PATH=/usr/bin:/bin
Start 2013-06-21T11:02:21
ActivePerl-1800 CPAN-2.00
Reading '/home/fly1800/var/cpan/Metadata'
Database was generated on Fri, 21 Jun 2013 16:08:34 GMT
Running make for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
Checksum for /net/nas/data/cpan/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz ok
BioPerl-1.6.1
BioPerl-1.6.1/AUTHORS
BioPerl-1.6.1/BioPerl.pm
BioPerl-1.6.1/BUGS
BioPerl-1.6.1/Build.PL
BioPerl-1.6.1/Changes
BioPerl-1.6.1/DEPENDENCIES
BioPerl-1.6.1/DEPRECATED
BioPerl-1.6.1/INSTALL
BioPerl-1.6.1/INSTALL.SKIP
BioPerl-1.6.1/INSTALL.WIN
BioPerl-1.6.1/LICENSE
BioPerl-1.6.1/Makefile.PL
BioPerl-1.6.1/MANIFEST
BioPerl-1.6.1/MANIFEST.SKIP
BioPerl-1.6.1/META.yml
BioPerl-1.6.1/README
BioPerl-1.6.1/Bio
BioPerl-1.6.1/Bio/AlignIO.pm
BioPerl-1.6.1/Bio/AnalysisI.pm
BioPerl-1.6.1/Bio/AnalysisParserI.pm
BioPerl-1.6.1/Bio/AnalysisResultI.pm
BioPerl-1.6.1/Bio/AnnotatableI.pm
BioPerl-1.6.1/Bio/AnnotationCollectionI.pm
BioPerl-1.6.1/Bio/AnnotationI.pm
BioPerl-1.6.1/Bio/Biblio.pm
BioPerl-1.6.1/Bio/ClusterI.pm
BioPerl-1.6.1/Bio/ClusterIO.pm
BioPerl-1.6.1/Bio/DasI.pm
BioPerl-1.6.1/Bio/DBLinkContainerI.pm
BioPerl-1.6.1/Bio/DescribableI.pm
BioPerl-1.6.1/Bio/FeatureHolderI.pm
BioPerl-1.6.1/Bio/FeatureIO.pm
BioPerl-1.6.1/Bio/HandlerBaseI.pm
BioPerl-1.6.1/Bio/IdCollectionI.pm
BioPerl-1.6.1/Bio/IdentifiableI.pm
BioPerl-1.6.1/Bio/LocatableSeq.pm
BioPerl-1.6.1/Bio/LocationI.pm
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BioPerl-1.6.1/Bio/OntologyIO.pm
BioPerl-1.6.1/Bio/ParameterBaseI.pm
BioPerl-1.6.1/Bio/Perl.pm
BioPerl-1.6.1/Bio/PhyloNetwork.pm
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BioPerl-1.6.1/Bio/RangeI.pm
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BioPerl-1.6.1/Bio/Species.pm
BioPerl-1.6.1/Bio/Taxon.pm
BioPerl-1.6.1/Bio/Taxonomy.pm
BioPerl-1.6.1/Bio/TreeIO.pm
BioPerl-1.6.1/Bio/UpdateableSeqI.pm
BioPerl-1.6.1/Bio/WebAgent.pm
BioPerl-1.6.1/Bio/Align
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BioPerl-1.6.1/Bio/Align/ProteinStatistics.pm
BioPerl-1.6.1/Bio/Align/StatisticsI.pm
BioPerl-1.6.1/Bio/Align/Utilities.pm
BioPerl-1.6.1/Bio/AlignIO
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BioPerl-1.6.1/Bio/AlignIO/Handler
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BioPerl-1.6.1/Bio/Annotation
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BioPerl-1.6.1/Bio/Annotation/Tree.pm
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BioPerl-1.6.1/Bio/Assembly/Contig.pm
BioPerl-1.6.1/Bio/Assembly/ContigAnalysis.pm
BioPerl-1.6.1/Bio/Assembly/IO.pm
BioPerl-1.6.1/Bio/Assembly/Scaffold.pm
BioPerl-1.6.1/Bio/Assembly/ScaffoldI.pm
BioPerl-1.6.1/Bio/Assembly/Singlet.pm
BioPerl-1.6.1/Bio/Assembly/IO
BioPerl-1.6.1/Bio/Assembly/IO/ace.pm
BioPerl-1.6.1/Bio/Assembly/IO/phrap.pm
BioPerl-1.6.1/Bio/Assembly/IO/tigr.pm
BioPerl-1.6.1/Bio/Assembly/Tools
BioPerl-1.6.1/Bio/Assembly/Tools/ContigSpectrum.pm
BioPerl-1.6.1/Bio/Biblio
BioPerl-1.6.1/Bio/Biblio/Article.pm
BioPerl-1.6.1/Bio/Biblio/BiblioBase.pm
BioPerl-1.6.1/Bio/Biblio/Book.pm
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BioPerl-1.6.1/Bio/Biblio/JournalArticle.pm
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BioPerl-1.6.1/Bio/Biblio/MedlineBookArticle.pm
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BioPerl-1.6.1/Bio/Biblio/Patent.pm
BioPerl-1.6.1/Bio/Biblio/Person.pm
BioPerl-1.6.1/Bio/Biblio/Proceeding.pm
BioPerl-1.6.1/Bio/Biblio/Provider.pm
BioPerl-1.6.1/Bio/Biblio/PubmedArticle.pm
BioPerl-1.6.1/Bio/Biblio/PubmedBookArticle.pm
BioPerl-1.6.1/Bio/Biblio/PubmedJournalArticle.pm
BioPerl-1.6.1/Bio/Biblio/Ref.pm
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BioPerl-1.6.1/Bio/Biblio/TechReport.pm
BioPerl-1.6.1/Bio/Biblio/Thesis.pm
BioPerl-1.6.1/Bio/Biblio/WebResource.pm
BioPerl-1.6.1/Bio/Biblio/IO
BioPerl-1.6.1/Bio/Biblio/IO/medline2ref.pm
BioPerl-1.6.1/Bio/Biblio/IO/medlinexml.pm
BioPerl-1.6.1/Bio/Biblio/IO/pubmed2ref.pm
BioPerl-1.6.1/Bio/Biblio/IO/pubmedxml.pm
BioPerl-1.6.1/Bio/Cluster
BioPerl-1.6.1/Bio/Cluster/ClusterFactory.pm
BioPerl-1.6.1/Bio/Cluster/FamilyI.pm
BioPerl-1.6.1/Bio/Cluster/SequenceFamily.pm
BioPerl-1.6.1/Bio/Cluster/UniGene.pm
BioPerl-1.6.1/Bio/Cluster/UniGeneI.pm
BioPerl-1.6.1/Bio/ClusterIO
BioPerl-1.6.1/Bio/ClusterIO/dbsnp.pm
BioPerl-1.6.1/Bio/ClusterIO/unigene.pm
BioPerl-1.6.1/Bio/CodonUsage
BioPerl-1.6.1/Bio/CodonUsage/IO.pm
BioPerl-1.6.1/Bio/CodonUsage/Table.pm
BioPerl-1.6.1/Bio/Coordinate
BioPerl-1.6.1/Bio/Coordinate/Chain.pm
BioPerl-1.6.1/Bio/Coordinate/Collection.pm
BioPerl-1.6.1/Bio/Coordinate/ExtrapolatingPair.pm
BioPerl-1.6.1/Bio/Coordinate/GeneMapper.pm
BioPerl-1.6.1/Bio/Coordinate/Graph.pm
BioPerl-1.6.1/Bio/Coordinate/MapperI.pm
BioPerl-1.6.1/Bio/Coordinate/Pair.pm
BioPerl-1.6.1/Bio/Coordinate/Result.pm
BioPerl-1.6.1/Bio/Coordinate/ResultI.pm
BioPerl-1.6.1/Bio/Coordinate/Utils.pm
BioPerl-1.6.1/Bio/Coordinate/Result
BioPerl-1.6.1/Bio/Coordinate/Result/Gap.pm
BioPerl-1.6.1/Bio/Coordinate/Result/Match.pm
BioPerl-1.6.1/Bio/Das
BioPerl-1.6.1/Bio/Das/FeatureTypeI.pm
BioPerl-1.6.1/Bio/Das/SegmentI.pm
BioPerl-1.6.1/Bio/DB
BioPerl-1.6.1/Bio/DB/Ace.pm
BioPerl-1.6.1/Bio/DB/BiblioI.pm
BioPerl-1.6.1/Bio/DB/BioFetch.pm
BioPerl-1.6.1/Bio/DB/CUTG.pm
BioPerl-1.6.1/Bio/DB/DBFetch.pm
BioPerl-1.6.1/Bio/DB/EMBL.pm
BioPerl-1.6.1/Bio/DB/EntrezGene.pm
BioPerl-1.6.1/Bio/DB/EUtilities.pm
BioPerl-1.6.1/Bio/DB/Expression.pm
BioPerl-1.6.1/Bio/DB/Failover.pm
BioPerl-1.6.1/Bio/DB/Fasta.pm
BioPerl-1.6.1/Bio/DB/FileCache.pm
BioPerl-1.6.1/Bio/DB/Flat.pm
BioPerl-1.6.1/Bio/DB/GenBank.pm
BioPerl-1.6.1/Bio/DB/GenericWebAgent.pm
BioPerl-1.6.1/Bio/DB/GenPept.pm
BioPerl-1.6.1/Bio/DB/GFF.pm
BioPerl-1.6.1/Bio/DB/HIV.pm
BioPerl-1.6.1/Bio/DB/InMemoryCache.pm
BioPerl-1.6.1/Bio/DB/LocationI.pm
BioPerl-1.6.1/Bio/DB/MeSH.pm
BioPerl-1.6.1/Bio/DB/NCBIHelper.pm
BioPerl-1.6.1/Bio/DB/Qual.pm
BioPerl-1.6.1/Bio/DB/QueryI.pm
BioPerl-1.6.1/Bio/DB/RandomAccessI.pm
BioPerl-1.6.1/Bio/DB/ReferenceI.pm
BioPerl-1.6.1/Bio/DB/RefSeq.pm
BioPerl-1.6.1/Bio/DB/Registry.pm
BioPerl-1.6.1/Bio/DB/SeqFeature.pm
BioPerl-1.6.1/Bio/DB/SeqHound.pm
BioPerl-1.6.1/Bio/DB/SeqI.pm
BioPerl-1.6.1/Bio/DB/SeqVersion.pm
BioPerl-1.6.1/Bio/DB/SwissProt.pm
BioPerl-1.6.1/Bio/DB/Taxonomy.pm
BioPerl-1.6.1/Bio/DB/TFBS.pm
BioPerl-1.6.1/Bio/DB/Universal.pm
BioPerl-1.6.1/Bio/DB/UpdateableSeqI.pm
BioPerl-1.6.1/Bio/DB/WebDBSeqI.pm
BioPerl-1.6.1/Bio/DB/Biblio
BioPerl-1.6.1/Bio/DB/Biblio/biofetch.pm
BioPerl-1.6.1/Bio/DB/Biblio/eutils.pm
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BioPerl-1.6.1/Bio/DB/Expression
BioPerl-1.6.1/Bio/DB/Expression/geo.pm
BioPerl-1.6.1/Bio/DB/Flat
BioPerl-1.6.1/Bio/DB/Flat/BDB.pm
BioPerl-1.6.1/Bio/DB/Flat/BinarySearch.pm
BioPerl-1.6.1/Bio/DB/Flat/BDB
BioPerl-1.6.1/Bio/DB/Flat/BDB/embl.pm
BioPerl-1.6.1/Bio/DB/Flat/BDB/fasta.pm
BioPerl-1.6.1/Bio/DB/Flat/BDB/genbank.pm
BioPerl-1.6.1/Bio/DB/Flat/BDB/swiss.pm
BioPerl-1.6.1/Bio/DB/GFF
BioPerl-1.6.1/Bio/DB/GFF/Aggregator.pm
BioPerl-1.6.1/Bio/DB/GFF/Featname.pm
BioPerl-1.6.1/Bio/DB/GFF/Feature.pm
BioPerl-1.6.1/Bio/DB/GFF/Homol.pm
BioPerl-1.6.1/Bio/DB/GFF/RelSegment.pm
BioPerl-1.6.1/Bio/DB/GFF/Segment.pm
BioPerl-1.6.1/Bio/DB/GFF/Typename.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/ace.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/berkeleydb.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/biofetch.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/biofetch_oracle.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/memory.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/berkeleydb
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi/iterator.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi/mysql.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi/oracle.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi/oracleace.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi/pg.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/memory
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
BioPerl-1.6.1/Bio/DB/GFF/Adaptor/memory/iterator.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/alignment.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/clone.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/coding.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/gene.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/match.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/none.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/orf.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/processed_transcript.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/so_transcript.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/transcript.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/ucsc_acembly.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/ucsc_genscan.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/ucsc_refgene.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/ucsc_softberry.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
BioPerl-1.6.1/Bio/DB/GFF/Aggregator/ucsc_unigene.pm
BioPerl-1.6.1/Bio/DB/GFF/Util
BioPerl-1.6.1/Bio/DB/GFF/Util/Binning.pm
BioPerl-1.6.1/Bio/DB/GFF/Util/Rearrange.pm
BioPerl-1.6.1/Bio/DB/HIV
BioPerl-1.6.1/Bio/DB/HIV/HIVAnnotProcessor.pm
BioPerl-1.6.1/Bio/DB/HIV/HIVQueryHelper.pm
BioPerl-1.6.1/Bio/DB/HIV/lanl-schema.xml
BioPerl-1.6.1/Bio/DB/Query
BioPerl-1.6.1/Bio/DB/Query/GenBank.pm
BioPerl-1.6.1/Bio/DB/Query/HIVQuery.pm
BioPerl-1.6.1/Bio/DB/Query/WebQuery.pm
BioPerl-1.6.1/Bio/DB/SeqFeature
BioPerl-1.6.1/Bio/DB/SeqFeature/NormalizedFeature.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/NormalizedFeatureI.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/NormalizedTableFeatureI.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/Segment.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/Store.pm
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BioPerl-1.6.1/Bio/DB/SeqFeature/Store/LoadHelper.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/Store/memory.pm
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BioPerl-1.6.1/Bio/DB/SeqFeature/Store/DBI/mysql.pm
BioPerl-1.6.1/Bio/DB/SeqFeature/Store/DBI/Pg.pm
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BioPerl-1.6.1/Bio/DB/Taxonomy/flatfile.pm
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BioPerl-1.6.1/Bio/Event
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BioPerl-1.6.1/Bio/Expression/Platform.pm
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BioPerl-1.6.1/Bio/Expression/Sample.pm
BioPerl-1.6.1/Bio/Expression/FeatureGroup
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BioPerl-1.6.1/Bio/Expression/FeatureSet
BioPerl-1.6.1/Bio/Expression/FeatureSet/FeatureSetMas50.pm
BioPerl-1.6.1/Bio/Factory
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BioPerl-1.6.1/Bio/Factory/ApplicationFactoryI.pm
BioPerl-1.6.1/Bio/Factory/DriverFactory.pm
BioPerl-1.6.1/Bio/Factory/FTLocationFactory.pm
BioPerl-1.6.1/Bio/Factory/LocationFactoryI.pm
BioPerl-1.6.1/Bio/Factory/MapFactoryI.pm
BioPerl-1.6.1/Bio/Factory/ObjectBuilderI.pm
BioPerl-1.6.1/Bio/Factory/ObjectFactory.pm
BioPerl-1.6.1/Bio/Factory/ObjectFactoryI.pm
BioPerl-1.6.1/Bio/Factory/SeqAnalysisParserFactory.pm
BioPerl-1.6.1/Bio/Factory/SeqAnalysisParserFactoryI.pm
BioPerl-1.6.1/Bio/Factory/SequenceFactoryI.pm
BioPerl-1.6.1/Bio/Factory/SequenceProcessorI.pm
BioPerl-1.6.1/Bio/Factory/SequenceStreamI.pm
BioPerl-1.6.1/Bio/Factory/TreeFactoryI.pm
BioPerl-1.6.1/Bio/FeatureIO
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BioPerl-1.6.1/Bio/Index/EMBL.pm
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BioPerl-1.6.1/Bio/Index/Qual.pm
BioPerl-1.6.1/Bio/Index/Stockholm.pm
BioPerl-1.6.1/Bio/Index/SwissPfam.pm
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BioPerl-1.6.1/examples
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BioPerl-1.6.1/examples/subsequence.cgi
BioPerl-1.6.1/examples/align
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BioPerl-1.6.1/examples/align/clustalw.pl
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BioPerl-1.6.1/examples/biblio/biblio_soap.pl
BioPerl-1.6.1/examples/Bio-DB-GFF
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BioPerl-1.6.1/examples/cluster
BioPerl-1.6.1/examples/cluster/dbsnp.pl
BioPerl-1.6.1/examples/contributed
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BioPerl-1.6.1/examples/contributed/prosite2perl.pl
BioPerl-1.6.1/examples/contributed/rebase2list.pl
BioPerl-1.6.1/examples/db
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BioPerl-1.6.1/examples/db/gb2features.pl
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BioPerl-1.6.1/examples/db/getGenBank.pl
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BioPerl-1.6.1/examples/liveseq
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BioPerl-1.6.1/examples/popgen
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BioPerl-1.6.1/examples/root
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BioPerl-1.6.1/examples/root/lib/Bio
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BioPerl-1.6.1/examples/searchio
