under perl version 5.018000 for darwin
# Current time local: Sun Jun 30 14:19:37 2013
# Current time GMT: Sun Jun 30 21:19:37 2013
# Using Test.pm version 1.26
shuggybus driver55
tamforklift driverchips
ok 1
$VAR1 = {
'personset' => {
'person' => [
{
'age' => '55',
'job' => 'bus driver',
'name' => 'shuggy'
},
{
'job' => 'forklift driver',
'name' => 'tam',
'favourite_food' => 'chips'
}
]
}
};
shuggy
bus driver
55
tam
forklift driver
chips
shuggy
bus driver
100
tam
forklift driver
chips
checking..
shuggy
bus driver
100
ok 2
ok 3
tam
forklift driver
chips
ok 4
ok 5
ok 6
yyy
tam
forklift driver
chips
ok 7
ok
t/xml2.t .............
1..4
# Running under perl version 5.018000 for darwin
# Current time local: Sun Jun 30 14:19:37 2013
# Current time GMT: Sun Jun 30 21:19:37 2013
# Using Test.pm version 1.26
$VAR1 = bless( [
'person',
[
bless( [
'name',
'davey'
], 'Data::Stag::StagImpl' ),
bless( [
'address',
'here'
], 'Data::Stag::StagImpl' ),
bless( [
'description',
[
bless( [
'hair',
'green'
], 'Data::Stag::StagImpl' ),
bless( [
'eyes',
'two'
], 'Data::Stag::StagImpl' ),
bless( [
'teeth',
5
], 'Data::Stag::StagImpl' )
]
], 'Data::Stag::StagImpl' ),
bless( [
'pets',
[
bless( [
'petname',
'igor'
], 'Data::Stag::StagImpl' ),
bless( [
'petname',
'ginger'
], 'Data::Stag::StagImpl' )
]
], 'Data::Stag::StagImpl' )
]
], 'Data::Stag::StagImpl' );
$VAR1 = bless( [
'person',
[
bless( [
'name',
'shuggy'
], 'Data::Stag::StagImpl' ),
bless( [
'address',
'there'
], 'Data::Stag::StagImpl' ),
bless( [
'description',
[
bless( [
'hair',
'red'
], 'Data::Stag::StagImpl' ),
bless( [
'eyes',
'three'
], 'Data::Stag::StagImpl' ),
bless( [
'teeth',
1
], 'Data::Stag::StagImpl' )
]
], 'Data::Stag::StagImpl' ),
bless( [
'pets',
[
bless( [
'petname',
'thud'
], 'Data::Stag::StagImpl' ),
bless( [
'petname',
'spud'
], 'Data::Stag::StagImpl' )
]
], 'Data::Stag::StagImpl' )
]
], 'Data::Stag::StagImpl' );
shuggy
there
red
three
1
thud
spud
desc
green
two
5
red
three
1
ok 1
shuggy
there
red
three
1
thud
spud
finding green haired people..
davey
here
green
two
5
igor
ginger
ok 2
shuggy
there
red
three
1
thud
spud
ok 3
'(a "")
'(foo
(bar "1"))
ok 4
ok
All tests successful.
Files=20, Tests=102, 4 wallclock secs ( 0.19 usr 0.05 sys + 1.65 cusr 0.25 csys = 2.14 CPU)
Result: PASS
CMUNGALL/Data-Stag-0.11.tar.gz
make test TEST_VERBOSE=1 -- OK
PPD for Data-Stag-0.11 already made
Running Build for C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz
Prepending /Users/fly1800/var/cpan/build/Data-Stag-0.11-S7GgSn/blib/arch /Users/fly1800/var/cpan/build/Data-Stag-0.11-S7GgSn/blib/lib to PERL5LIB for 'get'
Has already been unwrapped into directory /Users/fly1800/var/cpan/build/BioPerl-1.6.901-wrCmuT
Prepending /Users/fly1800/var/cpan/build/Data-Stag-0.11-S7GgSn/blib/arch /Users/fly1800/var/cpan/build/Data-Stag-0.11-S7GgSn/blib/lib to PERL5LIB for 'make'
CPAN.pm: Building C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz
>>> ./Build
Building BioPerl
CJFIELDS/BioPerl-1.6.901.tar.gz
./Build -- OK
Prepending /Users/fly1800/var/cpan/build/Data-Stag-0.11-S7GgSn/blib/arch /Users/fly1800/var/cpan/build/Data-Stag-0.11-S7GgSn/blib/lib to PERL5LIB for 'test'
Running Build test
>>> ./Build test verbose=1
Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS
Changing sharpbang in blib/script/search2tribe.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/search2tribe.PLS.bak
Copying scripts/DB-HIV/hivq.PLS -> blib/script/hivq.PLS
Changing sharpbang in blib/script/hivq.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/hivq.PLS.bak
Copying scripts/Bio-DB-EUtilities/einfo.PLS -> blib/script/einfo.PLS
Changing sharpbang in blib/script/einfo.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/einfo.PLS.bak
Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS
Changing sharpbang in blib/script/bp_fetch.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/bp_fetch.PLS.bak
Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS
Changing sharpbang in blib/script/split_seq.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/split_seq.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 /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/fast_load_gff.PLS.bak
Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS
Changing sharpbang in blib/script/bp_sreformat.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/bp_sreformat.PLS.bak
Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS
Changing sharpbang in blib/script/seqconvert.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/seqconvert.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 /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/hmmer_to_table.PLS.bak
Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS
Changing sharpbang in blib/script/meta_gff.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/meta_gff.PLS.bak
Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS
Changing sharpbang in blib/script/process_gadfly.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/process_gadfly.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 /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/extract_feature_seq.PLS.bak
Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS
Changing sharpbang in blib/script/genbank2gff.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/genbank2gff.PLS.bak
Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS
Changing sharpbang in blib/script/chaos_plot.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/chaos_plot.PLS.bak
Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS
Changing sharpbang in blib/script/bp_index.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/bp_index.PLS.bak
Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS
Changing sharpbang in blib/script/oligo_count.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/oligo_count.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 /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/query_entrez_taxa.PLS.bak
Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS
Changing sharpbang in blib/script/seqretsplit.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/seqretsplit.PLS.bak
Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS
Changing sharpbang in blib/script/biogetseq.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/biogetseq.PLS.bak
Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS
Changing sharpbang in blib/script/generate_histogram.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/generate_histogram.PLS.bak
Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS
Changing sharpbang in blib/script/translate_seq.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/translate_seq.PLS.bak
Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS
Changing sharpbang in blib/script/composite_LD.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/composite_LD.PLS.bak
Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS
Changing sharpbang in blib/script/bioflat_index.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/bioflat_index.PLS.bak
Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS
Changing sharpbang in blib/script/tree2pag.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/tree2pag.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 /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/mask_by_search.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 /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/bp_seqfeature_delete.PLS.bak
Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS
Changing sharpbang in blib/script/aacomp.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/aacomp.PLS.bak
Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS
Changing sharpbang in blib/script/bp_nrdb.PLS to /Users/fly1800/ap1800-297214/bin/perl-dynamic
Deleting blib/script/bp_nrdb.PLS.bak
Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS
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Deleting blib/script/dbsplit.PLS.bak
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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 ...........................