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BioPerl-1.6.1/examples/searchio/waba2gff.pl
BioPerl-1.6.1/examples/searchio/waba2gff3.pl
BioPerl-1.6.1/examples/sirna
BioPerl-1.6.1/examples/sirna/rnai_finder.cgi
BioPerl-1.6.1/examples/sirna/TAG
BioPerl-1.6.1/examples/structure
BioPerl-1.6.1/examples/structure/structure-io.pl
BioPerl-1.6.1/examples/tk
BioPerl-1.6.1/examples/tk/gsequence.pl
BioPerl-1.6.1/examples/tk/hitdisplay.pl
BioPerl-1.6.1/examples/tools
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BioPerl-1.6.1/examples/tools/seq_pattern.pl
BioPerl-1.6.1/examples/tools/standaloneblast.pl
BioPerl-1.6.1/examples/tree
BioPerl-1.6.1/examples/tree/paup2phylip.pl
BioPerl-1.6.1/ide
BioPerl-1.6.1/ide/bioperl.komodo
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BioPerl-1.6.1/t/SeqIO/embl.t
BioPerl-1.6.1/t/SeqIO/entrezgene.t
BioPerl-1.6.1/t/SeqIO/excel.t
BioPerl-1.6.1/t/SeqIO/exp.t
BioPerl-1.6.1/t/SeqIO/fasta.t
BioPerl-1.6.1/t/SeqIO/fastq.t
BioPerl-1.6.1/t/SeqIO/flybase_chadoxml.t
BioPerl-1.6.1/t/SeqIO/game.t
BioPerl-1.6.1/t/SeqIO/gcg.t
BioPerl-1.6.1/t/SeqIO/genbank.t
BioPerl-1.6.1/t/SeqIO/Handler.t
BioPerl-1.6.1/t/SeqIO/interpro.t
BioPerl-1.6.1/t/SeqIO/kegg.t
BioPerl-1.6.1/t/SeqIO/largefasta.t
BioPerl-1.6.1/t/SeqIO/lasergene.t
BioPerl-1.6.1/t/SeqIO/locuslink.t
BioPerl-1.6.1/t/SeqIO/metafasta.t
BioPerl-1.6.1/t/SeqIO/MultiFile.t
BioPerl-1.6.1/t/SeqIO/Multiple_fasta.t
BioPerl-1.6.1/t/SeqIO/phd.t
BioPerl-1.6.1/t/SeqIO/pir.t
BioPerl-1.6.1/t/SeqIO/pln.t
BioPerl-1.6.1/t/SeqIO/qual.t
BioPerl-1.6.1/t/SeqIO/raw.t
BioPerl-1.6.1/t/SeqIO/scf.t
BioPerl-1.6.1/t/SeqIO/SeqBuilder.t
BioPerl-1.6.1/t/SeqIO/Splicedseq.t
BioPerl-1.6.1/t/SeqIO/strider.t
BioPerl-1.6.1/t/SeqIO/swiss.t
BioPerl-1.6.1/t/SeqIO/tab.t
BioPerl-1.6.1/t/SeqIO/table.t
BioPerl-1.6.1/t/SeqIO/tigr.t
BioPerl-1.6.1/t/SeqIO/tigrxml.t
BioPerl-1.6.1/t/SeqIO/tinyseq.t
BioPerl-1.6.1/t/SeqIO/ztr.t
BioPerl-1.6.1/t/SeqTools
BioPerl-1.6.1/t/SeqTools/Backtranslate.t
BioPerl-1.6.1/t/SeqTools/CodonTable.t
BioPerl-1.6.1/t/SeqTools/ECnumber.t
BioPerl-1.6.1/t/SeqTools/GuessSeqFormat.t
BioPerl-1.6.1/t/SeqTools/OddCodes.t
BioPerl-1.6.1/t/SeqTools/SeqPattern.t
BioPerl-1.6.1/t/SeqTools/SeqStats.t
BioPerl-1.6.1/t/SeqTools/SeqUtils.t
BioPerl-1.6.1/t/SeqTools/SeqWords.t
BioPerl-1.6.1/t/Structure
BioPerl-1.6.1/t/Structure/IO.t
BioPerl-1.6.1/t/Structure/Structure.t
BioPerl-1.6.1/t/Tools
BioPerl-1.6.1/t/Tools/ePCR.t
BioPerl-1.6.1/t/Tools/Est2Genome.t
BioPerl-1.6.1/t/Tools/FootPrinter.t
BioPerl-1.6.1/t/Tools/Geneid.t
BioPerl-1.6.1/t/Tools/Genewise.t
BioPerl-1.6.1/t/Tools/Genomewise.t
BioPerl-1.6.1/t/Tools/Genpred.t
BioPerl-1.6.1/t/Tools/GFF.t
BioPerl-1.6.1/t/Tools/Hmmer.t
BioPerl-1.6.1/t/Tools/IUPAC.t
BioPerl-1.6.1/t/Tools/Lucy.t
BioPerl-1.6.1/t/Tools/Match.t
BioPerl-1.6.1/t/Tools/pICalculator.t
BioPerl-1.6.1/t/Tools/Primer3.t
BioPerl-1.6.1/t/Tools/Promoterwise.t
BioPerl-1.6.1/t/Tools/Pseudowise.t
BioPerl-1.6.1/t/Tools/QRNA.t
BioPerl-1.6.1/t/Tools/RandDistFunctions.t
BioPerl-1.6.1/t/Tools/RepeatMasker.t
BioPerl-1.6.1/t/Tools/rnamotif.t
BioPerl-1.6.1/t/Tools/Seg.t
BioPerl-1.6.1/t/Tools/Sigcleave.t
BioPerl-1.6.1/t/Tools/Signalp.t
BioPerl-1.6.1/t/Tools/Sim4.t
BioPerl-1.6.1/t/Tools/SiRNA.t
BioPerl-1.6.1/t/Tools/TandemRepeatsFinder.t
BioPerl-1.6.1/t/Tools/TargetP.t
BioPerl-1.6.1/t/Tools/Tmhmm.t
BioPerl-1.6.1/t/Tools/tRNAscanSE.t
BioPerl-1.6.1/t/Tools/Alignment
BioPerl-1.6.1/t/Tools/Alignment/Consed.t
BioPerl-1.6.1/t/Tools/Analysis
BioPerl-1.6.1/t/Tools/Analysis/DNA
BioPerl-1.6.1/t/Tools/Analysis/DNA/ESEfinder.t
BioPerl-1.6.1/t/Tools/Analysis/Protein
BioPerl-1.6.1/t/Tools/Analysis/Protein/Domcut.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/ELM.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/GOR4.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/HNN.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/Mitoprot.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/NetPhos.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/Scansite.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/Sopma.t
BioPerl-1.6.1/t/Tools/EMBOSS
BioPerl-1.6.1/t/Tools/EMBOSS/Palindrome.t
BioPerl-1.6.1/t/Tools/EUtilities
BioPerl-1.6.1/t/Tools/EUtilities/egquery.t
BioPerl-1.6.1/t/Tools/EUtilities/einfo.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_acheck.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_lcheck.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_llinks.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_ncheck.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_neighbor.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_neighbor_history.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_scores.t
BioPerl-1.6.1/t/Tools/EUtilities/epost.t
BioPerl-1.6.1/t/Tools/EUtilities/esearch.t
BioPerl-1.6.1/t/Tools/EUtilities/espell.t
BioPerl-1.6.1/t/Tools/EUtilities/esummary.t
BioPerl-1.6.1/t/Tools/EUtilities/EUtilParameters.t
BioPerl-1.6.1/t/Tools/Phylo
BioPerl-1.6.1/t/Tools/Phylo/Gerp.t
BioPerl-1.6.1/t/Tools/Phylo/Molphy.t
BioPerl-1.6.1/t/Tools/Phylo/PAML.t
BioPerl-1.6.1/t/Tools/Phylo/Phylip
BioPerl-1.6.1/t/Tools/Phylo/Phylip/ProtDist.t
BioPerl-1.6.1/t/Tools/Run
BioPerl-1.6.1/t/Tools/Run/RemoteBlast.t
BioPerl-1.6.1/t/Tools/Run/RemoteBlast_rpsblast.t
BioPerl-1.6.1/t/Tools/Run/StandAloneBlast.t
BioPerl-1.6.1/t/Tools/Run/WrapperBase.t
BioPerl-1.6.1/t/Tools/Signalp
BioPerl-1.6.1/t/Tools/Signalp/ExtendedSignalp.t
BioPerl-1.6.1/t/Tools/Spidey
BioPerl-1.6.1/t/Tools/Spidey/Spidey.t
BioPerl-1.6.1/t/Tree
BioPerl-1.6.1/t/Tree/Compatible.t
BioPerl-1.6.1/t/Tree/Node.t
BioPerl-1.6.1/t/Tree/RandomTreeFactory.t
BioPerl-1.6.1/t/Tree/Tree.t
BioPerl-1.6.1/t/Tree/TreeIO.t
BioPerl-1.6.1/t/Tree/TreeStatistics.t
BioPerl-1.6.1/t/Tree/PhyloNetwork
BioPerl-1.6.1/t/Tree/PhyloNetwork/Factory.t
BioPerl-1.6.1/t/Tree/PhyloNetwork/GraphViz.t
BioPerl-1.6.1/t/Tree/PhyloNetwork/MuVector.t
BioPerl-1.6.1/t/Tree/PhyloNetwork/PhyloNetwork.t
BioPerl-1.6.1/t/Tree/PhyloNetwork/RandomFactory.t
BioPerl-1.6.1/t/Tree/PhyloNetwork/TreeFactory.t
BioPerl-1.6.1/t/Tree/TreeIO
BioPerl-1.6.1/t/Tree/TreeIO/lintree.t
BioPerl-1.6.1/t/Tree/TreeIO/newick.t
BioPerl-1.6.1/t/Tree/TreeIO/nexus.t
BioPerl-1.6.1/t/Tree/TreeIO/nhx.t
BioPerl-1.6.1/t/Tree/TreeIO/phyloxml.t
BioPerl-1.6.1/t/Tree/TreeIO/svggraph.t
BioPerl-1.6.1/t/Tree/TreeIO/tabtree.t
BioPerl-1.6.1/t/Variation
BioPerl-1.6.1/t/Variation/AAChange.t
BioPerl-1.6.1/t/Variation/AAReverseMutate.t
BioPerl-1.6.1/t/Variation/Allele.t
BioPerl-1.6.1/t/Variation/DNAMutation.t
BioPerl-1.6.1/t/Variation/RNAChange.t
BioPerl-1.6.1/t/Variation/SeqDiff.t
BioPerl-1.6.1/t/Variation/SNP.t
BioPerl-1.6.1/t/Variation/Variation_IO.t
/bin/tar: Read 1536 bytes from -
CPAN.pm: Building C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
>>> /home/fly1800/ap1800-297235/bin/perl-static Makefile.PL
# running Build.PL
Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] Checking prerequisites...
recommends:
* Optional prerequisite Ace is not installed
(wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace)
* Optional prerequisite Bio::ASN1::EntrezGene is not installed
(wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!])
* Optional prerequisite Convert::Binary::C is not installed
(wanted for strider functionality, used by Bio::SeqIO::strider)
* Optional prerequisite GraphViz is not installed
(wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz)
* Optional prerequisite PostScript::TextBlock is not installed
(wanted for EPS output, used by Bio::Tree::Draw::Cladogram)
* Optional prerequisite SOAP::Lite is not installed
(wanted for Bibliographic queries, used by Bio::DB::Biblio::soap)
ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions
of the modules indicated above before proceeding with this installation
Checking features:
BioDBSeqFeature_Pg........enabled
BioDBSeqFeature_BDB.......enabled
BioDBGFF..................enabled
Network...................enabled
BioDBSeqFeature_mysql.....enabled
BioDBSeqFeature_SQLite....enabled
Do you want to run the Bio::DB::GFF or Bio::DB::SeqFeature::Store live database tests? y/n [n] - will not run the BioDBGFF or BioDBSeqFeature live database tests
Install [a]ll BioPerl scripts, [n]one, or choose groups [i]nteractively? [a] - will install all scripts
Do you want to run tests that require connection to servers across the internet
(likely to cause some failures)? y/n [n] Could not get valid metadata. Error is: Invalid metadata structure. Errors: Expected a map structure from string or file. (optional_features -> Bio::Tools::SeqPattern::BackTranslate -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Query::HIVQuery -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Biblio::eutils -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::* -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::EUtilParameters -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::WebAgent -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tree::Draw::Cladogram -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Draw::Pictogram -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::EUtilities -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::GFF::Adaptor::berkeleydb -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Analysis::DNA* -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::FeatureIO::interpro -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PopGen::HtSNP -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SearchIO::blastxml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::GFF::Adaptor::ace -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::game::gameWriter -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::chadoxml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tree::Compatible -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Microarray::Tools::ReseqChip -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::FeatureIO::gff -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::OntologyIO::InterProParser -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Query::GenBank -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Primer3 -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::SeqPattern -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PhyloNetwork -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::FileCache -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::entrezgene -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Analysis::DNA::ESEfinder -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::TreeIO::svggraph -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Variation::IO::xml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::agave -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Taxonomy::entrez -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PhyloNetwork::RandomFactory -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::excel -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Analysis::Protein* -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::tinyseq -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::HIV -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::NCBIHelper -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqFeature::Annotated -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::bsml_sax -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::ClusterIO::dbsnp -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Ace -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqFeature::Collection -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Tools::Run::RemoteBlast -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::Biblio::soap -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SearchIO::Writer::BSMLResultWriter -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::tigrxml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::strider -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::DB::SeqFeature::Store::FeatureFileLoader -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PopGen::TagHaplotype -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::PhyloNetwork::GraphViz -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::Biblio::IO::medlinexml -> requires) [Validation: 1.2], Expected a map structure from string or file. (optional_features -> Bio::SeqIO::game::gameSubs -> requires) [Validation: 1.2], 'Perl_5' for 'license' does not have a URL scheme (resources -> license) [Validation: 1.2]
at /home/fly1800/var/megalib/Module/Build/Base.pm line 4581.
Could not create MYMETA files
- will not run internet-requiring tests
Creating new 'Build' script for 'BioPerl' version '1.006001'
Could not read metadata file. Falling back to other methods to determine prerequisites
---- Unsatisfied dependencies detected during ----
---- CJFIELDS/BioPerl-1.6.1.tar.gz ----
Data::Stag [requires]
Running make 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
>>> /home/fly1800/ap1800-297235/bin/perl-static Makefile.PL
Checking if your kit is complete...
Looks good
Writing Makefile for Data
Writing MYMETA.yml and MYMETA.json
>>> make
cp Data/Stag/SxprParser.pm blib/lib/Data/Stag/SxprParser.pm
cp Data/Stag/SxprWriter.pm blib/lib/Data/Stag/SxprWriter.pm
cp Data/Stag/XSLTHandler.pm blib/lib/Data/Stag/XSLTHandler.pm
cp Data/Stag/SAX2Stag.pm blib/lib/Data/Stag/SAX2Stag.pm
cp Data/Stag/BaseGenerator.pm blib/lib/Data/Stag/BaseGenerator.pm
cp Data/Stag/PerlWriter.pm blib/lib/Data/Stag/PerlWriter.pm
cp Data/Stag/GraphHandler.pm blib/lib/Data/Stag/GraphHandler.pm
cp Data/Stag/Writer.pm blib/lib/Data/Stag/Writer.pm
cp Data/Stag/XMLWriter.pm blib/lib/Data/Stag/XMLWriter.pm
cp Data/Stag/StagImpl.pm blib/lib/Data/Stag/StagImpl.pm
cp Data/Stag/StagI.pm blib/lib/Data/Stag/StagI.pm
cp Data/Stag/IndentParser.pm blib/lib/Data/Stag/IndentParser.pm
cp Data/Stag/Util.pm blib/lib/Data/Stag/Util.pm
cp Data/Stag/Base.pm blib/lib/Data/Stag/Base.pm
cp Data/Stag/XSLHandler.pm blib/lib/Data/Stag/XSLHandler.pm
cp Data/Stag/XMLParser.pm blib/lib/Data/Stag/XMLParser.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/ChainHandler.pm blib/lib/Data/Stag/ChainHandler.pm
cp Data/Stag/BaseHandler.pm blib/lib/Data/Stag/BaseHandler.pm
cp Data/Stag/ITextWriter.pm blib/lib/Data/Stag/ITextWriter.pm
cp Data/Stag/Simple.pm blib/lib/Data/Stag/Simple.pm
cp Data/Stag.pm blib/lib/Data/Stag.pm
cp Data/Stag/Arr2HTML.pm blib/lib/Data/Stag/Arr2HTML.pm
cp Data/Stag/IndentWriter.pm blib/lib/Data/Stag/IndentWriter.pm
cp Data/Stag/null.pm blib/lib/Data/Stag/null.pm
cp Data/Stag/PodParser.pm blib/lib/Data/Stag/PodParser.pm
cp Data/Stag/DTDWriter.pm blib/lib/Data/Stag/DTDWriter.pm
cp Data/Stag/ITextParser.pm blib/lib/Data/Stag/ITextParser.pm
cp scripts/stag-handle.pl blib/script/stag-handle.pl
/home/fly1800/ap1800-297235/bin/perl-static -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-handle.pl
cp scripts/stag-view.pl blib/script/stag-view.pl
/home/fly1800/ap1800-297235/bin/perl-static -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-view.pl
cp scripts/stag-itext2sxpr.pl blib/script/stag-itext2sxpr.pl
/home/fly1800/ap1800-297235/bin/perl-static -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-itext2sxpr.pl
cp scripts/stag-autoschema.pl blib/script/stag-autoschema.pl
/home/fly1800/ap1800-297235/bin/perl-static -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-autoschema.pl
cp scripts/stag-grep.pl blib/script/stag-grep.pl
/home/fly1800/ap1800-297235/bin/perl-static -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-grep.pl
cp scripts/stag-join.pl blib/script/stag-join.pl
/home/fly1800/ap1800-297235/bin/perl-static -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-join.pl
cp scripts/stag-mogrify.pl blib/script/stag-mogrify.pl
/home/fly1800/ap1800-297235/bin/perl-static -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-mogrify.pl
cp scripts/stag-xml2itext.pl blib/script/stag-xml2itext.pl
/home/fly1800/ap1800-297235/bin/perl-static -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-xml2itext.pl
cp scripts/stag-filter.pl blib/script/stag-filter.pl
/home/fly1800/ap1800-297235/bin/perl-static -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-filter.pl
cp scripts/stag-query.pl blib/script/stag-query.pl
/home/fly1800/ap1800-297235/bin/perl-static -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-query.pl
cp scripts/stag-parse.pl blib/script/stag-parse.pl
/home/fly1800/ap1800-297235/bin/perl-static -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-parse.pl
cp scripts/stag-splitter.pl blib/script/stag-splitter.pl
/home/fly1800/ap1800-297235/bin/perl-static -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-splitter.pl
cp scripts/stag-findsubtree.pl blib/script/stag-findsubtree.pl
/home/fly1800/ap1800-297235/bin/perl-static -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-findsubtree.pl
cp scripts/stag-db.pl blib/script/stag-db.pl
/home/fly1800/ap1800-297235/bin/perl-static -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-db.pl
cp scripts/stag-flatten.pl blib/script/stag-flatten.pl
/home/fly1800/ap1800-297235/bin/perl-static -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-flatten.pl
cp scripts/stag-merge.pl blib/script/stag-merge.pl
/home/fly1800/ap1800-297235/bin/perl-static -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-merge.pl
cp scripts/stag-itext2simple.pl blib/script/stag-itext2simple.pl
/home/fly1800/ap1800-297235/bin/perl-static -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-itext2simple.pl
cp scripts/stag-drawtree.pl blib/script/stag-drawtree.pl
/home/fly1800/ap1800-297235/bin/perl-static -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-drawtree.pl
cp scripts/stag-itext2xml.pl blib/script/stag-itext2xml.pl
/home/fly1800/ap1800-297235/bin/perl-static -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-itext2xml.pl
cp scripts/stag-diff.pl blib/script/stag-diff.pl
/home/fly1800/ap1800-297235/bin/perl-static -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/stag-diff.pl
Manifying blib/man1/stag-diff.pl.1
Manifying blib/man1/stag-drawtree.pl.1
Manifying blib/man1/stag-merge.pl.1
Manifying blib/man1/stag-findsubtree.pl.1
Manifying blib/man1/stag-db.pl.1
Manifying blib/man1/stag-flatten.pl.1
Manifying blib/man1/stag-parse.pl.1
Manifying blib/man1/stag-splitter.pl.1
Manifying blib/man1/stag-query.pl.1
Manifying blib/man1/stag-filter.pl.1
Manifying blib/man1/stag-join.pl.1
Manifying blib/man1/stag-mogrify.pl.1
Manifying blib/man1/stag-autoschema.pl.1
Manifying blib/man1/stag-grep.pl.1
Manifying blib/man1/stag-view.pl.1
Manifying blib/man1/stag-handle.pl.1
Manifying blib/man3/Data::Stag::Simple.3
Manifying blib/man3/Data::Stag::BaseHandler.3
Manifying blib/man3/Data::Stag::PerlWriter.3
Manifying blib/man3/Data::Stag::StagDB.3
Manifying blib/man3/Data::Stag::StagImpl.3
Manifying blib/man3/Data::Stag::null.3
Manifying blib/man3/Data::Stag::ITextParser.3
Manifying blib/man3/Data::Stag::IndentWriter.3
Manifying blib/man3/Data::Stag::IndentParser.3
Manifying blib/man3/Data::Stag::Arr2HTML.3
Manifying blib/man3/Data::Stag::XSLHandler.3
Manifying blib/man3/Data::Stag::SxprParser.3
Manifying blib/man3/Data::Stag::SxprWriter.3
Manifying blib/man3/Data::Stag::GraphHandler.3
Manifying blib/man3/Data::Stag::ITextWriter.3
Manifying blib/man3/Data::Stag::BaseGenerator.3
Manifying blib/man3/Data::Stag::ChainHandler.3
Manifying blib/man3/Data::Stag.3
Manifying blib/man3/Data::Stag::HashDB.3
Manifying blib/man3/Data::Stag::XMLWriter.3
Manifying blib/man3/Data::Stag::Writer.3
Manifying blib/man3/Data::Stag::PodParser.3
Manifying blib/man3/Data::Stag::DTDWriter.3
Manifying blib/man3/Data::Stag::XMLParser.3
Manifying blib/man3/Data::Stag::XSLTHandler.3
Manifying blib/man3/Data::Stag::SAX2Stag.3
CMUNGALL/Data-Stag-0.11.tar.gz
make -- OK
Running make test
>>> make test TEST_VERBOSE=1
PERL_DL_NONLAZY=1 /home/fly1800/ap1800-297235/bin/perl-static "-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 linux
# Current time local: Fri Jun 21 11:02:36 2013
# Current time GMT: Fri Jun 21 18:02:36 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 linux
# Current time local: Fri Jun 21 11:02:36 2013
# Current time GMT: Fri Jun 21 18:02:36 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 linux
# Current time local: Fri Jun 21 11:02:37 2013
# Current time GMT: Fri Jun 21 18:02:37 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 linux
# Current time local: Fri Jun 21 11:02:37 2013
# Current time GMT: Fri Jun 21 18:02:37 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 linux
# Current time local: Fri Jun 21 11:02:37 2013
# Current time GMT: Fri Jun 21 18:02:37 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 linux
# Current time local: Fri Jun 21 11:02:37 2013
# Current time GMT: Fri Jun 21 18:02:37 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 linux
# Current time local: Fri Jun 21 11:02:37 2013
# Current time GMT: Fri Jun 21 18:02:37 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 linux
# Current time local: Fri Jun 21 11:02:37 2013
# Current time GMT: Fri Jun 21 18:02:37 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 linux
# Current time local: Fri Jun 21 11:02:37 2013
# Current time GMT: Fri Jun 21 18:02:37 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 linux
# Current time local: Fri Jun 21 11:02:37 2013
# Current time GMT: Fri Jun 21 18:02:37 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 linux
# Current time local: Fri Jun 21 11:02:38 2013
# Current time GMT: Fri Jun 21 18:02:38 2013
# Using Test.pm version 1.26
foo
methyl
big dave
auchtermuchty
bar
shuggy
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
1
2
2
ok 7
ok 8
2
ok 9
1
2
ok
t/roundtrip-attrs.t ..
1..5
# Running under perl version 5.018000 for linux
# Current time local: Fri Jun 21 11:02:38 2013
# Current time GMT: Fri Jun 21 18:02:38 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
88
http://sourceforge.net/sflogo.php?group_id=68482&type=1
31
SourceForge.net Logo
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 linux
# Current time local: Fri Jun 21 11:02:38 2013
# Current time GMT: Fri Jun 21 18:02:38 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 linux
# Current time local: Fri Jun 21 11:02:38 2013
# Current time GMT: Fri Jun 21 18:02:38 2013
# Using Test.pm version 1.26
Sherlock Holmes
detective
secret agent
James Bond
Sherlock Holmes
detective
London
221B Baker Street
Great Britain
secret agent
James Bond
ok 1
Sherlock Holmes
detective
London
221B Baker Street
Great Britain
secret agent
James Bond
ok 2
ok
t/sxpr.t .............
1..2
# Running under perl version 5.018000 for linux
# Current time local: Fri Jun 21 11:02:38 2013
# Current time GMT: Fri Jun 21 18:02:38 2013
# Using Test.pm version 1.26
ok 1
ok 2
ok
t/unhash.t ...........
1..4
# Running under perl version 5.018000 for linux
# Current time local: Fri Jun 21 11:02:38 2013
# Current time GMT: Fri Jun 21 18:02:38 2013
# Using Test.pm version 1.26
Hill
11291
The Manse
19 Chestnut Ln
Garden City
NY
James
34
James
Katonah
Hickory Street
10578
NY
Sarah
30
Hill
11291
Garden City
The Manse
19 Chestnut Ln
NY
James
34
Sarah
30
James
NY
10578
Hickory Street
Katonah
The Manse 19 Chestnut Ln
ok 1
Fred
blue
blonde
Jill
John
Gerald
Fred
blue
blonde
Jill
John
Gerald
Jill John Gerald
ok 2
ok 3
ok 4
ok
t/unset.t ............
1..4
# Running under perl version 5.018000 for linux
# Current time local: Fri Jun 21 11:02:38 2013
# Current time GMT: Fri Jun 21 18:02:38 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 linux
# Current time local: Fri Jun 21 11:02:38 2013
# Current time GMT: Fri Jun 21 18:02:38 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 linux
# Current time local: Fri Jun 21 11:02:38 2013
# Current time GMT: Fri Jun 21 18:02:38 2013
# Using Test.pm version 1.26
shuggybus driver55
tamforklift driverchips
ok 1
$VAR1 = {
'personset' => {
'person' => [
{
'age' => '55',
'name' => 'shuggy',
'job' => 'bus driver'
},
{
'name' => 'tam',
'favourite_food' => 'chips',
'job' => 'forklift driver'
}
]
}
};
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 linux
# Current time local: Fri Jun 21 11:02:38 2013
# Current time GMT: Fri Jun 21 18:02:38 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, 3 wallclock secs ( 0.15 usr 0.06 sys + 1.79 cusr 0.22 csys = 2.22 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 make for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
Prepending /home/fly1800/var/cpan/build/Data-Stag-0.11-1FpWA2/blib/arch /home/fly1800/var/cpan/build/Data-Stag-0.11-1FpWA2/blib/lib to PERL5LIB for 'get'
Has already been unwrapped into directory /home/fly1800/var/cpan/build/BioPerl-1.6.1-OeFNmD
Prepending /home/fly1800/var/cpan/build/Data-Stag-0.11-1FpWA2/blib/arch /home/fly1800/var/cpan/build/Data-Stag-0.11-1FpWA2/blib/lib to PERL5LIB for 'make'
CPAN.pm: Building C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
>>> make
/home/fly1800/ap1800-297235/bin/perl-static Build --makefile_env_macros 1
Building BioPerl
blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl
blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl
blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl
blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl
blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl
blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl
blib/script/search2table.PLS -> blib/script/bp_search2table.pl
blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl
blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl
blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl
blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl
blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl
blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl
blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl
blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl
blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl
blib/script/biblio.PLS -> blib/script/bp_biblio.pl
blib/script/einfo.PLS -> blib/script/bp_einfo.pl
blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl
blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl
blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl
blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl
blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl
blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl
blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl
blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl
blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl
blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl
blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl
blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl
blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl
blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl
blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl
blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl
blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl
blib/script/mutate.PLS -> blib/script/bp_mutate.pl
blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl
blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl
blib/script/hivq.PLS -> blib/script/bp_hivq.pl
blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl
blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl
blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl
blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl
blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl
blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl
blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl
blib/script/revtrans-motif.PLS -> blib/script/bp_revtrans-motif.pl
blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl
blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl
blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl
blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl
blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl
blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl
blib/script/bp_index.PLS -> blib/script/bp_index.pl
blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl
blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl
blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl
blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl
blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl
blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl
blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl
blib/script/flanks.PLS -> blib/script/bp_flanks.pl
blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl
blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl
CJFIELDS/BioPerl-1.6.1.tar.gz
make -- OK
Prepending /home/fly1800/var/cpan/build/Data-Stag-0.11-1FpWA2/blib/arch /home/fly1800/var/cpan/build/Data-Stag-0.11-1FpWA2/blib/lib to PERL5LIB for 'test'
Running make test
>>> make test TEST_VERBOSE=1
/home/fly1800/ap1800-297235/bin/perl-static Build --makefile_env_macros 1 test
Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS
Changing sharpbang in blib/script/flanks.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/flanks.PLS.bak
blib/script/flanks.PLS -> blib/script/bp_flanks.pl
Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS
Changing sharpbang in blib/script/filter_search.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/filter_search.PLS.bak
blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl
Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS
Changing sharpbang in blib/script/bp_fetch.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/bp_fetch.PLS.bak
blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl
Copying scripts/utilities/download_query_genbank.PLS -> blib/script/download_query_genbank.PLS
Changing sharpbang in blib/script/download_query_genbank.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/download_query_genbank.PLS.bak
blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl
Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS
Changing sharpbang in blib/script/search2table.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/search2table.PLS.bak
blib/script/search2table.PLS -> blib/script/bp_search2table.pl
Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS
Changing sharpbang in blib/script/search2gff.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/search2gff.PLS.bak
blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl
Copying scripts/tree/blast2tree.PLS -> blib/script/blast2tree.PLS
Changing sharpbang in blib/script/blast2tree.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/blast2tree.PLS.bak
blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl
Copying scripts/Bio-DB-GFF/process_wormbase.PLS -> blib/script/process_wormbase.PLS
Changing sharpbang in blib/script/process_wormbase.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/process_wormbase.PLS.bak
blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl
Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS
Changing sharpbang in blib/script/biblio.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/biblio.PLS.bak
blib/script/biblio.PLS -> blib/script/bp_biblio.pl
Copying scripts/popgen/composite_LD.PLS -> blib/script/composite_LD.PLS
Changing sharpbang in blib/script/composite_LD.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/composite_LD.PLS.bak
blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl
Copying scripts/taxa/classify_hits_kingdom.PLS -> blib/script/classify_hits_kingdom.PLS
Changing sharpbang in blib/script/classify_hits_kingdom.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/classify_hits_kingdom.PLS.bak
blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl
Copying scripts/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS
Changing sharpbang in blib/script/biofetch_genbank_proxy.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/biofetch_genbank_proxy.PLS.bak
blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl
Copying scripts/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS
Changing sharpbang in blib/script/process_gadfly.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/process_gadfly.PLS.bak
blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl
Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS
Changing sharpbang in blib/script/genbank2gff3.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/genbank2gff3.PLS.bak
blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl
Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS
Changing sharpbang in blib/script/remote_blast.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/remote_blast.PLS.bak
blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl
Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS
Changing sharpbang in blib/script/tree2pag.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/tree2pag.PLS.bak
blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl
Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS
Changing sharpbang in blib/script/generate_histogram.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/generate_histogram.PLS.bak
blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl
Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS
Changing sharpbang in blib/script/make_mrna_protein.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/make_mrna_protein.PLS.bak
blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl
Copying scripts/Bio-DB-GFF/load_gff.PLS -> blib/script/load_gff.PLS
Changing sharpbang in blib/script/load_gff.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/load_gff.PLS.bak
blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl
Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS
Changing sharpbang in blib/script/bulk_load_gff.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/bulk_load_gff.PLS.bak
blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl
Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS
Changing sharpbang in blib/script/bp_mrtrans.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/bp_mrtrans.PLS.bak
blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl
Copying scripts/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS
Changing sharpbang in blib/script/fastam9_to_table.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/fastam9_to_table.PLS.bak
blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl
Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS
Changing sharpbang in blib/script/seqconvert.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/seqconvert.PLS.bak
blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl
Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS
Changing sharpbang in blib/script/local_taxonomydb_query.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/local_taxonomydb_query.PLS.bak
blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl
Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS
Changing sharpbang in blib/script/search2tribe.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/search2tribe.PLS.bak
blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl
Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS
Changing sharpbang in blib/script/parse_hmmsearch.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/parse_hmmsearch.PLS.bak
blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl
Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS
Changing sharpbang in blib/script/nexus2nh.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/nexus2nh.PLS.bak
blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl
Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS
Changing sharpbang in blib/script/bp_index.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/bp_index.PLS.bak
blib/script/bp_index.PLS -> blib/script/bp_index.pl
Copying scripts/utilities/dbsplit.PLS -> blib/script/dbsplit.PLS
Changing sharpbang in blib/script/dbsplit.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/dbsplit.PLS.bak
blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl
Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.PLS
Changing sharpbang in blib/script/bp_seqfeature_load.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/bp_seqfeature_load.PLS.bak
blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl
Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS
Changing sharpbang in blib/script/heterogeneity_test.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/heterogeneity_test.PLS.bak
blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl
Copying scripts/utilities/seq_length.PLS -> blib/script/seq_length.PLS
Changing sharpbang in blib/script/seq_length.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/seq_length.PLS.bak
blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl
Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS
Changing sharpbang in blib/script/unflatten_seq.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/unflatten_seq.PLS.bak
blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl
Copying scripts/searchio/hmmer_to_table.PLS -> blib/script/hmmer_to_table.PLS
Changing sharpbang in blib/script/hmmer_to_table.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/hmmer_to_table.PLS.bak
blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl
Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS
Changing sharpbang in blib/script/gccalc.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/gccalc.PLS.bak
blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl
Copying scripts/Bio-DB-EUtilities/einfo.PLS -> blib/script/einfo.PLS
Changing sharpbang in blib/script/einfo.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/einfo.PLS.bak
blib/script/einfo.PLS -> blib/script/bp_einfo.pl
Copying scripts/seqstats/aacomp.PLS -> blib/script/aacomp.PLS
Changing sharpbang in blib/script/aacomp.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/aacomp.PLS.bak
blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl
Copying scripts/utilities/revtrans-motif.PLS -> blib/script/revtrans-motif.PLS
Changing sharpbang in blib/script/revtrans-motif.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/revtrans-motif.PLS.bak
blib/script/revtrans-motif.PLS -> blib/script/bp_revtrans-motif.pl
Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS
Changing sharpbang in blib/script/taxid4species.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/taxid4species.PLS.bak
blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl
Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS
Changing sharpbang in blib/script/bp_seqret.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/bp_seqret.PLS.bak
blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl
Copying scripts/seq/extract_feature_seq.PLS -> blib/script/extract_feature_seq.PLS
Changing sharpbang in blib/script/extract_feature_seq.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/extract_feature_seq.PLS.bak
blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl
Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS
Changing sharpbang in blib/script/biogetseq.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/biogetseq.PLS.bak
blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl
Copying scripts/utilities/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS
Changing sharpbang in blib/script/pairwise_kaks.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/pairwise_kaks.PLS.bak
blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl
Copying scripts/Bio-DB-GFF/fast_load_gff.PLS -> blib/script/fast_load_gff.PLS
Changing sharpbang in blib/script/fast_load_gff.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/fast_load_gff.PLS.bak
blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl
Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS
Changing sharpbang in blib/script/translate_seq.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/translate_seq.PLS.bak
blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl
Copying scripts/DB-HIV/hivq.PLS -> blib/script/hivq.PLS
Changing sharpbang in blib/script/hivq.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/hivq.PLS.bak
blib/script/hivq.PLS -> blib/script/bp_hivq.pl
Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS
Changing sharpbang in blib/script/meta_gff.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/meta_gff.PLS.bak
blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl
Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS
Changing sharpbang in blib/script/taxonomy2tree.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/taxonomy2tree.PLS.bak
blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl
Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS
Changing sharpbang in blib/script/bioflat_index.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/bioflat_index.PLS.bak
blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl
Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS
Changing sharpbang in blib/script/mutate.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/mutate.PLS.bak
blib/script/mutate.PLS -> blib/script/bp_mutate.pl
Copying scripts/seq/seqretsplit.PLS -> blib/script/seqretsplit.PLS
Changing sharpbang in blib/script/seqretsplit.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/seqretsplit.PLS.bak
blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl
Copying scripts/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS
Changing sharpbang in blib/script/query_entrez_taxa.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/query_entrez_taxa.PLS.bak
blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl
Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS
Changing sharpbang in blib/script/search2alnblocks.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/search2alnblocks.PLS.bak
blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl
Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS
Changing sharpbang in blib/script/bp_sreformat.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/bp_sreformat.PLS.bak
blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl
Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS
Changing sharpbang in blib/script/bp_nrdb.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/bp_nrdb.PLS.bak
blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl
Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS
Changing sharpbang in blib/script/oligo_count.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/oligo_count.PLS.bak
blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl
Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS
Changing sharpbang in blib/script/mask_by_search.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/mask_by_search.PLS.bak
blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl
Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.PLS
Changing sharpbang in blib/script/bp_seqfeature_delete.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/bp_seqfeature_delete.PLS.bak
blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl
Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS
Changing sharpbang in blib/script/process_sgd.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/process_sgd.PLS.bak
blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl
Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS
Changing sharpbang in blib/script/chaos_plot.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/chaos_plot.PLS.bak
blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl
Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS
Changing sharpbang in blib/script/split_seq.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/split_seq.PLS.bak
blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl
Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS
Changing sharpbang in blib/script/genbank2gff.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/genbank2gff.PLS.bak
blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl
Copying scripts/utilities/search2BSML.PLS -> blib/script/search2BSML.PLS
Changing sharpbang in blib/script/search2BSML.PLS to /home/fly1800/ap1800-297235/bin/perl-static
Deleting blib/script/search2BSML.PLS.bak
blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl
Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS
blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Align/AlignStats.t .........................