1..41
ok 1 - use Bio::Align::Graphics;
ok 2 - require Bio::Align::Graphics;
ok 3 - Bio::Align::Graphics->can(...)
ok 4 - input is defined
ok 5 - AlignIO object is defined
ok 6 - The object isa Bio::AlignIO
ok 7 - alignment is there and defined
ok 8 - all starts are present
ok 9 - all ends are present
ok 10 - all colors are present
ok 11 - first end is further than first start
ok 12 - second end is further than second start
ok 13 - third end is further than third start
ok 14 - domain labels are present
ok 15 - domain starts are present
ok 16 - domain ends are present
ok 17 - domain colors are present
ok 18 - label - first end is further than first start
ok 19 - label - second end is further than second start
ok 20 - label - third end is further than third start
ok 21 - first label start is within domain range
ok 22 - second label start is within domain range
ok 23 - third label start is within domain range
ok 24 - first label end is within domain range
ok 25 - second label end is within domain range
ok 26 - third label end is within domain range
ok 27 - individual labels work
ok 28 - The object isa Bio::Align::Graphics
ok 29 - new object is defined
ok 30 - pad_bottom is right
ok 31 - default pad_top is right
ok 32 - start point loaded
ok 33 - end point loaded
ok 34 - color of domain loaded
ok 35 - domain labels loaded
ok 36 - label starts loaded
ok 37 - label ends loaded
ok 38 - label colors loaded
ok 39 - labels loaded
ok 40 - output file is png
ok 41 - wrapping length is not zero
ok
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: Test::Exception::lives_ok t/Align/SimpleAlign.t:421
# STACK: t/Align/SimpleAlign.t:421
# -----------------------------------------------------------
# )
ok 94 - slice 1 len
ok 95 - correct masked seq
ok 96 - correct masked seq
ok 97 - correct masked seq
not ok 98 # TODO This should pass but dies; see bug 2842
# Failed (TODO) test at t/Align/SimpleAlign.t line 421.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 3.
# Overriding value [2] with value 3 for Bio::LocatableSeq::end().
# ?
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm: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: Test::Exception::lives_ok t/Align/SimpleAlign.t:421
# STACK: t/Align/SimpleAlign.t:421
# -----------------------------------------------------------
# )
ok 99 - slice 2 len
ok 100 - correct masked seq
ok 101 - correct masked seq
ok 102 - correct masked seq
not ok 103 # TODO This should pass but dies; see bug 2842
# Failed (TODO) test at t/Align/SimpleAlign.t line 421.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 3.
# Overriding value [1] with value 3 for Bio::LocatableSeq::end().
# ??
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm: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: Test::Exception::lives_ok t/Align/SimpleAlign.t:421