1..43
ok 1 - use Bio::Align::DNAStatistics;
ok 2 - use Bio::Align::ProteinStatistics;
ok 3 - use Bio::AlignIO;
ok 4 - The object isa Bio::Align::AlignI
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17 - The object isa Bio::Align::AlignI
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31 - The object isa Bio::Align::AlignI
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - The object isa Bio::Align::AlignI
ok 38 - The object isa Bio::Matrix::PhylipDist
ok 39
ok 40
ok 41
ok 42 - The object isa Bio::PrimarySeqI
ok 43
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118, line 120.
t/Align/SimpleAlign.t ........................
1..179
ok 1 - use Bio::SimpleAlign;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::SeqFeature::Generic;
ok 4 - use Bio::Location::Simple;
ok 5 - use Bio::Location::Split;
ok 6 - The object isa Bio::AlignIO
ok 7 - pfam input test
ok 8 - match_line
ok 9 - The object isa Bio::Align::AlignI
ok 10 - num_sequences
ok 11 - num_sequences
ok 12 - select_noncont
ok 13 - select_noncont
ok 14 - num_sequences
ok 15 - select_noncont
ok 16 - select_noncont
ok 17 - each_seq
ok 18 - get_nse
ok 19 - id
ok 20 - num_gaps
ok 21 - each_alphabetically
ok 22 - column_from_residue_number
ok 23 - display_name get/set
ok 24 - display_name get
ok 25 - consensus_string
ok 26 - consensus_string
ok 27 - consensus_string
ok 28
ok 29 - each_seq_with_id
ok 30 - is_flush
ok 31 - id get/set
ok 32 - length
ok 33 - num_residues
ok 34 - num_sequences
ok 35 - overall_percentage_identity
ok 36 - overall_percentage_identity
ok 37 - overall_percentage_identity
ok 38 - overall_percentage_identity
ok 39 - average_percentage_identity
ok 40
ok 41 - set_displayname_count
ok 42
ok 43 - set_displayname_flat
ok 44
ok 45 - set_displayname_normal
ok 46
ok 47
ok 48 - uppercase, map_chars
ok 49 - match_line
ok 50 - remove_seqs
ok 51 - remove_seqs
ok 52 - add_seq
ok 53 - add_seq
ok 54 - get_seq_by_pos
ok 55 - get_seq_by_pos
ok 56
ok 57
ok 58
ok 59 - purge
ok 60 - purge
ok 61 - IO::String consensus_iupac
ok 62 - IO::String write_aln normal
ok 63 - IO::String write_aln slice
ok 64 - IO::String write_aln slice
ok 65 - IO::String write_aln slice
ok 66 - IO::String write_aln slice
ok 67 - IO::String write_aln slice
ok 68
ok 69 - remove_columns by position
ok 70 - remove_columns by position (wrong order)
ok 71 - cigar_line
ok 72 - cigar_line
ok 73 - cigar_line
ok 74 - cigar_line
ok 75 - sort_alphabetically - before
ok 76
ok 77 - sort_alphabetically - after
ok 78 - remove_gaps
ok 79 - remove_gaps all_gaps_only
ok 80 - set_new_reference
ok 81 - set_new_reference
ok 82 - uniq_seq
ok 83 - bug 2099
ok 84 - bug 2099
ok 85 - bug 2793
ok 86 - bug 2793
ok 87 - bug 2793
ok 88 - bug 2793
ok 89 - Bad sequence, bad!
ok 90 - added 3 seqs
ok 91 - first 2 features added
ok 92 - 3rd feature added
not ok 93 # TODO This should pass but dies; see bug 2842
# Failed (TODO) test at t/Align/SimpleAlign.t line 421.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 1.
# Overriding value [0] with value 1 for Bio::LocatableSeq::end().
# ?
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:181
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:196
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1143
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421
# STACK: t/Align/SimpleAlign.t:421
# -----------------------------------------------------------
# )
ok 94 - slice 1 len
ok 95 - correct masked seq
ok 96 - correct masked seq
ok 97 - correct masked seq
not ok 98 # TODO This should pass but dies; see bug 2842
# Failed (TODO) test at t/Align/SimpleAlign.t line 421.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 3.
# Overriding value [2] with value 3 for Bio::LocatableSeq::end().
# ?
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:181
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:196
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1143
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421
# STACK: t/Align/SimpleAlign.t:421
# -----------------------------------------------------------
# )
ok 99 - slice 2 len
ok 100 - correct masked seq
ok 101 - correct masked seq
ok 102 - correct masked seq
not ok 103 # TODO This should pass but dies; see bug 2842
# Failed (TODO) test at t/Align/SimpleAlign.t line 421.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 3.
# Overriding value [1] with value 3 for Bio::LocatableSeq::end().
# ??
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:181
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:196
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1143
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421
# STACK: t/Align/SimpleAlign.t:421
# -----------------------------------------------------------
# )
ok 104 - slice 3 len
ok 105 - correct masked seq
ok 106 - correct masked seq
ok 107 - correct masked seq
not ok 108 # TODO This should pass but dies; see bug 2842
# Failed (TODO) test at t/Align/SimpleAlign.t line 421.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 6.
# Overriding value [4] with value 6 for Bio::LocatableSeq::end().
# ??
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:181
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:196
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1143
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421
# STACK: t/Align/SimpleAlign.t:421
# -----------------------------------------------------------
# )
ok 109 - slice 4 len
ok 110 - correct masked seq
ok 111 - correct masked seq
ok 112 - correct masked seq
ok 113 - initial display id ok
ok 114 - safe display id ok
ok 115 - restored display id ok
ok 116 - sort by list ok
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123 - BIC:GGATCCATT[C/C]CTACT
ok 124 - BIC:GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT
ok 125 - BIC:G[G/C]ATCCATT[C/G]CTACT
ok 126 - BIC:GGATCCATT[C/G]CTACT
ok 127 - BIC:GGATCCATT[C/G]CTAC[T/A]
ok 128 - BIC:GGATCCATT[C/G]CTA[C/G][T/A]
ok 129 - BIC:GGATCCATT[C/G]CTACT
ok 130 - BIC:GGATCCATT{C.C}CTACT
ok 131 - BIC:GGAT{C.-}{C.-}ATT{C.C}CT{A.C}CT
ok 132 - BIC:G{G.C}ATCCATT{C.G}CTACT
ok 133 - BIC:GGATCCATT{C.G}CTACT
ok 134 - BIC:GGATCCATT{C.G}CTAC{T.A}
ok 135 - BIC:GGATCCATT{C.G}CTA{C.G}{T.A}
ok 136 - BIC:GGATCCATT{C.G}CTACT
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174 - The object isa Bio::SimpleAlign
ok 175 - consensus string looks ok
ok 176 - looks like correct unmasked alignment (from clustalw)
ok 177 - looks like correct masked alignment (from clustalw)
ok 178
ok 179 - align after looks ok
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/AlignIO/AlignIO.t ..........................
1..28
ok 1 - use Bio::AlignIO;
ok 2 - input filehandle method test : clustalw
ok 3 - input filehandle method test : xmfa
ok 4 - input filehandle method test : pfam
ok 5 - input filehandle method test : nexus
ok 6 - input filehandle method test : arp
ok 7 - input filehandle method test : psi
ok 8 - input filehandle method test : phylip
ok 9 - input filehandle method test : msf
ok 10 - input filehandle method test : po
ok 11 - input filehandle method test : metafasta
ok 12 - input filehandle method test : mase
ok 13 - input filehandle method test : prodom
ok 14 - input filehandle method test : selex
ok 15 - input filehandle method test : stockholm
ok 16 - input filehandle method test : fasta
ok 17 - filehandle output test : clustalw
ok 18 - filehandle output test : xmfa
ok 19 - filehandle output test : pfam
ok 20 - filehandle output test : nexus
ok 21 - filehandle output test : psi
ok 22 - filehandle output test : phylip
ok 23 - filehandle output test : msf
ok 24 - filehandle output test : po
ok 25 - filehandle output test : metafasta
ok 26 - filehandle output test : selex
ok 27 - filehandle output test : stockholm
ok 28 - filehandle output test : fasta
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/AlignIO/phylip.t ...........................
1..11
ok 1 - use Bio::AlignIO::phylip;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4
ok 5 - phylip output test
ok 6 - The object isa Bio::Align::AlignI
ok 7
ok 8 - The object isa Bio::AlignIO
ok 9 - The object isa Bio::Align::AlignI
ok 10
ok 11
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/AlignIO/stockholm.t ........................
1..83
ok 1 - use Bio::AlignIO::stockholm;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9 - The object isa Bio::Annotation::Comment
ok 10 - Stockholm annotation
ok 11 - Stockholm annotation
ok 12 - stockholm output test
ok 13 - The object isa Bio::Align::AlignI
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20 - Stockholm annotation isa Bio::Annotation::Reference
ok 21 - Stockholm annotation
ok 22 - Stockholm annotation
ok 23 - Stockholm annotation
ok 24 - Stockholm annotation
ok 25 - The object isa Bio::Seq::MetaI
ok 26 - Rfam meta data
ok 27 - Rfam meta data
ok 28
ok 29 - The object isa Bio::Align::AlignI
ok 30
ok 31
ok 32
ok 33
ok 34 - The object isa Bio::Seq::MetaI
ok 35 - Rfam meta data
ok 36 - Rfam meta data
ok 37 - The object isa Bio::AlignIO
ok 38
ok 39 - The object isa Bio::Align::AlignI
ok 40
ok 41
ok 42
ok 43
ok 44 - The object isa Bio::Annotation::SimpleValue
ok 45 - Pfam annotation
ok 46
ok 47 - The object isa Bio::Align::AlignI
ok 48
ok 49
ok 50
ok 51
ok 52 - The object isa Bio::Align::AlignI
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58 - The object isa Bio::Seq::MetaI
ok 59 - Pfam aln meta data
ok 60 - Pfam aln meta data
ok 61 - Pfam aln meta data
ok 62 - Pfam aln meta data
ok 63 - Pfam aln meta data
ok 64 - Pfam aln meta data
ok 65 - Pfam seq meta data
ok 66 - Pfam seq meta data
ok 67 - Pfam seq meta data
ok 68 - Pfam seq meta data
ok 69
ok 70 - The object isa Bio::SeqFeatureI
ok 71 - The object isa Bio::Seq::Meta
ok 72 - The object isa Bio::AnnotationI
ok 73 - The object isa Bio::Annotation::DBLink
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/AlignIO/xmfa.t .............................
1..16
ok 1 - use Bio::AlignIO::xmfa;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - xmfa input test
ok 4 - xmfa input test for description
ok 5 - xmfa input test for id
ok 6 - xmfa input test for end
ok 7 - xmfa input test for end
ok 8 - xmfa alignment score
ok 9 - The object isa Bio::Align::AlignI
ok 10 - xmfa input test
ok 11 - xmfa input test for description
ok 12 - xmfa input test for id
ok 13 - xmfa input test for end
ok 14 - xmfa input test for end
ok 15 - xmfa alignment score
ok 16 - xmfa output test
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Annotation/Annotation.t ....................
1..158
ok 1 - use Bio::Annotation::Collection;
ok 2 - use Bio::Annotation::DBLink;
ok 3 - use Bio::Annotation::Comment;
ok 4 - use Bio::Annotation::Reference;
ok 5 - use Bio::Annotation::SimpleValue;
ok 6 - use Bio::Annotation::Target;
ok 7 - use Bio::Annotation::AnnotationFactory;
ok 8 - use Bio::Annotation::StructuredValue;
ok 9 - use Bio::Annotation::TagTree;
ok 10 - use Bio::Annotation::Tree;
ok 11 - use Bio::Seq;
ok 12 - use Bio::SimpleAlign;
ok 13 - use Bio::Cluster::UniGene;
ok 14 - The object isa Bio::AnnotationI
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21 - The object isa Bio::AnnotationI
ok 22
ok 23
ok 24
ok 25 - The object isa Bio::AnnotationCollectionI
ok 26
ok 27
ok 28 - The object isa Bio::AnnotationI
ok 29
ok 30 - The object isa Bio::AnnotationI
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53 - The object isa Bio::AnnotationI
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68 - The object isa Bio::AnnotationCollectionI
ok 69
ok 70
ok 71
ok 72
ok 73 - The object isa Bio::Annotation::StructuredValue
ok 74
ok 75
ok 76
ok 77
ok 78 - use Bio::Annotation::OntologyTerm;
ok 79 - The object isa Bio::Ontology::Term
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85 - The object isa Bio::AnnotatableI
ok 86 - isa SeqFeatureI isa Bio::SeqFeatureI
ok 87 - isa AnnotatableI isa Bio::AnnotatableI
ok 88 - isa SeqFeatureI isa Bio::SeqFeatureI
ok 89 - isa AnnotatableI isa Bio::AnnotatableI
ok 90 - The object isa Bio::AnnotatableI
ok 91 - The object isa Bio::AnnotatableI
ok 92 - The object isa Bio::Factory::ObjectFactoryI
ok 93 - The object isa Bio::Annotation::SimpleValue
ok 94
ok 95 - The object isa Bio::Annotation::OntologyTerm
ok 96 - Bio::Annotation::Comment
ok 97 - The object isa Bio::Annotation::Comment
ok 98
ok 99 - Bio::Annotation::Comment
ok 100 - The object isa Bio::Annotation::Comment
ok 101 - Bio::Annotation::Comment
ok 102 - The object isa Bio::Annotation::Comment
ok 103
ok 104 - The object isa Bio::Annotation::Target
ok 105
ok 106
ok 107 - The object isa Bio::AnnotationI
ok 108 - tree_id()
ok 109 - tagname()
ok 110 - The object isa Bio::AnnotatableI
ok 111 - add tree to AlignI
ok 112 - get seq from node id
ok 113
ok 114 - The object isa Bio::Annotation::Tree
ok 115 - The object isa Bio::AnnotationI
ok 116 - default itext
ok 117 - roundtrip
ok 118 - itext
ok 119 - spxr
ok 120 - indent
ok 121 - xml
ok 122 - The object isa Data::Stag::StagI
ok 123
ok 124 - child changes
ok 125 - The object isa Data::Stag::StagI
ok 126
ok 127 - child changes
ok 128 - The object isa Data::Stag::StagI
ok 129
ok 130 - child changes
ok 131 - child changes in parent node
ok 132 - no tags
ok 133 - before Stag node
ok 134 - after Stag node
ok 135 - both stag nodes
ok 136 - different instances
ok 137 - before TagTree
ok 138 - after TagTree
ok 139 - both stag nodes
ok 140 - different instances
ok 141 - before TagTree
ok 142 - after TagTree
ok 143 - stag nodes
ok 144 - same instance
ok 145 - before TagTree
ok 146 - after TagTree
ok 147 - stag nodes
ok 148 - different instance
ok 149 - The object isa Bio::AnnotationI
ok 150 - The object isa Data::Stag::StagI
ok 151 - child changes
ok 152 - The object isa Data::Stag::StagI
ok 153 - child changes
ok 154 - The object isa Data::Stag::StagI
ok 155 - child changes
ok 156
ok 157
ok 158 - The object isa Bio::Annotation::TagTree
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
Use of uninitialized value in lc at Bio/Assembly/Contig.pm line 1143, line 412.
Use of uninitialized value in lc at Bio/Assembly/Contig.pm line 1143, line 412.