# STACK: t/Align/SimpleAlign.t:421
# -----------------------------------------------------------
# )
ok 104 - slice 3 len
ok 105 - correct masked seq
ok 106 - correct masked seq
ok 107 - correct masked seq
not ok 108 # TODO This should pass but dies; see bug 2842
# Failed (TODO) test at t/Align/SimpleAlign.t line 421.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 6.
# Overriding value [4] with value 6 for Bio::LocatableSeq::end().
# ??
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm: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: Test::Exception::lives_ok t/Align/SimpleAlign.t:421
# STACK: t/Align/SimpleAlign.t:421
# -----------------------------------------------------------
# )
ok 109 - slice 4 len
ok 110 - correct masked seq
ok 111 - correct masked seq
ok 112 - correct masked seq
ok 113 - initial display id ok
ok 114 - safe display id ok
ok 115 - restored display id ok
ok 116 - sort by list ok
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123 - BIC:GGATCCATT[C/C]CTACT
ok 124 - BIC:GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT
ok 125 - BIC:G[G/C]ATCCATT[C/G]CTACT
ok 126 - BIC:GGATCCATT[C/G]CTACT
ok 127 - BIC:GGATCCATT[C/G]CTAC[T/A]
ok 128 - BIC:GGATCCATT[C/G]CTA[C/G][T/A]
ok 129 - BIC:GGATCCATT[C/G]CTACT
ok 130 - BIC:GGATCCATT{C.C}CTACT
ok 131 - BIC:GGAT{C.-}{C.-}ATT{C.C}CT{A.C}CT
ok 132 - BIC:G{G.C}ATCCATT{C.G}CTACT
ok 133 - BIC:GGATCCATT{C.G}CTACT
ok 134 - BIC:GGATCCATT{C.G}CTAC{T.A}
ok 135 - BIC:GGATCCATT{C.G}CTA{C.G}{T.A}
ok 136 - BIC:GGATCCATT{C.G}CTACT
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
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 : clustalw
ok 3 - input filehandle method test : selex
ok 4 - input filehandle method test : stockholm
ok 5 - input filehandle method test : msf
ok 6 - input filehandle method test : po
ok 7 - input filehandle method test : xmfa
ok 8 - input filehandle method test : psi
ok 9 - input filehandle method test : phylip
ok 10 - input filehandle method test : pfam
ok 11 - input filehandle method test : fasta
ok 12 - input filehandle method test : arp
ok 13 - input filehandle method test : prodom
ok 14 - input filehandle method test : metafasta
ok 15 - input filehandle method test : mase
ok 16 - input filehandle method test : nexus
ok 17 - filehandle output test : clustalw
ok 18 - filehandle output test : selex
ok 19 - filehandle output test : stockholm
ok 20 - filehandle output test : msf
ok 21 - filehandle output test : po
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 : fasta
ok 27 - filehandle output test : metafasta
ok 28 - filehandle output test : nexus
ok
t/AlignIO/arp.t ..............................
1..48
ok 1 - use Bio::AlignIO::arp;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4 - ARP get_nse()
ok 5
ok 6 - ARP num_sequences()
ok 7 - ARP id()
ok 8 - ARP description()
ok 9 - The object isa Bio::AnnotationCollectionI
ok 10 - The object isa Bio::AnnotationI
ok 11
ok 12
ok 13
ok 14
ok 15 - The object isa Bio::AlignIO
ok 16 - The object isa Bio::Align::AlignI
ok 17 - ARP get_nse()
ok 18 - ARP num_sequences()
ok 19 - ARP id()
ok 20 - ARP description()
ok 21 - The object isa Bio::AnnotationCollectionI
ok 22 - The object isa Bio::AnnotationI
ok 23
ok 24
ok 25
ok 26
ok 27 - The object isa Bio::Align::AlignI
ok 28 - ARP get_nse()
ok 29 - ARP num_sequences()
ok 30 - ARP id()
ok 31 - ARP description()
ok 32 - The object isa Bio::AnnotationCollectionI
ok 33 - The object isa Bio::AnnotationI
ok 34
ok 35
ok 36
ok 37
ok 38 - The object isa Bio::Align::AlignI
ok 39 - ARP get_nse()
ok 40 - ARP num_sequences()
ok 41 - ARP id()
ok 42 - ARP description()
ok 43 - The object isa Bio::AnnotationCollectionI
ok 44 - The object isa Bio::AnnotationI
ok 45
ok 46
ok 47
ok 48
ok
t/AlignIO/bl2seq.t ...........................
1..3
ok 1 - use Bio::AlignIO::bl2seq;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - BLAST bl2seq format test
ok
t/AlignIO/clustalw.t .........................
1..6
ok 1 - use Bio::AlignIO::clustalw;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - clustalw consensus_string test
ok 4 - clustalw (.aln) output test
ok 5 - The object isa Bio::Align::AlignI
ok 6 - clustalw (.aln) input test
ok
t/AlignIO/emboss.t ...........................
1..37
ok 1 - use Bio::AlignIO::emboss;
ok 2 - The object isa Bio::Align::AlignI
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10 - The object isa Bio::Align::AlignI
ok 11
ok 12
ok 13
ok 14 - The object isa Bio::Align::AlignI
ok 15
ok 16
ok 17
ok 18 - The object isa Bio::Align::AlignI
ok 19
ok 20
ok 21 - The object isa Bio::Align::AlignI
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32 - The object isa Bio::Align::AlignI
ok 33
ok 34
ok 35
ok 36
ok 37
ok
t/AlignIO/fasta.t ............................
1..10
ok 1 - use Bio::AlignIO::fasta;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - fasta input test
ok 4 - fasta input test for description
ok 5 - fasta input test for id
ok 6 - fasta input test for end
ok 7 - fasta input test for description
ok 8 - fasta output test
ok 9 - filehandle input test
ok 10 - filehandle output test
ok
t/AlignIO/largemultifasta.t ..................
1..7
ok 1 - use Bio::AlignIO::largemultifasta;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - fasta input test
ok 4 - fasta input test for description
ok 5 - fasta input test for id
ok 6 - fasta input test for description
ok 7 - fasta output test
ok
t/AlignIO/maf.t ..............................
1..11
ok 1 - use Bio::AlignIO::maf;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - maf input test
ok 4
ok 5 - The object isa Bio::Align::AlignI
ok 6 - maf input test
ok 7
ok 8 - maf input test
ok 9
ok 10 - maf input test
ok 11
ok
t/AlignIO/mase.t .............................
1..3
ok 1 - use Bio::AlignIO::mase;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - mase input test
ok
t/AlignIO/mega.t .............................
1..6
ok 1 - use Bio::AlignIO::mega;
ok 2 - The object isa Bio::Align::AlignI
ok 3
ok 4
ok 5
ok 6 - mega output test
ok
t/AlignIO/meme.t .............................