Use of uninitialized value in lc at Bio/Assembly/Contig.pm line 1143, line 412.
Use of uninitialized value in lc at Bio/Assembly/Contig.pm line 1143, line 412.
Use of uninitialized value in lc at Bio/Assembly/Contig.pm line 1143, line 413.
Use of uninitialized value in lc at Bio/Assembly/Contig.pm line 1143, line 413.
t/Assembly/Assembly.t ........................
1..51
ok 1 - use Bio::Assembly::IO;
ok 2 - The object isa Bio::Assembly::IO
not ok 3 # TODO phrap parser doesn't include the sequence string in the sequence objects.
# Failed (TODO) test at t/Assembly/Assembly.t line 35.
ok 4 - The object isa Bio::Assembly::Scaffold
ok 5
ok 6
ok 7 - The object isa Bio::AnnotationCollectionI
ok 8 - no annotations in Annotation collection?
ok 9
ok 10
ok 11 - get_nof_singlets
ok 12 - get_contig_seq_ids
ok 13 - get_contig_ids
ok 14 - get_singlet_ids
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23 - get_nof_singlets
ok 24 - get_contig_seq_ids
ok 25 - get_contig_ids
ok 26 - get_singlet_ids
ok 27
ok 28 - the contig is a Bio::Assembly::Contig isa Bio::Assembly::Contig
ok 29
ok 30 - get_nof_singlets
ok 31 - the singlet is a Bio::Assembly::Contig isa Bio::Assembly::Contig
ok 32 - the singlet is a Bio::Assembly::Singlet isa Bio::Assembly::Singlet
ok 33 - get_contig_seq_ids
ok 34 - get_contig_ids
ok 35 - get_singlet_ids
ok 36 - The object isa Bio::Assembly::Scaffold
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44 - The object isa Bio::LocatableSeq
ok 45 - The object isa Bio::Assembly::Contig
ok 46
ok 47
ok 48
ok 49 - The object isa Bio::AnnotationCollectionI
ok 50 - no annotations in Annotation collection?
ok 51
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Assembly/ContigSpectrum.t ..................
1..134
ok 1 - use Bio::Assembly::IO;
ok 2 - use Bio::Assembly::Tools::ContigSpectrum;
ok 3 - The object isa Bio::Assembly::IO
ok 4 - The object isa Bio::Assembly::Scaffold
ok 5
ok 6 - The object isa Bio::Assembly::Tools::ContigSpectrum
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
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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
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
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
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
Replacement list is longer than search list at Bio/Range.pm line 251, chunk 1.
t/ClusterIO/unigene.t ........................
1..73
ok 1 - use Bio::ClusterIO;
ok 2 - new Bio::ClusterIO object defined
ok 3
ok 4 - The object isa Bio::Cluster::UniGeneI
ok 5 - The object isa Bio::ClusterI
ok 6 - The object isa Bio::IdentifiableI
ok 7 - The object isa Bio::DescribableI
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48 - The object isa Bio::PrimarySeqI
ok 49
ok 50
ok 51 - annotation object defined
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66 - The object isa Bio::PrimarySeqI
ok 67
ok 68 - next cluster
ok 69
ok 70
ok 71
ok 72
ok 73
ok
t/Coordinate/CoordinateGraph.t ...............
1..7
ok 1 - use Bio::Coordinate::Graph;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
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
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
t/Coordinate/GeneCoordinateMapper.t ..........
1..116
ok 1 - use Bio::Location::Simple;
ok 2 - use Bio::Coordinate::Pair;
ok 3 - use Bio::Coordinate::ExtrapolatingPair;
ok 4 - use Bio::Coordinate::GeneMapper;
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14 - The object isa Bio::Location::Simple
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75 - The object isa Bio::Location::Simple
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok
t/LiveSeq/Chain.t ............................
1..45
ok 1 - use Bio::LiveSeq::Chain;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/LocalDB/BioDBGFF.t .........................
1..279
ok 1 - use Bio::DB::GFF;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103 # skip fetch_feature_by_gid() not implemented by this adaptor
ok 104 # skip fetch_feature_by_gid() not implemented by this adaptor
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134 # skip delete_groups() not implemented by this adaptor
ok 135 # skip delete_groups() not implemented by this adaptor
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok 176
ok 177
ok 178
ok 179
ok 180
ok 181
ok 182
ok 183
ok 184
ok 185
ok 186
ok 187
ok 188
ok 189
ok 190
ok 191
ok 192
ok 193
ok 194
ok 195
ok 196
ok 197
ok 198
ok 199
ok 200
ok 201
ok 202
ok 203
ok 204
ok 205
ok 206
ok 207
ok 208
ok 209
ok 210
ok 211
ok 212
ok 213
ok 214
ok 215
ok 216
ok 217
ok 218
ok 219
ok 220
ok 221
ok 222
ok 223
ok 224
ok 225
ok 226
ok 227
ok 228
ok 229
ok 230
ok 231
ok 232
ok 233
ok 234
ok 235
ok 236
ok 237
ok 238
ok 239
ok 240
ok 241
ok 242 # skip fetch_feature_by_gid() not implemented by this adaptor
ok 243 # skip fetch_feature_by_gid() not implemented by this adaptor
ok 244
ok 245
ok 246
ok 247
ok 248
ok 249
ok 250 # skip preferred groups are not supported by gff3
ok 251 # skip preferred groups are not supported by gff3
ok 252 # skip preferred groups are not supported by gff3
ok 253
ok 254
ok 255
ok 256
ok 257
ok 258
ok 259
ok 260
ok 261
ok 262
ok 263
ok 264
ok 265
ok 266
ok 267
ok 268
ok 269
ok 270
ok 271
ok 272
ok 273 # skip delete_groups() not implemented by this adaptor
ok 274 # skip delete_groups() not implemented by this adaptor
ok 275
ok 276
ok 277
ok 278
ok 279
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/LocalDB/BlastIndex.t .......................
1..26
ok 1 - use Cwd;
ok 2 - use Bio::SearchIO;
ok 3 - use Bio::Index::Blast;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/LocalDB/DBFasta.t ..........................
1..15
ok 1 - use Bio::Root::IO;
ok 2 - use File::Copy;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok
t/LocalDB/DBQual.t ...........................
1..38
ok 1 - use Bio::Root::IO;
ok 2 - use File::Copy;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13 - The object isa Bio::Seq::PrimaryQual
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25 - The object isa Bio::Seq::PrimaryQual
ok 26
ok 27
ok 28 - The object isa Bio::Seq::PrimaryQual
ok 29
ok 30
ok 31
ok 32 - The object isa Bio::Seq::PrimaryQual
ok 33
ok 34 - The object isa Bio::Seq::PrimaryQual
ok 35
ok 36
ok 37
ok 38
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/LocalDB/Index.t ............................
1..64
ok 1 - use Bio::Index::Fasta;
ok 2 - use Bio::Index::Qual;
ok 3 - use Bio::Index::SwissPfam;
ok 4 - use Bio::Index::EMBL;
ok 5 - use Bio::Index::GenBank;
ok 6 - use Bio::Index::Swissprot;
ok 7 - use Bio::DB::InMemoryCache;
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16 - The object isa Bio::PrimarySeqI
ok 17
ok 18
ok 19
ok 20 - The object isa Bio::SeqI
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
"my" variable %h masks earlier declaration in same statement at Bio/DB/SeqFeature/Store/LoadHelper.pm line 74.
"my" variable $tmp masks earlier declaration in same scope at Bio/DB/SeqFeature/Store/LoadHelper.pm line 74.
"my" variable $dbname masks earlier declaration in same statement at Bio/DB/SeqFeature/Store/LoadHelper.pm line 74.
"my" variable $hash_options masks earlier declaration in same scope at Bio/DB/SeqFeature/Store/LoadHelper.pm line 75.
"my" variable %self masks earlier declaration in same scope at Bio/DB/SeqFeature/Store/LoadHelper.pm line 76.
"my" variable $dbname masks earlier declaration in same scope at Bio/DB/SeqFeature/Store/LoadHelper.pm line 76.
"my" variable %h masks earlier declaration in same scope at Bio/DB/SeqFeature/Store/LoadHelper.pm line 76.
"my" variable $self masks earlier declaration in same scope at Bio/DB/SeqFeature/Store/LoadHelper.pm line 99.
"my" variable $id masks earlier declaration in same scope at Bio/DB/SeqFeature/Store/LoadHelper.pm line 100.
"my" variable $self masks earlier declaration in same scope at Bio/DB/SeqFeature/Store/LoadHelper.pm line 106.
"my" variable $id masks earlier declaration in same scope at Bio/DB/SeqFeature/Store/LoadHelper.pm line 107.
"my" variable $self masks earlier declaration in same scope at Bio/DB/SeqFeature/Store/LoadHelper.pm line 112.
"my" variable $id masks earlier declaration in same scope at Bio/DB/SeqFeature/Store/LoadHelper.pm line 113.
"my" variable $self masks earlier declaration in same scope at Bio/DB/SeqFeature/Store/LoadHelper.pm line 119.
# Failed test 'use Bio::DB::SeqFeature::Store::GFF3Loader;'
# at t/LocalDB/SeqFeature.t line 17.
# Tried to use 'Bio::DB::SeqFeature::Store::GFF3Loader'.
# Error: syntax error at Bio/DB/SeqFeature/Store/LoadHelper.pm line 72, near "$dbname qw(IndexIt TopLevel Local2Global)"
# Global symbol "$tmp" requires explicit package name at Bio/DB/SeqFeature/Store/LoadHelper.pm line 84.
# Global symbol "%self" requires explicit package name at Bio/DB/SeqFeature/Store/LoadHelper.pm line 86.
# Global symbol "%self" requires explicit package name at Bio/DB/SeqFeature/Store/LoadHelper.pm line 88.
# syntax error at Bio/DB/SeqFeature/Store/LoadHelper.pm line 89, near "}"
# syntax error at Bio/DB/SeqFeature/Store/LoadHelper.pm line 96, near "}"
# syntax error at Bio/DB/SeqFeature/Store/LoadHelper.pm line 103, near "}"
# syntax error at Bio/DB/SeqFeature/Store/LoadHelper.pm line 109, near "}"
# syntax error at Bio/DB/SeqFeature/Store/LoadHelper.pm line 116, near "}"
# syntax error at Bio/DB/SeqFeature/Store/LoadHelper.pm line 123, near "}"
# Bio/DB/SeqFeature/Store/LoadHelper.pm has too many errors.
# Compilation failed in require at Bio/DB/SeqFeature/Store/GFF3Loader.pm line 73.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/GFF3Loader.pm line 73.
# Compilation failed in require at (eval 78) line 2.
# BEGIN failed--compilation aborted at (eval 78) line 2.
# Looks like you failed 1 test of 69.
t/LocalDB/SeqFeature.t .......................
1..69
ok 1 - use Bio::DB::SeqFeature::Store;
not ok 2 - use Bio::DB::SeqFeature::Store::GFF3Loader;
ok 3 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 4 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 5 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 6 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 7 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 8 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 9 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 10 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 11 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 12 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 13 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 14 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 15 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 16 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 17 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 18 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 19 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 20 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 21 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 22 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 23 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 24 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 25 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 26 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 27 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 28 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 29 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 30 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 31 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 32 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 33 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 34 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 35 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 36 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 37 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 38 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 39 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 40 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 41 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 42 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 43 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 44 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 45 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 46 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 47 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 48 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 49 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 50 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 51 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 52 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 53 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 54 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 55 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 56 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 57 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 58 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 59 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 60 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 61 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 62 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 63 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 64 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 65 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 66 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 67 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 68 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
ok 69 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 80) line 2.
# at t/LocalDB/SeqFeature.t line 28.
#
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/69 subtests
(less 67 skipped subtests: 1 okay)
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
Replacement list is longer than search list at Bio/Range.pm line 251.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable %model masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable $let masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable %model masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable $let masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable $self masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 374.
"my" variable $self masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 374.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 408.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 425.
"my" variable $prev masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 426.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 442.
"my" variable $prev masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 443.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 460.
"my" variable $prev masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 461.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 479.
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::TFBS::transfac_pro. syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 346, near "$let qw(probA probC probG probT)"
Global symbol "$self" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 357.
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 358, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 394, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 412, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 429, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 446, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 464, near "}"
Can't use global @_ in "my" at Bio/Matrix/PSM/SiteMatrix.pm line 479, near "= @_"
Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 480.
Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 483.
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 491, near "}"
Bio/Matrix/PSM/SiteMatrix.pm has too many errors.
Compilation failed in require at Bio/DB/TFBS/transfac_pro.pm line 112.
BEGIN failed--compilation aborted at Bio/DB/TFBS/transfac_pro.pm line 112.
Compilation failed in require at Bio/Root/Root.pm line 439.
STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441
STACK: Bio::DB::TFBS::_load_tax_module Bio/DB/TFBS.pm:151
STACK: Bio::DB::TFBS::new Bio/DB/TFBS.pm:130
STACK: t/LocalDB/transfac_pro.t:25
-----------------------------------------------------------
Bio::DB::TFBS: transfac_pro cannot be found
Exception
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::TFBS::transfac_pro. syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 346, near "$let qw(probA probC probG probT)"
Global symbol "$self" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 357.
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 358, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 394, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 412, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 429, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 446, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 464, near "}"
Can't use global @_ in "my" at Bio/Matrix/PSM/SiteMatrix.pm line 479, near "= @_"
Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 480.
Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 483.
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 491, near "}"
Bio/Matrix/PSM/SiteMatrix.pm has too many errors.
Compilation failed in require at Bio/DB/TFBS/transfac_pro.pm line 112.
BEGIN failed--compilation aborted at Bio/DB/TFBS/transfac_pro.pm line 112.
Compilation failed in require at Bio/Root/Root.pm line 439.
STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441
STACK: Bio::DB::TFBS::_load_tax_module Bio/DB/TFBS.pm:151
STACK: Bio::DB::TFBS::new Bio/DB/TFBS.pm:130
STACK: t/LocalDB/transfac_pro.t:25
-----------------------------------------------------------
For more information about the Bio::DB::TFBS system please see
the Bio::DB::TFBS docs. This includes ways of checking for
formats at compile time, not run time.
# Failed test at t/LocalDB/transfac_pro.t line 25.
Can't call method "get_reference_ids" on an undefined value at t/LocalDB/transfac_pro.t line 33.
# Looks like you planned 115 tests but ran 4.
# Looks like you failed 1 test of 4 run.
# Looks like your test exited with 255 just after 4.
t/LocalDB/transfac_pro.t .....................
1..115
ok 1 - use Bio::Matrix::PSM::IO;
ok 2 - use Bio::DB::TFBS;
ok 3 - use Bio::DB::Taxonomy;
not ok 4
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 112/115 subtests
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
# Failed test at t/Map/Map.t line 322.
# got: 'Bio::Map::Position=HASH(0x168874f8)'
# expected: 'Bio::Map::Position=HASH(0x16886418)'
# Failed test at t/Map/Map.t line 323.
# got: 'Bio::Map::Position=HASH(0x16886418)'
# expected: 'Bio::Map::Position=HASH(0x168874f8)'
# Failed test at t/Map/Map.t line 324.
# got: undef
# expected: 'Bio::Map::Position=HASH(0x168878d0)'
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
Replacement list is longer than search list at Bio/Range.pm line 251, line 16.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
# Failed test at t/Map/Physical.t line 96.
# got: '1248'
# expected: '1249'
# Looks like you failed 1 test of 39.
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
not ok 39
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/39 subtests
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable %model masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable $let masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable %model masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable $let masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable $self masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 374.
"my" variable $self masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 374.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 408.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 425.
"my" variable $prev masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 426.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 442.
"my" variable $prev masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 443.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 460.
"my" variable $prev masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 461.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 479.
Bio::Matrix::PSM::IO: masta cannot be found
Exception
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::Matrix::PSM::IO::masta. syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 346, near "$let qw(probA probC probG probT)"
Global symbol "$self" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 357.
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 358, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 394, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 412, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 429, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 446, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 464, near "}"
Can't use global @_ in "my" at Bio/Matrix/PSM/SiteMatrix.pm line 479, near "= @_"
Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 480.
Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 483.
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 491, near "}"
Bio/Matrix/PSM/SiteMatrix.pm has too many errors.
Compilation failed in require at Bio/Matrix/PSM/IO/masta.pm line 79.
BEGIN failed--compilation aborted at Bio/Matrix/PSM/IO/masta.pm line 79.
Compilation failed in require at Bio/Root/Root.pm line 439.
STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441
STACK: Bio::Matrix::PSM::IO::_load_format_module Bio/Matrix/PSM/IO.pm:195
STACK: Bio::Matrix::PSM::IO::new Bio/Matrix/PSM/IO.pm:155
STACK: t/Matrix/IO/masta.t:16
-----------------------------------------------------------
For more information about the Matrix::PSM::IO system please see the
Matrix::PSM::IO docs. This includes ways of checking for formats at
compile time, not run time
Bio::Matrix::PSM::IO: masta cannot be found
Exception
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::Matrix::PSM::IO::masta. Attempt to reload Bio/Matrix/PSM/IO/masta.pm aborted.
Compilation failed in require at Bio/Root/Root.pm line 439.
STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441
STACK: Bio::Matrix::PSM::IO::_load_format_module Bio/Matrix/PSM/IO.pm:195
STACK: Bio::Matrix::PSM::IO::new Bio/Matrix/PSM/IO.pm:155
STACK: t/Matrix/IO/masta.t:19
-----------------------------------------------------------
For more information about the Matrix::PSM::IO system please see the
Matrix::PSM::IO docs. This includes ways of checking for formats at
compile time, not run time
Can't call method "_flush_on_write" on an undefined value at t/Matrix/IO/masta.t line 21.
# Looks like you planned 16 tests but ran 1.
# Looks like your test exited with 25 just after 1.
t/Matrix/IO/masta.t ..........................