1..14
ok 1 - use Bio::AlignIO::meme;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4
ok 5
ok 6
ok 7
ok 8 - The object isa Bio::AlignIO
ok 9 - The object isa Bio::Align::AlignI
ok 10
ok 11
ok 12
ok 13
ok 14
ok
t/AlignIO/metafasta.t ........................
1..4
ok 1 - use Bio::AlignIO::metafasta;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - consensus_string on metafasta
ok 4 - symbol_chars() using metafasta
ok
t/AlignIO/msf.t ..............................
1..4
ok 1 - use Bio::AlignIO::msf;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - msf input test
ok 4 - msf output test
ok
t/AlignIO/nexml.t ............................ skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
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
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not find sequence species1635|5973 in contig contig00001_6
STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472
STACK: Bio::Assembly::Contig::get_seq_by_name Bio/Assembly/Contig.pm:1063
STACK: t/Assembly/ContigSpectrum.t:336
-----------------------------------------------------------
# Looks like you planned 236 tests but ran 215.
# Looks like your test exited with 255 just after 215.
t/Assembly/ContigSpectrum.t ..................
1..236
ok 1 - use Bio::Assembly::IO;
ok 2 - use Bio::Assembly::Tools::ContigSpectrum;
ok 3 - The object isa Bio::Assembly::IO
ok 4 - The object isa Bio::Assembly::Scaffold
ok 5 - get/set methods
ok 6 - The object isa Bio::Assembly::Tools::ContigSpectrum
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29 - simple spectrum
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 - mixed contig spectrum
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 - dissolved contig spectrum
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 - cross-contig spectrum
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130 - cross-contig spectrum
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142 - cross-contig spectrum
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151 - contig spectrum sum
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 - average contig spectrum
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 - drop assembly
ok 181
ok 182 - contig spectrum score
ok 183
ok 184
ok 185
ok 186
ok 187
ok 188
ok 189
ok 190
ok 191 - The object isa Bio::Assembly::IO
ok 192 - The object isa Bio::Assembly::Scaffold
ok 193 - large contig spectrum
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 - large cross-contig spectrum
ok 207
ok 208
ok 209
ok 210
ok 211
ok 212
ok 213
ok 214
ok 215
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 21/236 subtests
t/Assembly/IO/bowtie.t ....................... skipped: The optional module Bio::Tools::Run::Samtools (or dependencies thereof) was not installed
t/Assembly/IO/sam.t .......................... skipped: The optional module Bio::DB::Sam (or dependencies thereof) was not installed
--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------
t/Assembly/core.t ............................
1..890
ok 1 - use Bio::Seq;
ok 2 - use Bio::LocatableSeq;
ok 3 - use Bio::Seq::Quality;
ok 4 - use Bio::Assembly::IO;
ok 5 - use Bio::Assembly::Singlet;
ok 6 - singlet from Bio::PrimarySeq
ok 7 - The object isa Bio::Assembly::Contig
ok 8 - The object isa Bio::Assembly::Singlet
ok 9
ok 10
ok 11 - The object isa Bio::LocatableSeq
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 - singlet from Bio::Seq::Quality
ok 25
ok 26
ok 27 - The object isa Bio::Seq::QualI
ok 28
ok 29 - singlet from LocatableSeq
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38 - singlet from LocatableSeq with set coordinates
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::Assembly::IO
ok 54 - The object isa Bio::Assembly::Contig
ok 55 - The object isa Bio::Assembly::Contig
ok 56 - The object isa Bio::Assembly::Contig
ok 57 - The object isa Bio::Assembly::IO
not ok 58 # TODO phrap parser doesn't include the sequence string in the sequence objects.
# Failed (TODO) test at t/Assembly/core.t line 126.
ok 59
ok 60 - The object isa Bio::Assembly::Scaffold
ok 61
ok 62
ok 63 - The object isa Bio::AnnotationCollectionI
ok 64 - no annotations in Annotation collection?
ok 65
ok 66
ok 67 - get_nof_singlets
ok 68 - get_contig_seq_ids
ok 69 - get_contig_ids
ok 70 - get_singlet_ids
ok 71 - the contig is a Bio::Assembly::Contig isa Bio::Assembly::Contig
ok 72 - the singlet is a Bio::Assembly::Contig isa Bio::Assembly::Contig
ok 73 - the singlet is a Bio::Assembly::Singlet isa Bio::Assembly::Singlet
ok 74 - get_contig_seq_ids
ok 75
ok 76
ok 77
ok 78 - get_contig_ids
ok 79
ok 80
ok 81 - get_singlet_ids
ok 82
ok 83
ok 84
ok 85 - get_all_seq_ids
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92 - contig features