1..16
ok 1 - use Bio::Matrix::PSM::IO;
Dubious, test returned 25 (wstat 6400, 0x1900)
Failed 15/16 subtests
Replacement list is longer than search list at Bio/Range.pm line 251.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable %model masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable $let masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable %model masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable $let masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable $self masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 374.
"my" variable $self masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 374.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 408.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 425.
"my" variable $prev masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 426.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 442.
"my" variable $prev masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 443.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 460.
"my" variable $prev masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 461.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 479.
Bio::Matrix::PSM::IO: meme cannot be found
Exception
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::Matrix::PSM::IO::meme. syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 346, near "$let qw(probA probC probG probT)"
Global symbol "$self" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 357.
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 358, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 394, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 412, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 429, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 446, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 464, near "}"
Can't use global @_ in "my" at Bio/Matrix/PSM/SiteMatrix.pm line 479, near "= @_"
Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 480.
Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 483.
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 491, near "}"
Bio/Matrix/PSM/SiteMatrix.pm has too many errors.
Compilation failed in require at Bio/Matrix/PSM/IO/meme.pm line 59.
BEGIN failed--compilation aborted at Bio/Matrix/PSM/IO/meme.pm line 59.
Compilation failed in require at Bio/Root/Root.pm line 439.
STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441
STACK: Bio::Matrix::PSM::IO::_load_format_module Bio/Matrix/PSM/IO.pm:195
STACK: Bio::Matrix::PSM::IO::new Bio/Matrix/PSM/IO.pm:155
STACK: t/Matrix/IO/psm.t:35
-----------------------------------------------------------
For more information about the Matrix::PSM::IO system please see the
Matrix::PSM::IO docs. This includes ways of checking for formats at
compile time, not run time
# Failed test at t/Matrix/IO/psm.t line 37.
Can't call method "unstructured" on an undefined value at t/Matrix/IO/psm.t line 39.
# Looks like you planned 63 tests but ran 2.
# Looks like you failed 1 test of 2 run.
# Looks like your test exited with 255 just after 2.
t/Matrix/IO/psm.t ............................
1..63
ok 1 - use Bio::Matrix::PSM::IO;
not ok 2
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 62/63 subtests
Replacement list is longer than search list at Bio/Range.pm line 251.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable %model masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable $let masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable %model masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable $let masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable $self masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 374.
"my" variable $self masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 374.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 408.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 425.
"my" variable $prev masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 426.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 442.
"my" variable $prev masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 443.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 460.
"my" variable $prev masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 461.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 479.
Bio::Matrix::PSM::IO: psiblast cannot be found
Exception
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::Matrix::PSM::IO::psiblast. syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 346, near "$let qw(probA probC probG probT)"
Global symbol "$self" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 357.
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 358, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 394, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 412, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 429, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 446, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 464, near "}"
Can't use global @_ in "my" at Bio/Matrix/PSM/SiteMatrix.pm line 479, near "= @_"
Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 480.
Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 483.
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 491, near "}"
Bio/Matrix/PSM/SiteMatrix.pm has too many errors.
Compilation failed in require at (eval 57) line 2.
...propagated at /home/fly1800/var/megalib/base.pm line 84.
BEGIN failed--compilation aborted at Bio/Matrix/PSM/Psm.pm line 131.
Compilation failed in require at Bio/Matrix/PSM/IO/psiblast.pm line 58.
BEGIN failed--compilation aborted at Bio/Matrix/PSM/IO/psiblast.pm line 58.
Compilation failed in require at Bio/Root/Root.pm line 439.
STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441
STACK: Bio::Matrix::PSM::IO::_load_format_module Bio/Matrix/PSM/IO.pm:195
STACK: Bio::Matrix::PSM::IO::new Bio/Matrix/PSM/IO.pm:155
STACK: t/Matrix/ProtPsm.t:17
-----------------------------------------------------------
For more information about the Matrix::PSM::IO system please see the
Matrix::PSM::IO docs. This includes ways of checking for formats at
compile time, not run time
# Failed test at t/Matrix/ProtPsm.t line 19.
Can't call method "next_psm" on an undefined value at t/Matrix/ProtPsm.t line 21.
# Looks like you planned 14 tests but ran 2.
# Looks like you failed 1 test of 2 run.
# Looks like your test exited with 255 just after 2.
t/Matrix/ProtPsm.t ...........................
1..14
ok 1 - use Bio::Matrix::PSM::IO;
not ok 2
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 13/14 subtests
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable %model masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable $let masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable %model masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable $let masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 348.
"my" variable $self masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 374.
"my" variable $self masks earlier declaration in same statement at Bio/Matrix/PSM/SiteMatrix.pm line 374.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 408.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 425.
"my" variable $prev masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 426.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 442.
"my" variable $prev masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 443.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 460.
"my" variable $prev masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 461.
"my" variable $self masks earlier declaration in same scope at Bio/Matrix/PSM/SiteMatrix.pm line 479.
# Failed test 'use Bio::Matrix::PSM::SiteMatrix;'
# at t/Matrix/SiteMatrix.t line 13.
# Tried to use 'Bio::Matrix::PSM::SiteMatrix'.
# Error: syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 346, near "$let qw(probA probC probG probT)"
# Global symbol "$self" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 357.
# syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 358, near "}"
# syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 394, near "}"
# syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 412, near "}"
# syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 429, near "}"
# syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 446, near "}"
# syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 464, near "}"
# Can't use global @_ in "my" at Bio/Matrix/PSM/SiteMatrix.pm line 479, near "= @_"
# Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 480.
# Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 483.
# syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 491, near "}"
# Bio/Matrix/PSM/SiteMatrix.pm has too many errors.
# Compilation failed in require at (eval 18) line 2.
# BEGIN failed--compilation aborted at (eval 18) line 2.
Undefined subroutine &Bio::Matrix::PSM::SiteMatrix::_to_IUPAC called at Bio/Matrix/PSM/SiteMatrix.pm line 321.
# Looks like you planned 14 tests but ran 1.
# Looks like you failed 1 test of 1 run.
# Looks like your test exited with 255 just after 1.
t/Matrix/SiteMatrix.t ........................
1..14
not ok 1 - use Bio::Matrix::PSM::SiteMatrix;
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 14/14 subtests
t/Ontology/GOterm.t ..........................
1..62
ok 1 - use Bio::Ontology::GOterm;
ok 2 - use Bio::Ontology::Ontology;
ok 3 - use Bio::Annotation::DBLink;
ok 4 - The object isa Bio::Ontology::GOterm
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok
t/Ontology/GraphAdaptor.t ....................
1..28
ok 1 - use Bio::Ontology::SimpleGOEngine::GraphAdaptor;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok
t/Ontology/IO/go.t ...........................
1..102
ok 1 - use Bio::OntologyIO;
ok 2
ok 3 - The object isa Bio::Ontology::OntologyI
ok 4
ok 5 - The object isa Bio::Ontology::OntologyEngineI
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok
t/Ontology/IO/interpro.t .....................
1..47
ok 1 - use Bio::OntologyIO;
ok 2
ok 3
ok 4
ok 5
ok 6 - term Kringle in ontology InterPro
ok 7
ok 8 - term Integrins alpha chain in ontology InterPro
ok 9
ok 10 - term post-translational modification in ontology InterPro
ok 11
ok 12 - term Helix-turn-helix, AraC type in ontology InterPro
ok 13
ok 14 - term Binding Site in ontology InterPro
ok 15
ok 16 - term Active Site in ontology InterPro
ok 17
ok 18 - term Cdc20/Fizzy in ontology InterPro
ok 19
ok 20 - term Repeat in ontology InterPro
ok 21
ok 22 - term Active Site in ontology InterPro
ok 23
ok 24 - term Binding Site in ontology InterPro
ok 25
ok 26 - term Domain in ontology InterPro
ok 27
ok 28 - term Family in ontology InterPro
ok 29
ok 30 - term Repeat in ontology InterPro
ok 31
ok 32 - term post-translational modification in ontology InterPro
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok
# Failed test at t/Ontology/IO/obo.t line 47.
# got: '3'
# expected: '5'
# Failed test at t/Ontology/IO/obo.t line 49.
# Failed test at t/Ontology/IO/obo.t line 51.
# Failed test at t/Ontology/IO/obo.t line 53.
# Failed test at t/Ontology/IO/obo.t line 55.
# Failed test at t/Ontology/IO/obo.t line 57.
# Failed test at t/Ontology/IO/obo.t line 61.
# got: '7'
# expected: '2'
# Looks like you failed 7 tests of 83.
t/Ontology/IO/obo.t ..........................
1..83
ok 1 - use Bio::OntologyIO;
ok 2 - use Bio::Ontology::RelationshipType;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
not ok 14
not ok 15
not ok 16
not ok 17
not ok 18
not ok 19
not 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
Dubious, test returned 7 (wstat 1792, 0x700)
Failed 7/83 subtests
t/Ontology/Ontology.t ........................
1..52
ok 1 - use Bio::OntologyIO;
ok 2 - use Bio::Ontology::RelationshipType;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok
t/Ontology/OntologyEngine.t ..................
1..27
ok 1 - use Bio::Ontology::Term;
ok 2 - use Bio::Ontology::Relationship;
ok 3 - use Bio::Ontology::RelationshipType;
ok 4 - use Bio::Ontology::SimpleOntologyEngine;
ok 5 - use Bio::Ontology::Ontology;
ok 6 - The object isa Bio::Ontology::OntologyEngineI
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok
t/Ontology/OntologyStore.t ................... skipped: Network tests have not been requested
t/Ontology/Relationship.t ....................
1..12
ok 1 - use Bio::Ontology::Relationship;
ok 2 - use Bio::Ontology::GOterm;
ok 3 - use Bio::Ontology::RelationshipType;
ok 4 - The object isa Bio::Ontology::RelationshipType
ok 5 - The object isa Bio::Ontology::GOterm
ok 6 - The object isa Bio::Ontology::GOterm
ok 7 - The object isa Bio::Ontology::Relationship
ok 8
ok 9
ok 10
ok 11
ok 12
ok
t/Ontology/RelationshipType.t ................
1..23
ok 1 - use Bio::Ontology::RelationshipType;
ok 2 - use Bio::Ontology::Ontology;
ok 3 - The object isa Bio::Ontology::RelationshipType
ok 4 - The object isa Bio::Ontology::TermI
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok
t/Ontology/Term.t ............................
1..54
ok 1 - use Bio::Ontology::Term;
ok 2 - use Bio::Ontology::TermFactory;
ok 3 - use Bio::Annotation::DBLink;
ok 4 - The object isa Bio::Ontology::TermI
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44 - The object isa Bio::Ontology::TermI
ok 45
ok 46 - The object isa Bio::Ontology::TermI
ok 47 - The object isa Bio::Ontology::GOterm
ok 48
ok 49
ok 50 - The object isa Bio::Ontology::TermI
ok 51 - The object isa Bio::AnnotationI
ok 52
ok 53
ok 54
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Replacement list is longer than search list at Bio/Perl.pm line 627.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Perl.t .....................................
1..29
ok 1 - use Bio::Perl;
ok 2
ok 3 - The object isa Bio::SeqI
ok 4
ok 5 - The object isa Bio::SeqI
ok 6
ok 7 - The object isa Bio::SeqI
ok 8 - The object isa Bio::SeqI
ok 9
ok 10
ok 11 - The object isa Bio::SeqI
ok 12
ok 13 - The object isa Bio::SeqI
ok 14
ok 15 - The object isa Bio::PrimarySeqI
ok 16
ok 17
ok 18
ok 19
ok 20 # skip Network tests have not been requested
ok 21 # skip Network tests have not been requested
ok 22 # skip Network tests have not been requested
ok 23 # skip Network tests have not been requested
ok 24 # skip Network tests have not been requested
ok 25 # skip Network tests have not been requested
ok 26 # skip Network tests have not been requested
ok 27 # skip Network tests have not been requested
ok 28 # skip Network tests have not been requested
ok 29 # skip Network tests have not been requested
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
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
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
Replacement list is longer than search list at Bio/Range.pm line 251.
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
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Phenotype/OMIMparser.t .....................
1..175
ok 1 - use Bio::Phenotype::OMIM::OMIMparser;
ok 2 - The object isa Bio::Phenotype::OMIM::OMIMparser
ok 3 - The object isa Bio::Phenotype::OMIM::OMIMentry
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19 - The object isa Bio::Phenotype::OMIM::MiniMIMentry
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89 - The object isa Bio::Phenotype::OMIM::OMIMentry
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105 - The object isa Bio::Phenotype::OMIM::MiniMIMentry
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175 - missing linebreak caught
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Phenotype/Phenotype.t ......................
1..116
ok 1 - use Bio::Phenotype::Phenotype;
ok 2 - use Bio::Species;
ok 3 - use Bio::Annotation::Reference;
ok 4 - use Bio::Map::CytoPosition;
ok 5 - use Bio::Phenotype::Correlate;
ok 6 - use Bio::Phenotype::Measure;
ok 7 - use Bio::Annotation::DBLink;
ok 8 - The object isa Bio::Phenotype::PhenotypeI
ok 9 - The object isa Bio::Phenotype::Phenotype
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42 - operator overloading in AnnotationI is deprecated
ok 43 - operator overloading in AnnotationI is deprecated
ok 44
ok 45
ok 46 - operator overloading in AnnotationI is deprecated
ok 47 - operator overloading in AnnotationI is deprecated
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99 - operator overloading in AnnotationI is deprecated
ok 100 - operator overloading in AnnotationI is deprecated
ok 101
ok 102
ok 103 - operator overloading in AnnotationI is deprecated
ok 104 - operator overloading in AnnotationI is deprecated
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok
# Failed test 'POD test for Bio/Tree/Statistics.pm'
# at /home/fly1800/var/megalib/Test/Pod.pm line 186.
Wide character in print at /home/fly1800/ap1800-297235/lib/Test/Builder.pm line 1759.
# Bio/Tree/Statistics.pm (215): Non-ASCII character seen before =encoding in 'deï¬ning'. Assuming UTF-8
# Failed test 'POD test for Bio/Tools/Geneid.pm'
# at /home/fly1800/var/megalib/Test/Pod.pm line 186.
# Bio/Tools/Geneid.pm (38): Non-ASCII character seen before =encoding in 'Guigó'. Assuming ISO8859-1
# Failed test 'POD test for Bio/Tools/GuessSeqFormat.pm'
# at /home/fly1800/var/megalib/Test/Pod.pm line 186.
# Bio/Tools/GuessSeqFormat.pm (226): Non-ASCII character seen before =encoding in 'Kähäri,'. Assuming ISO8859-1
# Failed test 'POD test for Bio/Tools/Run/WrapperBase.pm'
# at /home/fly1800/var/megalib/Test/Pod.pm line 186.
# Bio/Tools/Run/WrapperBase.pm (182): Non-ASCII character seen before =encoding in 'NB:ÊThis'. Assuming ISO8859-1
# Failed test 'POD test for examples/biblio/biblio-eutils-example.pl'
# at /home/fly1800/var/megalib/Test/Pod.pm line 186.
# examples/biblio/biblio-eutils-example.pl (109): Non-ASCII character seen before =encoding in 'Kubícková'. Assuming ISO8859-1
# Looks like you failed 5 tests of 999.
t/PodSyntax.t ................................