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99 - get_nof_singlets
ok 100 - get_contig_seq_ids
ok 101 - get_contig_ids
ok 102 - get_singlet_ids
ok 103 - The object isa Bio::Assembly::Contig
ok 104 - The object isa Bio::Assembly::Contig
ok 105 - The object isa Bio::Assembly::Contig
ok 106 - The object isa Bio::Assembly::Contig
ok 107 - The object isa Bio::Assembly::Contig
ok 108 - The object isa Bio::Assembly::Contig
ok 109 - The object isa Bio::Assembly::Contig
ok 110 - The object isa Bio::Assembly::Contig
ok 111 - The object isa Bio::Assembly::Contig
ok 112 - The object isa Bio::Assembly::Contig
ok 113 - The object isa Bio::Assembly::Contig
ok 114 - The object isa Bio::Assembly::Contig
ok 115 - The object isa Bio::Assembly::Contig
ok 116 - The object isa Bio::Assembly::Contig
ok 117 - The object isa Bio::Assembly::Contig
ok 118 - The object isa Bio::Assembly::Contig
ok 119 - The object isa Bio::Assembly::Contig
ok 120 - The object isa Bio::Assembly::Contig
ok 121 - The object isa Bio::Assembly::Contig
ok 122 - The object isa Bio::Assembly::Contig
ok 123 - The object isa Bio::Assembly::Contig
ok 124 - The object isa Bio::Assembly::Contig
ok 125 - The object isa Bio::Assembly::Contig
ok 126 - The object isa Bio::Assembly::Contig
ok 127 - The object isa Bio::Assembly::Contig
ok 128 - The object isa Bio::Assembly::Contig
ok 129 - The object isa Bio::Assembly::Contig
ok 130 - The object isa Bio::Assembly::Contig
ok 131 - The object isa Bio::Assembly::Contig
ok 132 - The object isa Bio::Assembly::Contig
ok 133 - The object isa Bio::Assembly::Contig
ok 134 - The object isa Bio::Assembly::Contig
ok 135 - The object isa Bio::Assembly::Contig
ok 136 - The object isa Bio::Assembly::Contig
ok 137 - The object isa Bio::Assembly::Contig
ok 138 - The object isa Bio::Assembly::Contig
ok 139
ok 140 - the contig is a Bio::Assembly::Contig isa Bio::Assembly::Contig
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146 - get_nof_singlets
ok 147 - the singlet is a Bio::Assembly::Contig isa Bio::Assembly::Contig
ok 148 - the singlet is a Bio::Assembly::Singlet isa Bio::Assembly::Singlet
ok 149 - get_contig_seq_ids
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157 - get_contig_ids
ok 158
ok 159
ok 160
ok 161
ok 162 - get_singlet_ids
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 - get_all_seq_ids
ok 198
ok 199
ok 200
ok 201
ok 202
ok 203
ok 204
ok 205
ok 206
ok 207
ok 208
ok 209
ok 210
ok 211
ok 212
ok 213
ok 214
ok 215
ok 216
ok 217
ok 218
ok 219
ok 220
ok 221
ok 222
ok 223
ok 224
ok 225
ok 226
ok 227
ok 228
ok 229
ok 230
ok 231
ok 232
ok 233
ok 234
ok 235
ok 236
ok 237
ok 238
ok 239 - 454 ACE variant coordinates check
ok 240
ok 241 - 454 ACE variant consensus check
ok 242
ok 243
ok 244
ok 245
ok 246 - writing in the ACE format
ok 247
ok 248
ok 249
ok 250
ok 251
ok 252 - The object isa Bio::Assembly::Contig
ok 253 - The object isa Bio::Assembly::Contig
ok 254 - The object isa Bio::Assembly::Contig
ok 255 - The object isa Bio::Assembly::Contig
ok 256 - The object isa Bio::Assembly::Contig
ok 257 - The object isa Bio::Assembly::Contig
ok 258 - The object isa Bio::Assembly::Contig
ok 259 - The object isa Bio::Assembly::Contig
ok 260 - The object isa Bio::Assembly::Contig
ok 261 - The object isa Bio::Assembly::Contig
ok 262 - The object isa Bio::Assembly::Contig
ok 263 - The object isa Bio::Assembly::Contig
ok 264 - The object isa Bio::Assembly::Contig
ok 265 - The object isa Bio::Assembly::Contig
ok 266 - The object isa Bio::Assembly::Scaffold
ok 267
ok 268
ok 269
ok 270
ok 271
ok 272
ok 273
ok 274 - The object isa Bio::LocatableSeq
ok 275 - The object isa Bio::Assembly::Contig
ok 276
ok 277
ok 278
ok 279 - The object isa Bio::AnnotationCollectionI
ok 280 - no annotations in Annotation collection?
ok 281 - writing in the TIGR format
ok 282 - init maq IO object
ok 283 - get maq assy
ok 284 - got all contigs
ok 285 - read test file as text
ok 286 - recorded all maq reads
ok 287 - no singlets
ok 288
ok 289 - The object isa Bio::Assembly::IO
ok 290 - The object isa Bio::Assembly::Contig
ok 291 - The object isa Bio::Assembly::Contig
ok 292 - The object isa Bio::Assembly::Contig
ok 293 - The object isa Bio::Assembly::Contig
ok 294 - The object isa Bio::Assembly::Contig
ok 295 - The object isa Bio::Assembly::Contig
ok 296 - The object isa Bio::Assembly::Contig
ok 297 - The object isa Bio::Assembly::Contig
ok 298 - The object isa Bio::Assembly::Contig
ok 299 - The object isa Bio::Assembly::Contig
ok 300 - The object isa Bio::Assembly::Contig
ok 301
ok 302 - get maq assy
ok 303 - The object isa Bio::Assembly::IO
ok 304 - get_contig_seq_ids
ok 305
ok 306
ok 307
ok 308
ok 309
ok 310
ok 311
ok 312
ok 313
ok 314
ok 315
ok 316
ok 317
ok 318
ok 319
ok 320
ok 321
ok 322
ok 323
ok 324
ok 325
ok 326
ok 327
ok 328
ok 329
ok 330
ok 331
ok 332
ok 333
ok 334
ok 335
ok 336
ok 337
ok 338
ok 339
ok 340
ok 341
ok 342
ok 343
ok 344
ok 345
ok 346
ok 347
ok 348
ok 349
ok 350
ok 351
ok 352
ok 353
ok 354
ok 355
ok 356
ok 357
ok 358
ok 359
ok 360
ok 361
ok 362
ok 363
ok 364
ok 365
ok 366
ok 367
ok 368
ok 369
ok 370
ok 371
ok 372
ok 373
ok 374
ok 375
ok 376
ok 377
ok 378
ok 379
ok 380
ok 381
ok 382
ok 383
ok 384
ok 385
ok 386
ok 387
ok 388
ok 389
ok 390
ok 391
ok 392
ok 393
ok 394
ok 395
ok 396
ok 397
ok 398
ok 399
ok 400
ok 401
ok 402
ok 403
ok 404
ok 405
ok 406
ok 407
ok 408
ok 409
ok 410
ok 411
ok 412
ok 413
ok 414
ok 415
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ok 417
ok 418
ok 419
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ok 421
ok 422
ok 423
ok 424
ok 425
ok 426
ok 427
ok 428
ok 429
ok 430
ok 431
ok 432
ok 433
ok 434
ok 435
ok 436
ok 437
ok 438
ok 439
ok 440
ok 441
ok 442
ok 443
ok 444
ok 445
ok 446
ok 447
ok 448
ok 449
ok 450
ok 451
ok 452
ok 453
ok 454
ok 455
ok 456
ok 457
ok 458
ok 459
ok 460
ok 461
ok 462
ok 463
ok 464
ok 465
ok 466
ok 467
ok 468
ok 469
ok 470
ok 471
ok 472
ok 473
ok 474
ok 475
ok 476
ok 477
ok 478
ok 479
ok 480
ok 481
ok 482
ok 483
ok 484
ok 485
ok 486
ok 487
ok 488
ok 489
ok 490
ok 491
ok 492
ok 493
ok 494
ok 495
ok 496
ok 497
ok 498
ok 499
ok 500
ok 501
ok 502
ok 503
ok 504
ok 505
ok 506
ok 507
ok 508
ok 509
ok 510
ok 511
ok 512
ok 513
ok 514
ok 515
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ok 517
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ok 520
ok 521
ok 522
ok 523
ok 524
ok 525
ok 526
ok 527
ok 528
ok 529
ok 530
ok 531
ok 532
ok 533
ok 534
ok 535
ok 536
ok 537
ok 538
ok 539
ok 540
ok 541
ok 542
ok 543
ok 544
ok 545
ok 546
ok 547
ok 548
ok 549
ok 550
ok 551
ok 552 - get_contig_ids
ok 553
ok 554
ok 555
ok 556
ok 557
ok 558
ok 559
ok 560
ok 561
ok 562
ok 563
ok 564
ok 565
ok 566
ok 567
ok 568
ok 569
ok 570
ok 571
ok 572
ok 573
ok 574
ok 575
ok 576
ok 577
ok 578
ok 579
ok 580
ok 581
ok 582
ok 583
ok 584
ok 585
ok 586
ok 587
ok 588
ok 589
ok 590
ok 591 - get_singlet_ids
ok 592
ok 593
ok 594
ok 595
ok 596
ok 597 - get_all_seq_ids
ok 598
ok 599
ok 600
ok 601
ok 602
ok 603
ok 604
ok 605
ok 606
ok 607
ok 608
ok 609
ok 610
ok 611
ok 612
ok 613
ok 614
ok 615
ok 616
ok 617
ok 618
ok 619
ok 620
ok 621
ok 622
ok 623
ok 624
ok 625
ok 626
ok 627
ok 628
ok 629
ok 630
ok 631
ok 632
ok 633
ok 634
ok 635
ok 636
ok 637
ok 638
ok 639
ok 640
ok 641
ok 642
ok 643
ok 644
ok 645
ok 646
ok 647
ok 648
ok 649
ok 650
ok 651
ok 652
ok 653
ok 654
ok 655
ok 656
ok 657
ok 658
ok 659
ok 660
ok 661
ok 662
ok 663
ok 664
ok 665
ok 666
ok 667
ok 668
ok 669
ok 670
ok 671
ok 672
ok 673
ok 674
ok 675
ok 676
ok 677
ok 678
ok 679
ok 680
ok 681
ok 682
ok 683
ok 684
ok 685
ok 686
ok 687
ok 688
ok 689
ok 690
ok 691
ok 692
ok 693
ok 694
ok 695
ok 696
ok 697
ok 698
ok 699
ok 700
ok 701
ok 702
ok 703
ok 704
ok 705
ok 706
ok 707
ok 708
ok 709
ok 710
ok 711
ok 712
ok 713
ok 714
ok 715
ok 716
ok 717
ok 718
ok 719
ok 720
ok 721
ok 722
ok 723
ok 724
ok 725
ok 726
ok 727
ok 728
ok 729
ok 730
ok 731
ok 732
ok 733
ok 734
ok 735
ok 736
ok 737
ok 738
ok 739
ok 740
ok 741
ok 742
ok 743
ok 744
ok 745
ok 746
ok 747
ok 748
ok 749
ok 750
ok 751
ok 752
ok 753
ok 754
ok 755
ok 756
ok 757
ok 758
ok 759
ok 760
ok 761
ok 762
ok 763
ok 764
ok 765
ok 766
ok 767
ok 768
ok 769
ok 770
ok 771
ok 772
ok 773
ok 774
ok 775
ok 776
ok 777
ok 778
ok 779
ok 780
ok 781
ok 782
ok 783
ok 784
ok 785
ok 786
ok 787
ok 788
ok 789
ok 790
ok 791
ok 792
ok 793
ok 794
ok 795
ok 796
ok 797
ok 798
ok 799
ok 800
ok 801
ok 802
ok 803
ok 804
ok 805
ok 806
ok 807
ok 808
ok 809
ok 810
ok 811
ok 812
ok 813
ok 814
ok 815
ok 816
ok 817
ok 818
ok 819
ok 820
ok 821
ok 822
ok 823
ok 824
ok 825
ok 826
ok 827
ok 828
ok 829
ok 830
ok 831
ok 832
ok 833
ok 834
ok 835
ok 836
ok 837
ok 838
ok 839
ok 840
ok 841
ok 842
ok 843
ok 844
ok 845
ok 846
ok 847
ok 848
ok 849
ok 850 - The object isa Bio::Assembly::Contig
ok 851 - The object isa Bio::Assembly::Contig
ok 852 - The object isa Bio::Assembly::Contig
ok 853 - The object isa Bio::Assembly::Contig
ok 854 - The object isa Bio::Assembly::Contig
ok 855 - The object isa Bio::Assembly::Contig
ok 856 - The object isa Bio::Assembly::Contig
ok 857 - The object isa Bio::Assembly::Contig
ok 858 - The object isa Bio::Assembly::Contig
ok 859 - The object isa Bio::Assembly::Contig
ok 860 - The object isa Bio::Assembly::Contig
ok 861 - The object isa Bio::Assembly::Contig
ok 862 - The object isa Bio::Assembly::Contig
ok 863 - The object isa Bio::Assembly::Contig
ok 864 - The object isa Bio::Assembly::Contig
ok 865 - The object isa Bio::Assembly::Contig