1..999
ok 1 - POD test for Bio/Perl.pm
ok 2 - POD test for Bio/Taxonomy.pm
ok 3 - POD test for Bio/DescribableI.pm
ok 4 - POD test for Bio/HandlerBaseI.pm
ok 5 - POD test for Bio/SeqIO.pm
ok 6 - POD test for Bio/PrimarySeq.pm
ok 7 - POD test for Bio/Species.pm
ok 8 - POD test for Bio/ClusterI.pm
ok 9 - POD test for Bio/ParameterBaseI.pm
ok 10 - POD test for Bio/FeatureHolderI.pm
ok 11 - POD test for Bio/SeqI.pm
ok 12 - POD test for Bio/OntologyIO.pm
ok 13 - POD test for Bio/AnalysisResultI.pm
ok 14 - POD test for Bio/LocatableSeq.pm
ok 15 - POD test for Bio/PhyloNetwork.pm
ok 16 - POD test for Bio/DBLinkContainerI.pm
ok 17 - POD test for Bio/FeatureIO.pm
ok 18 - POD test for Bio/AnalysisParserI.pm
ok 19 - POD test for Bio/SearchDist.pm
ok 20 - POD test for Bio/SimpleAnalysisI.pm
ok 21 - POD test for Bio/AnnotationI.pm
ok 22 - POD test for Bio/Range.pm
ok 23 - POD test for Bio/SeqUtils.pm
ok 24 - POD test for Bio/AlignIO.pm
ok 25 - POD test for Bio/SeqAnalysisParserI.pm
ok 26 - POD test for Bio/UpdateableSeqI.pm
ok 27 - POD test for Bio/Seq.pm
ok 28 - POD test for Bio/LocationI.pm
ok 29 - POD test for Bio/Taxon.pm
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ok 466 - POD test for Bio/AlignIO/maf.pm
ok 467 - POD test for Bio/AlignIO/arp.pm
ok 468 - POD test for Bio/AlignIO/proda.pm
ok 469 - POD test for Bio/AlignIO/meme.pm
ok 470 - POD test for Bio/AlignIO/psi.pm
ok 471 - POD test for Bio/AlignIO/Handler/GenericAlignHandler.pm
ok 472 - POD test for Bio/Location/NarrowestCoordPolicy.pm
ok 473 - POD test for Bio/Location/FuzzyLocationI.pm
ok 474 - POD test for Bio/Location/SplitLocationI.pm
ok 475 - POD test for Bio/Location/AvWithinCoordPolicy.pm
ok 476 - POD test for Bio/Location/WidestCoordPolicy.pm
ok 477 - POD test for Bio/Location/Fuzzy.pm
ok 478 - POD test for Bio/Location/Simple.pm
ok 479 - POD test for Bio/Location/Atomic.pm
ok 480 - POD test for Bio/Location/CoordinatePolicyI.pm
ok 481 - POD test for Bio/Location/Split.pm
ok 482 - POD test for Bio/PopGen/TagHaplotype.pm
ok 483 - POD test for Bio/PopGen/PopStats.pm
ok 484 - POD test for Bio/PopGen/Marker.pm
ok 485 - POD test for Bio/PopGen/Population.pm
ok 486 - POD test for Bio/PopGen/Statistics.pm
ok 487 - POD test for Bio/PopGen/IndividualI.pm
ok 488 - POD test for Bio/PopGen/HtSNP.pm
ok 489 - POD test for Bio/PopGen/GenotypeI.pm
ok 490 - POD test for Bio/PopGen/Genotype.pm
ok 491 - POD test for Bio/PopGen/Individual.pm
ok 492 - POD test for Bio/PopGen/MarkerI.pm
ok 493 - POD test for Bio/PopGen/Utilities.pm
ok 494 - POD test for Bio/PopGen/PopulationI.pm
ok 495 - POD test for Bio/PopGen/IO.pm
ok 496 - POD test for Bio/PopGen/Simulation/GeneticDrift.pm
ok 497 - POD test for Bio/PopGen/Simulation/Coalescent.pm
ok 498 - POD test for Bio/PopGen/IO/phase.pm
ok 499 - POD test for Bio/PopGen/IO/prettybase.pm
ok 500 - POD test for Bio/PopGen/IO/csv.pm
ok 501 - POD test for Bio/PopGen/IO/hapmap.pm
ok 502 - POD test for Bio/DB/Universal.pm
ok 503 - POD test for Bio/DB/SeqVersion.pm
ok 504 - POD test for Bio/DB/MeSH.pm
ok 505 - POD test for Bio/DB/HIV.pm
ok 506 - POD test for Bio/DB/Fasta.pm
ok 507 - POD test for Bio/DB/CUTG.pm
ok 508 - POD test for Bio/DB/BioFetch.pm
ok 509 - POD test for Bio/DB/Taxonomy.pm
ok 510 - POD test for Bio/DB/SeqHound.pm
ok 511 - POD test for Bio/DB/BiblioI.pm
ok 512 - POD test for Bio/DB/Expression.pm
ok 513 - POD test for Bio/DB/EUtilities.pm
ok 514 - POD test for Bio/DB/Registry.pm
ok 515 - POD test for Bio/DB/SeqI.pm
ok 516 - POD test for Bio/DB/QueryI.pm
ok 517 - POD test for Bio/DB/Failover.pm
ok 518 - POD test for Bio/DB/Ace.pm
ok 519 - POD test for Bio/DB/TFBS.pm
ok 520 - POD test for Bio/DB/InMemoryCache.pm
ok 521 - POD test for Bio/DB/GenericWebAgent.pm
ok 522 - POD test for Bio/DB/RandomAccessI.pm
ok 523 - POD test for Bio/DB/EntrezGene.pm
ok 524 - POD test for Bio/DB/UpdateableSeqI.pm
ok 525 - POD test for Bio/DB/SeqFeature.pm
ok 526 - POD test for Bio/DB/LocationI.pm
ok 527 - POD test for Bio/DB/EMBL.pm
ok 528 - POD test for Bio/DB/GenBank.pm
ok 529 - POD test for Bio/DB/Flat.pm
ok 530 - POD test for Bio/DB/DBFetch.pm
ok 531 - POD test for Bio/DB/GFF.pm
ok 532 - POD test for Bio/DB/NCBIHelper.pm
ok 533 - POD test for Bio/DB/GenPept.pm
ok 534 - POD test for Bio/DB/ReferenceI.pm
ok 535 - POD test for Bio/DB/FileCache.pm
ok 536 - POD test for Bio/DB/WebDBSeqI.pm
ok 537 - POD test for Bio/DB/RefSeq.pm
ok 538 - POD test for Bio/DB/SwissProt.pm
ok 539 - POD test for Bio/DB/Qual.pm
ok 540 - POD test for Bio/DB/Query/WebQuery.pm
ok 541 - POD test for Bio/DB/Query/HIVQuery.pm
ok 542 - POD test for Bio/DB/Query/GenBank.pm
ok 543 - POD test for Bio/DB/Expression/geo.pm
ok 544 - POD test for Bio/DB/Taxonomy/list.pm
ok 545 - POD test for Bio/DB/Taxonomy/flatfile.pm
ok 546 - POD test for Bio/DB/Taxonomy/entrez.pm
ok 547 - POD test for Bio/DB/SeqFeature/NormalizedTableFeatureI.pm
ok 548 - POD test for Bio/DB/SeqFeature/Store.pm
ok 549 - POD test for Bio/DB/SeqFeature/NormalizedFeature.pm
ok 550 - POD test for Bio/DB/SeqFeature/Segment.pm
ok 551 - POD test for Bio/DB/SeqFeature/NormalizedFeatureI.pm
ok 552 - POD test for Bio/DB/SeqFeature/Store/GFF3Loader.pm
ok 553 - POD test for Bio/DB/SeqFeature/Store/memory.pm
ok 554 - POD test for Bio/DB/SeqFeature/Store/LoadHelper.pm
ok 555 - POD test for Bio/DB/SeqFeature/Store/bdb.pm
ok 556 - POD test for Bio/DB/SeqFeature/Store/FeatureFileLoader.pm
ok 557 - POD test for Bio/DB/SeqFeature/Store/berkeleydb3.pm
ok 558 - POD test for Bio/DB/SeqFeature/Store/GFF2Loader.pm
ok 559 - POD test for Bio/DB/SeqFeature/Store/berkeleydb.pm
ok 560 - POD test for Bio/DB/SeqFeature/Store/Loader.pm
ok 561 - POD test for Bio/DB/SeqFeature/Store/DBI/Iterator.pm
ok 562 - POD test for Bio/DB/SeqFeature/Store/DBI/SQLite.pm
ok 563 - POD test for Bio/DB/SeqFeature/Store/DBI/Pg.pm
ok 564 - POD test for Bio/DB/SeqFeature/Store/DBI/mysql.pm
ok 565 - POD test for Bio/DB/Biblio/eutils.pm
ok 566 - POD test for Bio/DB/Biblio/soap.pm
ok 567 - POD test for Bio/DB/Biblio/biofetch.pm
ok 568 - POD test for Bio/DB/Flat/BDB.pm
ok 569 - POD test for Bio/DB/Flat/BinarySearch.pm
ok 570 - POD test for Bio/DB/Flat/BDB/fasta.pm
ok 571 - POD test for Bio/DB/Flat/BDB/genbank.pm
ok 572 - POD test for Bio/DB/Flat/BDB/embl.pm
ok 573 - POD test for Bio/DB/Flat/BDB/swiss.pm
ok 574 - POD test for Bio/DB/HIV/HIVAnnotProcessor.pm
ok 575 - POD test for Bio/DB/HIV/HIVQueryHelper.pm
ok 576 - POD test for Bio/DB/SeqVersion/gi.pm
ok 577 - POD test for Bio/DB/GFF/Typename.pm
ok 578 - POD test for Bio/DB/GFF/RelSegment.pm
ok 579 - POD test for Bio/DB/GFF/Feature.pm
ok 580 - POD test for Bio/DB/GFF/Featname.pm
ok 581 - POD test for Bio/DB/GFF/Homol.pm
ok 582 - POD test for Bio/DB/GFF/Aggregator.pm
ok 583 - POD test for Bio/DB/GFF/Segment.pm
ok 584 - POD test for Bio/DB/GFF/Util/Rearrange.pm
ok 585 - POD test for Bio/DB/GFF/Util/Binning.pm
ok 586 - POD test for Bio/DB/GFF/Adaptor/memory.pm
ok 587 - POD test for Bio/DB/GFF/Adaptor/biofetch_oracle.pm
ok 588 - POD test for Bio/DB/GFF/Adaptor/ace.pm
ok 589 - POD test for Bio/DB/GFF/Adaptor/berkeleydb.pm
ok 590 - POD test for Bio/DB/GFF/Adaptor/biofetch.pm
ok 591 - POD test for Bio/DB/GFF/Adaptor/dbi.pm
ok 592 - POD test for Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
ok 593 - POD test for Bio/DB/GFF/Adaptor/memory/iterator.pm
ok 594 - POD test for Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
ok 595 - POD test for Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm
ok 596 - POD test for Bio/DB/GFF/Adaptor/dbi/mysqlace.pm
ok 597 - POD test for Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
ok 598 - POD test for Bio/DB/GFF/Adaptor/dbi/pg.pm
ok 599 - POD test for Bio/DB/GFF/Adaptor/dbi/oracleace.pm
ok 600 - POD test for Bio/DB/GFF/Adaptor/dbi/oracle.pm
ok 601 - POD test for Bio/DB/GFF/Adaptor/dbi/iterator.pm
ok 602 - POD test for Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm
ok 603 - POD test for Bio/DB/GFF/Adaptor/dbi/mysql.pm
ok 604 - POD test for Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
ok 605 - POD test for Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
ok 606 - POD test for Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm
ok 607 - POD test for Bio/DB/GFF/Aggregator/ucsc_sanger22.pm
ok 608 - POD test for Bio/DB/GFF/Aggregator/ucsc_refgene.pm
ok 609 - POD test for Bio/DB/GFF/Aggregator/transcript.pm
ok 610 - POD test for Bio/DB/GFF/Aggregator/so_transcript.pm
ok 611 - POD test for Bio/DB/GFF/Aggregator/coding.pm
ok 612 - POD test for Bio/DB/GFF/Aggregator/none.pm
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ok 614 - POD test for Bio/DB/GFF/Aggregator/match.pm
ok 615 - POD test for Bio/DB/GFF/Aggregator/ucsc_acembly.pm
ok 616 - POD test for Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
ok 617 - POD test for Bio/DB/GFF/Aggregator/ucsc_softberry.pm
ok 618 - POD test for Bio/DB/GFF/Aggregator/ucsc_genscan.pm
ok 619 - POD test for Bio/DB/GFF/Aggregator/ucsc_unigene.pm
ok 620 - POD test for Bio/DB/GFF/Aggregator/clone.pm
ok 621 - POD test for Bio/DB/GFF/Aggregator/processed_transcript.pm
ok 622 - POD test for Bio/DB/GFF/Aggregator/alignment.pm
ok 623 - POD test for Bio/DB/GFF/Aggregator/gene.pm
ok 624 - POD test for Bio/DB/TFBS/transfac_pro.pm
ok 625 - POD test for Bio/MolEvol/CodonModel.pm
ok 626 - POD test for Bio/Structure/Atom.pm
ok 627 - POD test for Bio/Structure/Model.pm
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ok 630 - POD test for Bio/Structure/Residue.pm
ok 631 - POD test for Bio/Structure/Entry.pm
ok 632 - POD test for Bio/Structure/IO.pm
ok 633 - POD test for Bio/Structure/SecStr/STRIDE/Res.pm
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ok 636 - POD test for Bio/Symbol/DNAAlphabet.pm
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ok 643 - POD test for Bio/Seq/Meta.pm
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ok 647 - POD test for Bio/Seq/Quality.pm
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ok 649 - POD test for Bio/Seq/MetaI.pm
ok 650 - POD test for Bio/Seq/BaseSeqProcessor.pm
ok 651 - POD test for Bio/Seq/QualI.pm
ok 652 - POD test for Bio/Seq/PrimedSeq.pm
ok 653 - POD test for Bio/Seq/RichSeqI.pm
ok 654 - POD test for Bio/Seq/LargeSeqI.pm
ok 655 - POD test for Bio/Seq/LargeSeq.pm
ok 656 - POD test for Bio/Seq/LargeLocatableSeq.pm
ok 657 - POD test for Bio/Seq/SequenceTrace.pm
ok 658 - POD test for Bio/Seq/SeqBuilder.pm
ok 659 - POD test for Bio/Seq/EncodedSeq.pm
ok 660 - POD test for Bio/Seq/LargePrimarySeq.pm
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ok 662 - POD test for Bio/Seq/Meta/Array.pm
ok 663 - POD test for Bio/Phenotype/PhenotypeI.pm
ok 664 - POD test for Bio/Phenotype/Correlate.pm
ok 665 - POD test for Bio/Phenotype/Phenotype.pm
ok 666 - POD test for Bio/Phenotype/Measure.pm
ok 667 - POD test for Bio/Phenotype/OMIM/MiniMIMentry.pm
ok 668 - POD test for Bio/Phenotype/OMIM/OMIMparser.pm
ok 669 - POD test for Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm
ok 670 - POD test for Bio/Phenotype/OMIM/OMIMentry.pm
ok 671 - POD test for Bio/Phenotype/MeSH/Twig.pm
ok 672 - POD test for Bio/Phenotype/MeSH/Term.pm
ok 673 - POD test for Bio/SeqEvolution/DNAPoint.pm
ok 674 - POD test for Bio/SeqEvolution/Factory.pm
ok 675 - POD test for Bio/SeqEvolution/EvolutionI.pm
ok 676 - POD test for Bio/MapIO/fpc.pm
ok 677 - POD test for Bio/MapIO/mapmaker.pm
ok 678 - POD test for Bio/Tools/Seg.pm
ok 679 - POD test for Bio/Tools/Eponine.pm
ok 680 - POD test for Bio/Tools/CodonTable.pm
ok 681 - POD test for Bio/Tools/Hmmpfam.pm
ok 682 - POD test for Bio/Tools/SiRNA.pm
ok 683 - POD test for Bio/Tools/Lucy.pm
ok 684 - POD test for Bio/Tools/Gel.pm
ok 685 - POD test for Bio/Tools/OddCodes.pm
ok 686 - POD test for Bio/Tools/QRNA.pm
ok 687 - POD test for Bio/Tools/Pseudowise.pm
ok 688 - POD test for Bio/Tools/Genomewise.pm
ok 689 - POD test for Bio/Tools/Protparam.pm
ok 690 - POD test for Bio/Tools/RepeatMasker.pm
ok 691 - POD test for Bio/Tools/ipcress.pm
ok 692 - POD test for Bio/Tools/PrositeScan.pm
ok 693 - POD test for Bio/Tools/RandomDistFunctions.pm
ok 694 - POD test for Bio/Tools/EUtilities.pm
ok 695 - POD test for Bio/Tools/Signalp.pm
ok 696 - POD test for Bio/Tools/Tmhmm.pm
ok 697 - POD test for Bio/Tools/ESTScan.pm
ok 698 - POD test for Bio/Tools/Promoterwise.pm
ok 699 - POD test for Bio/Tools/RNAMotif.pm
ok 700 - POD test for Bio/Tools/Coil.pm
not ok 701 - POD test for Bio/Tools/Geneid.pm
ok 702 - POD test for Bio/Tools/Genewise.pm
ok 703 - POD test for Bio/Tools/dpAlign.pm
ok 704 - POD test for Bio/Tools/Sigcleave.pm
ok 705 - POD test for Bio/Tools/Est2Genome.pm
ok 706 - POD test for Bio/Tools/Infernal.pm
ok 707 - POD test for Bio/Tools/SeqPattern.pm
ok 708 - POD test for Bio/Tools/AnalysisResult.pm
ok 709 - POD test for Bio/Tools/TargetP.pm
ok 710 - POD test for Bio/Tools/Blat.pm
ok 711 - POD test for Bio/Tools/Genemark.pm
ok 712 - POD test for Bio/Tools/EPCR.pm
ok 713 - POD test for Bio/Tools/ERPIN.pm
ok 714 - POD test for Bio/Tools/tRNAscanSE.pm
ok 715 - POD test for Bio/Tools/isPcr.pm
ok 716 - POD test for Bio/Tools/Genscan.pm
ok 717 - POD test for Bio/Tools/Profile.pm
ok 718 - POD test for Bio/Tools/GFF.pm
ok 719 - POD test for Bio/Tools/AlignFactory.pm
ok 720 - POD test for Bio/Tools/FootPrinter.pm
ok 721 - POD test for Bio/Tools/SeqWords.pm
ok 722 - POD test for Bio/Tools/pSW.pm
ok 723 - POD test for Bio/Tools/Grail.pm
ok 724 - POD test for Bio/Tools/pICalculator.pm
ok 725 - POD test for Bio/Tools/IUPAC.pm
ok 726 - POD test for Bio/Tools/TandemRepeatsFinder.pm
ok 727 - POD test for Bio/Tools/SeqStats.pm
ok 728 - POD test for Bio/Tools/Prints.pm
ok 729 - POD test for Bio/Tools/Match.pm
ok 730 - POD test for Bio/Tools/Glimmer.pm
ok 731 - POD test for Bio/Tools/MZEF.pm
ok 732 - POD test for Bio/Tools/ECnumber.pm
ok 733 - POD test for Bio/Tools/Primer3.pm
not ok 734 - POD test for Bio/Tools/GuessSeqFormat.pm
ok 735 - POD test for Bio/Tools/Fgenesh.pm
ok 736 - POD test for Bio/Tools/HMMER/Domain.pm
ok 737 - POD test for Bio/Tools/HMMER/Results.pm
ok 738 - POD test for Bio/Tools/HMMER/Set.pm
ok 739 - POD test for Bio/Tools/Signalp/ExtendedSignalp.pm
ok 740 - POD test for Bio/Tools/SeqPattern/Backtranslate.pm
ok 741 - POD test for Bio/Tools/Phylo/Gumby.pm