ok 866 - The object isa Bio::Assembly::Contig
ok 867 - The object isa Bio::Assembly::Contig
ok 868 - The object isa Bio::Assembly::Contig
ok 869 - The object isa Bio::Assembly::Contig
ok 870 - The object isa Bio::Assembly::Contig
ok 871 - The object isa Bio::Assembly::Contig
ok 872 - The object isa Bio::Assembly::Contig
ok 873 - The object isa Bio::Assembly::Contig
ok 874 - The object isa Bio::Assembly::Contig
ok 875 - The object isa Bio::Assembly::Contig
ok 876 - The object isa Bio::Assembly::Contig
ok 877 - The object isa Bio::Assembly::Contig
ok 878 - The object isa Bio::Assembly::Contig
ok 879 - The object isa Bio::Assembly::Contig
ok 880 - The object isa Bio::Assembly::Contig
ok 881 - The object isa Bio::Assembly::Contig
ok 882 - The object isa Bio::Assembly::Contig
ok 883 - The object isa Bio::Assembly::Contig
ok 884 - The object isa Bio::Assembly::Contig
ok 885 - The object isa Bio::Assembly::Contig
ok 886 - The object isa Bio::Assembly::Contig
ok 887 - The object isa Bio::Assembly::Contig
ok 888 - The object isa Bio::Assembly::Contig
ok 889 - The object isa Bio::Assembly::Contig
ok 890 - The object isa Bio::Assembly::Contig
ok
t/Biblio/Biblio.t ............................
1..24
ok 1 - use Bio::Biblio;
ok 2 - use Bio::Biblio::IO;
ok 3 # skip The optional module SOAP::Lite (or dependencies thereof) was not installed
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
t/LocalDB/DBFasta.t ..........................
1..17
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8 - bug 3126
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17 - threw Regexp ((?^:FASTA header doesn't match))
ok
t/LocalDB/DBQual.t ...........................
1..38
ok 1 - use Bio::Root::IO;
ok 2 - use File::Copy;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13 - The object isa Bio::Seq::PrimaryQual
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25 - The object isa Bio::Seq::PrimaryQual
ok 26
ok 27
ok 28 - The object isa Bio::Seq::PrimaryQual
ok 29
ok 30
ok 31
ok 32 - The object isa Bio::Seq::PrimaryQual
ok 33
ok 34 - The object isa Bio::Seq::PrimaryQual
ok 35
ok 36
ok 37
ok 38
ok
t/LocalDB/Flat.t .............................
1..24
ok 1 - use Bio::DB::Flat;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok
t/LocalDB/Index/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 ......................
1..64
ok 1 - use Bio::Index::Fasta;
ok 2 - use Bio::Index::Qual;
ok 3 - use Bio::Index::SwissPfam;
ok 4 - use Bio::Index::EMBL;
ok 5 - use Bio::Index::GenBank;
ok 6 - use Bio::Index::Swissprot;
ok 7 - use Bio::DB::InMemoryCache;
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16 - The object isa Bio::PrimarySeqI
ok 17
ok 18
ok 19
ok 20 - The object isa Bio::SeqI
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok
t/LocalDB/Registry.t .........................
1..14
ok 1 - use Bio::DB::Registry;
ok 2 - use Bio::DB::Flat;
ok 3
ok 4
ok 5
ok 6 # skip Network tests have not been requested
ok 7 # skip Network tests have not been requested
ok 8 # skip Network tests have not been requested
ok 9 # skip Network tests have not been requested
ok 10 # skip Network tests have not been requested
ok 11 # skip Network tests have not been requested
ok 12 # skip Network tests have not been requested
ok 13 # skip Network tests have not been requested
ok 14 # skip Network tests have not been requested
ok
t/LocalDB/SeqFeature.t .......................
1..116
ok 1 - use Bio::SeqFeature::Generic;
ok 2 - use Bio::DB::SeqFeature::Store;
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
ok 10 - adding a feature
ok 11
ok 12
ok 13
ok 14 - adding a feature with no primary_id
ok 15
ok 16 - searching for a feature that shouldnt exist
ok 17 - simple type
ok 18 - base type with colon
ok 19 - base type alone
ok 20 - queried types are not interpolated
ok 21
ok 22
ok 23 - The object isa Bio::DB::GFF::Typename
ok 24 - feature deletion
ok 25
ok 26
ok 27 - adding subfeatures
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 - feature names should be case insensitive
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 - base type
ok 65 - base:source type
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73 - The object isa Bio::Location::Split
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 - keyword search; 1 term
ok 103 - keyword search; 2 terms
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 112 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 113 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 114 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 115 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 116 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok
t/LocalDB/transfac_pro.t .....................
1..115
ok 1 - use Bio::Matrix::PSM::IO;
ok 2 - use Bio::DB::TFBS;
ok 3 - use Bio::DB::Taxonomy;
ok 4
ok 5
ok 6
ok 7
ok 8 - The object isa Bio::Annotation::Reference
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39 - The object isa Bio::Seq
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57 - The object isa Bio::Matrix::PSM::SiteMatrix
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69 - The object isa Bio::SimpleAlign
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96 - The object isa Bio::SeqI
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107 - The object isa Bio::Map::TranscriptionFactor
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok
t/Map/Cyto.t .................................
1..110
ok 1 - use Bio::Map::CytoMap;
ok 2 - use Bio::Map::CytoPosition;
ok 3 - use Bio::Map::CytoMarker;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14 - The object isa Bio::Map::CytoPosition
ok 15
ok 16
ok 17
ok 18 - The object isa Bio::Range
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok
t/Map/Linkage.t ..............................
1..18
ok 1 - use Bio::Map::LinkagePosition;
ok 2 - use Bio::Map::Microsatellite;
ok 3 - use Bio::Map::LinkageMap;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok
# Failed test at t/Map/Map.t line 322.
# got: 'Bio::Map::Position=HASH(0x101567e30)'
# expected: 'Bio::Map::Position=HASH(0x101567a30)'
# Failed test at t/Map/Map.t line 323.
# got: 'Bio::Map::Position=HASH(0x101567a30)'
# expected: 'Bio::Map::Position=HASH(0x101567e30)'
# Failed test at t/Map/Map.t line 324.
# got: undef
# expected: 'Bio::Map::Position=HASH(0x1015681f0)'
Can't call method "toString" on an undefined value at t/Map/Map.t line 325.
# Looks like you planned 267 tests but ran 134.
# Looks like you failed 3 tests of 134 run.
# Looks like your test exited with 255 just after 134.
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
not ok 132
not ok 133
not ok 134
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 136/267 subtests
t/Map/MapIO.t ................................
1..51
ok 1 - use Bio::MapIO;
ok 2
ok 3 - The object isa Bio::Map::MapI
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok
t/Map/MicrosatelliteMarker.t .................
1..8
ok 1 - use Bio::Map::SimpleMap;
ok 2 - use Bio::Map::Position;
ok 3 - use Bio::Map::Microsatellite;
ok 4
ok 5
ok 6
ok 7
ok 8
ok
t/Map/Physical.t .............................
1..39
ok 1 - use Bio::Map::Physical;
ok 2 - use Bio::MapIO;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12 - code holds and returns a string, definition requires a boolean
ok 13 - code holds and returns a string, definition requires a boolean
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok
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
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok
t/Matrix/InstanceSite.t ......................
1..6
ok 1 - use Bio::Matrix::PSM::InstanceSite;
ok 2
ok 3
ok 4
ok 5
ok 6
ok
t/Matrix/Matrix.t ............................
1..77
ok 1 - use Bio::Matrix::Generic;
ok 2 - use Bio::Matrix::IO;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30 - The object isa Bio::Matrix::Scoring
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42 - The object isa Bio::Matrix::Scoring
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok
t/Matrix/ProtMatrix.t ........................
1..14
ok 1 - use Bio::Matrix::PSM::ProtMatrix;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok
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
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok
t/Ontology/GraphAdaptor.t ....................
1..28
ok 1 - use Bio::Ontology::SimpleGOEngine::GraphAdaptor;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok
t/Ontology/IO/go.t ...........................
1..102
ok 1 - use Bio::OntologyIO;
ok 2
ok 3 - The object isa Bio::Ontology::OntologyI
ok 4
ok 5 - The object isa Bio::Ontology::OntologyEngineI
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok
t/Ontology/IO/interpro.t .....................
1..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 Helix-turn-helix, AraC type in ontology InterPro
ok 21 - The object isa Bio::Ontology::Ontology
ok 22 - term Binding Site in ontology InterPro
ok 23 - The object isa Bio::Ontology::Ontology
ok 24 - term Kringle in ontology InterPro
ok 25 - The object isa Bio::Ontology::Ontology
ok 26 - term Conserved Site in ontology InterPro
ok 27 - The object isa Bio::Ontology::Ontology
ok 28 - term Active Site in ontology InterPro
ok 29 - The object isa Bio::Ontology::Ontology
ok 30 - term Region in ontology InterPro
ok 31 - The object isa Bio::Ontology::Ontology
ok 32 - term post-translational modification in ontology InterPro
ok 33 - The object isa Bio::Ontology::Ontology
ok 34 - term Cdc20/Fizzy in ontology InterPro
ok 35 - The object isa Bio::Ontology::Ontology
ok 36 - term Integrins alpha chain in ontology InterPro
ok 37 - The object isa Bio::Ontology::Ontology
ok 38 - term Repeat 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 - Helix-turn-helix, AraC type term has one parent
ok 62 - Helix-turn-helix, AraC type term has one ancestor
ok 63 - Kringle term has one parent
ok 64 - Kringle term has one ancestor
ok 65 - Cdc20/Fizzy term has one parent
ok 66 - Cdc20/Fizzy term has one ancestor
ok 67 - Integrins alpha chain term has one parent
ok 68 - Integrins alpha chain 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
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok
Timeout (max run time is 300s)
/Users/fly1800/ap1800-297214/bin/perl-dynamic killed by signal 15.