ok 742 - POD test for Bio/Tools/Phylo/PAML.pm
ok 743 - POD test for Bio/Tools/Phylo/Molphy.pm
ok 744 - POD test for Bio/Tools/Phylo/Gerp.pm
ok 745 - POD test for Bio/Tools/Phylo/Molphy/Result.pm
ok 746 - POD test for Bio/Tools/Phylo/PAML/Result.pm
ok 747 - POD test for Bio/Tools/Phylo/PAML/ModelResult.pm
ok 748 - POD test for Bio/Tools/Phylo/Phylip/ProtDist.pm
ok 749 - POD test for Bio/Tools/EMBOSS/Palindrome.pm
ok 750 - POD test for Bio/Tools/EUtilities/Summary.pm
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ok 752 - POD test for Bio/Tools/EUtilities/EUtilDataI.pm
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ok 754 - POD test for Bio/Tools/EUtilities/HistoryI.pm
ok 755 - POD test for Bio/Tools/EUtilities/Query.pm
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ok 757 - POD test for Bio/Tools/EUtilities/Info.pm
ok 758 - POD test for Bio/Tools/EUtilities/EUtilParameters.pm
ok 759 - POD test for Bio/Tools/EUtilities/Query/GlobalQuery.pm
ok 760 - POD test for Bio/Tools/EUtilities/Summary/DocSum.pm
ok 761 - POD test for Bio/Tools/EUtilities/Summary/Item.pm
ok 762 - POD test for Bio/Tools/EUtilities/Summary/ItemContainerI.pm
ok 763 - POD test for Bio/Tools/EUtilities/Info/FieldInfo.pm
ok 764 - POD test for Bio/Tools/EUtilities/Info/LinkInfo.pm
ok 765 - POD test for Bio/Tools/EUtilities/Link/UrlLink.pm
ok 766 - POD test for Bio/Tools/EUtilities/Link/LinkSet.pm
ok 767 - POD test for Bio/Tools/Sim4/Exon.pm
ok 768 - POD test for Bio/Tools/Sim4/Results.pm
ok 769 - POD test for Bio/Tools/Prediction/Exon.pm
ok 770 - POD test for Bio/Tools/Prediction/Gene.pm
ok 771 - POD test for Bio/Tools/SiRNA/Ruleset/saigo.pm
ok 772 - POD test for Bio/Tools/SiRNA/Ruleset/tuschl.pm
ok 773 - POD test for Bio/Tools/Alignment/Trim.pm
ok 774 - POD test for Bio/Tools/Alignment/Consed.pm
ok 775 - POD test for Bio/Tools/Primer/Feature.pm
ok 776 - POD test for Bio/Tools/Primer/Pair.pm
ok 777 - POD test for Bio/Tools/Primer/AssessorI.pm
ok 778 - POD test for Bio/Tools/Primer/Assessor/Base.pm
ok 779 - POD test for Bio/Tools/Run/RemoteBlast.pm
ok 780 - POD test for Bio/Tools/Run/GenericParameters.pm
ok 781 - POD test for Bio/Tools/Run/StandAloneNCBIBlast.pm
ok 782 - POD test for Bio/Tools/Run/StandAloneBlast.pm
ok 783 - POD test for Bio/Tools/Run/StandAloneWUBlast.pm
not ok 784 - POD test for Bio/Tools/Run/WrapperBase.pm
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ok 786 - POD test for Bio/Tools/Analysis/SimpleAnalysisBase.pm
ok 787 - POD test for Bio/Tools/Analysis/Protein/ELM.pm
ok 788 - POD test for Bio/Tools/Analysis/Protein/Mitoprot.pm
ok 789 - POD test for Bio/Tools/Analysis/Protein/Sopma.pm
ok 790 - POD test for Bio/Tools/Analysis/Protein/Scansite.pm
ok 791 - POD test for Bio/Tools/Analysis/Protein/Domcut.pm
ok 792 - POD test for Bio/Tools/Analysis/Protein/GOR4.pm
ok 793 - POD test for Bio/Tools/Analysis/Protein/HNN.pm
ok 794 - POD test for Bio/Tools/Analysis/Protein/NetPhos.pm
ok 795 - POD test for Bio/Tools/Analysis/DNA/ESEfinder.pm
ok 796 - POD test for Bio/Tools/Spidey/Exon.pm
ok 797 - POD test for Bio/Tools/Spidey/Results.pm
ok 798 - POD test for Bio/Cluster/UniGeneI.pm
ok 799 - POD test for Bio/Cluster/UniGene.pm
ok 800 - POD test for Bio/Cluster/SequenceFamily.pm
ok 801 - POD test for Bio/Cluster/ClusterFactory.pm
ok 802 - POD test for Bio/Cluster/FamilyI.pm
ok 803 - POD test for Bio/ClusterIO/dbsnp.pm
ok 804 - POD test for Bio/ClusterIO/unigene.pm
ok 805 - POD test for Bio/Align/AlignI.pm
ok 806 - POD test for Bio/Align/DNAStatistics.pm
ok 807 - POD test for Bio/Align/PairwiseStatistics.pm
ok 808 - POD test for Bio/Align/StatisticsI.pm
ok 809 - POD test for Bio/Align/ProteinStatistics.pm
ok 810 - POD test for Bio/Align/Utilities.pm
ok 811 - POD test for Bio/Coordinate/Utils.pm
ok 812 - POD test for Bio/Coordinate/Pair.pm
ok 813 - POD test for Bio/Coordinate/Chain.pm
ok 814 - POD test for Bio/Coordinate/MapperI.pm
ok 815 - POD test for Bio/Coordinate/Graph.pm
ok 816 - POD test for Bio/Coordinate/Collection.pm
ok 817 - POD test for Bio/Coordinate/ExtrapolatingPair.pm
ok 818 - POD test for Bio/Coordinate/GeneMapper.pm
ok 819 - POD test for Bio/Coordinate/ResultI.pm
ok 820 - POD test for Bio/Coordinate/Result.pm
ok 821 - POD test for Bio/Coordinate/Result/Gap.pm
ok 822 - POD test for Bio/Coordinate/Result/Match.pm
ok 823 - POD test for Bio/Matrix/MatrixI.pm
ok 824 - POD test for Bio/Matrix/Scoring.pm
ok 825 - POD test for Bio/Matrix/Mlagan.pm
ok 826 - POD test for Bio/Matrix/Generic.pm
ok 827 - POD test for Bio/Matrix/PhylipDist.pm
ok 828 - POD test for Bio/Matrix/IO.pm
ok 829 - POD test for Bio/Matrix/IO/mlagan.pm
ok 830 - POD test for Bio/Matrix/IO/scoring.pm
ok 831 - POD test for Bio/Matrix/IO/phylip.pm
ok 832 - POD test for Bio/Matrix/PSM/InstanceSiteI.pm
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ok 835 - POD test for Bio/Matrix/PSM/PsmHeaderI.pm
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ok 839 - POD test for Bio/Matrix/PSM/PsmI.pm
ok 840 - POD test for Bio/Matrix/PSM/Psm.pm
ok 841 - POD test for Bio/Matrix/PSM/IO.pm
ok 842 - POD test for Bio/Matrix/PSM/SiteMatrix.pm
ok 843 - POD test for Bio/Matrix/PSM/IO/masta.pm
ok 844 - POD test for Bio/Matrix/PSM/IO/mast.pm
ok 845 - POD test for Bio/Matrix/PSM/IO/transfac.pm
ok 846 - POD test for Bio/Matrix/PSM/IO/psiblast.pm
ok 847 - POD test for Bio/Matrix/PSM/IO/meme.pm
ok 848 - POD test for Bio/Variation/AAChange.pm
ok 849 - POD test for Bio/Variation/DNAMutation.pm
ok 850 - POD test for Bio/Variation/AAReverseMutate.pm
ok 851 - POD test for Bio/Variation/VariantI.pm
ok 852 - POD test for Bio/Variation/RNAChange.pm
ok 853 - POD test for Bio/Variation/SNP.pm
ok 854 - POD test for Bio/Variation/SeqDiff.pm
ok 855 - POD test for Bio/Variation/Allele.pm
ok 856 - POD test for Bio/Variation/IO.pm
ok 857 - POD test for Bio/Variation/IO/flat.pm
ok 858 - POD test for Bio/Variation/IO/xml.pm
ok 859 - POD test for scripts/taxa/classify_hits_kingdom.PLS
ok 860 - POD test for scripts/taxa/query_entrez_taxa.PLS
ok 861 - POD test for scripts/taxa/local_taxonomydb_query.PLS
ok 862 - POD test for scripts/taxa/taxid4species.PLS
ok 863 - POD test for scripts/taxa/taxonomy2tree.PLS
ok 864 - POD test for scripts/tree/blast2tree.PLS
ok 865 - POD test for scripts/tree/tree2pag.PLS
ok 866 - POD test for scripts/tree/nexus2nh.PLS
ok 867 - POD test for scripts/popgen/heterogeneity_test.PLS
ok 868 - POD test for scripts/popgen/composite_LD.PLS
ok 869 - POD test for scripts/seq/extract_feature_seq.PLS
ok 870 - POD test for scripts/seq/split_seq.PLS
ok 871 - POD test for scripts/seq/make_mrna_protein.PLS
ok 872 - POD test for scripts/seq/seqconvert.PLS
ok 873 - POD test for scripts/seq/translate_seq.PLS
ok 874 - POD test for scripts/seq/unflatten_seq.PLS
ok 875 - POD test for scripts/seq/seqretsplit.PLS
ok 876 - POD test for scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS (no pod)
ok 877 - POD test for scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS (no pod)
ok 878 - POD test for scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS (no pod)
ok 879 - POD test for scripts/index/bp_fetch.PLS
ok 880 - POD test for scripts/index/bp_index.PLS
ok 881 - POD test for scripts/index/bp_seqret.PLS
ok 882 - POD test for scripts/Bio-DB-EUtilities/einfo.PLS
ok 883 - POD test for scripts/DB-HIV/hivq.PLS
ok 884 - POD test for scripts/seqstats/aacomp.PLS
ok 885 - POD test for scripts/seqstats/chaos_plot.PLS
ok 886 - POD test for scripts/seqstats/oligo_count.PLS
ok 887 - POD test for scripts/seqstats/gccalc.PLS
ok 888 - POD test for scripts/DB/bioflat_index.PLS
ok 889 - POD test for scripts/DB/biofetch_genbank_proxy.PLS
ok 890 - POD test for scripts/DB/biogetseq.PLS
ok 891 - POD test for scripts/DB/flanks.PLS
ok 892 - POD test for scripts/searchio/filter_search.PLS
ok 893 - POD test for scripts/searchio/hmmer_to_table.PLS
ok 894 - POD test for scripts/searchio/search2table.PLS
ok 895 - POD test for scripts/searchio/fastam9_to_table.PLS
ok 896 - POD test for scripts/searchio/parse_hmmsearch.PLS
ok 897 - POD test for scripts/Bio-DB-GFF/process_gadfly.PLS
ok 898 - POD test for scripts/Bio-DB-GFF/genbank2gff.PLS
ok 899 - POD test for scripts/Bio-DB-GFF/generate_histogram.PLS
ok 900 - POD test for scripts/Bio-DB-GFF/bulk_load_gff.PLS
ok 901 - POD test for scripts/Bio-DB-GFF/genbank2gff3.PLS
ok 902 - POD test for scripts/Bio-DB-GFF/load_gff.PLS
ok 903 - POD test for scripts/Bio-DB-GFF/process_sgd.PLS
ok 904 - POD test for scripts/Bio-DB-GFF/fast_load_gff.PLS
ok 905 - POD test for scripts/Bio-DB-GFF/meta_gff.PLS
ok 906 - POD test for scripts/Bio-DB-GFF/process_wormbase.PLS
ok 907 - POD test for scripts/utilities/mutate.PLS
ok 908 - POD test for scripts/utilities/bp_sreformat.PLS
ok 909 - POD test for scripts/utilities/seq_length.PLS
ok 910 - POD test for scripts/utilities/download_query_genbank.PLS
ok 911 - POD test for scripts/utilities/dbsplit.PLS
ok 912 - POD test for scripts/utilities/bp_nrdb.PLS
ok 913 - POD test for scripts/utilities/search2alnblocks.PLS
ok 914 - POD test for scripts/utilities/remote_blast.PLS
ok 915 - POD test for scripts/utilities/revtrans-motif.PLS
ok 916 - POD test for scripts/utilities/search2gff.PLS
ok 917 - POD test for scripts/utilities/search2BSML.PLS
ok 918 - POD test for scripts/utilities/search2tribe.PLS
ok 919 - POD test for scripts/utilities/mask_by_search.PLS
ok 920 - POD test for scripts/utilities/pairwise_kaks.PLS
ok 921 - POD test for scripts/utilities/bp_mrtrans.PLS
ok 922 - POD test for scripts/biblio/biblio.PLS
ok 923 - POD test for examples/bioperl.pl (no pod)
ok 924 - POD test for examples/longorf.pl
ok 925 - POD test for examples/subsequence.cgi (no pod)
ok 926 - POD test for examples/generate_random_seq.pl (no pod)
ok 927 - POD test for examples/make_primers.pl (no pod)
ok 928 - POD test for examples/revcom_dir.pl (no pod)
ok 929 - POD test for examples/rev_and_trans.pl (no pod)
ok 930 - POD test for examples/tools/gff2ps.pl
ok 931 - POD test for examples/tools/psw.pl (no pod)
ok 932 - POD test for examples/tools/seq_pattern.pl (no pod)
ok 933 - POD test for examples/tools/run_primer3.pl
ok 934 - POD test for examples/tools/run_genscan.pl (no pod)
ok 935 - POD test for examples/tools/parse_codeml.pl (no pod)
ok 936 - POD test for examples/tools/reverse-translate.pl
ok 937 - POD test for examples/tools/gb_to_gff.pl (no pod)
ok 938 - POD test for examples/tools/extract_genes.pl
ok 939 - POD test for examples/tools/standaloneblast.pl (no pod)
ok 940 - POD test for examples/tree/paup2phylip.pl (no pod)
ok 941 - POD test for examples/cluster/dbsnp.pl (no pod)
ok 942 - POD test for examples/popgen/parse_calc_stats.pl (no pod)
ok 943 - POD test for examples/sirna/rnai_finder.cgi
ok 944 - POD test for examples/tk/gsequence.pl (no pod)
ok 945 - POD test for examples/tk/hitdisplay.pl (no pod)
ok 946 - POD test for examples/root/exceptions3.pl (no pod)
ok 947 - POD test for examples/root/exceptions4.pl (no pod)
ok 948 - POD test for examples/root/exceptions2.pl (no pod)
ok 949 - POD test for examples/root/exceptions1.pl (no pod)
ok 950 - POD test for examples/root/lib/TestObject.pm
ok 951 - POD test for examples/root/lib/TestInterface.pm
ok 952 - POD test for examples/root/lib/Bio/PrimarySeq.pm
ok 953 - POD test for examples/root/lib/Bio/SeqI.pm
ok 954 - POD test for examples/root/lib/Bio/Seq.pm
ok 955 - POD test for examples/root/lib/Bio/PrimarySeqI.pm
ok 956 - POD test for examples/liveseq/change_gene.pl (no pod)
ok 957 - POD test for examples/contributed/rebase2list.pl (no pod)
ok 958 - POD test for examples/contributed/prosite2perl.pl (no pod)
ok 959 - POD test for examples/contributed/nmrpdb_parse.pl (no pod)
ok 960 - POD test for examples/db/use_registry.pl (no pod)
ok 961 - POD test for examples/db/getGenBank.pl (no pod)
ok 962 - POD test for examples/db/est_tissue_query.pl (no pod)
ok 963 - POD test for examples/db/rfetch.pl (no pod)
ok 964 - POD test for examples/db/dbfetch
ok 965 - POD test for examples/db/gb2features.pl (no pod)
ok 966 - POD test for examples/db/get_seqs.pl (no pod)
ok 967 - POD test for examples/quality/svgtrace.pl (no pod)
ok 968 - POD test for examples/searchio/hspwriter.pl (no pod)
ok 969 - POD test for examples/searchio/blast_example.pl (no pod)
ok 970 - POD test for examples/searchio/rawwriter.pl (no pod)
ok 971 - POD test for examples/searchio/waba2gff3.pl
ok 972 - POD test for examples/searchio/hitwriter.pl (no pod)
ok 973 - POD test for examples/searchio/waba2gff.pl (no pod)
ok 974 - POD test for examples/searchio/psiblast_features.pl (no pod)
ok 975 - POD test for examples/searchio/htmlwriter.pl (no pod)
ok 976 - POD test for examples/searchio/custom_writer.pl (no pod)
ok 977 - POD test for examples/searchio/resultwriter.pl (no pod)
ok 978 - POD test for examples/searchio/psiblast_iterations.pl (no pod)
ok 979 - POD test for examples/Bio-DB-GFF/load_ucsc.pl (no pod)
ok 980 - POD test for examples/structure/structure-io.pl (no pod)
ok 981 - POD test for examples/align/clustalw.pl (no pod)
ok 982 - POD test for examples/align/aligntutorial.pl (no pod)
ok 983 - POD test for examples/align/align_on_codons.pl (no pod)
ok 984 - POD test for examples/align/simplealign.pl (no pod)
ok 985 - POD test for examples/biblio/biblio-soap-example.pl
ok 986 - POD test for examples/biblio/biblio_soap.pl (no pod)
not ok 987 - POD test for examples/biblio/biblio-eutils-example.pl
ok 988 - POD test for maintenance/dependencies.pl
ok 989 - POD test for maintenance/authors.pl
ok 990 - POD test for maintenance/version.pl
ok 991 - POD test for maintenance/pod.pl
ok 992 - POD test for maintenance/check_NAME.pl
ok 993 - POD test for maintenance/check_URLs.pl
ok 994 - POD test for maintenance/module_usage.pl (no pod)
ok 995 - POD test for maintenance/cvs2cl_by_file.pl
ok 996 - POD test for maintenance/symlink_script.pl
ok 997 - POD test for maintenance/deprecated.pl
ok 998 - POD test for maintenance/ncbi_blast_switches.pl (no pod)
ok 999 - POD test for maintenance/modules.pl
Dubious, test returned 5 (wstat 1280, 0x500)
Failed 5/999 subtests
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/PopGen/Coalescent.t ........................
1..13
ok 1 - use Bio::PopGen::Simulation::Coalescent;
ok 2 - use Bio::PopGen::Statistics;
ok 3 - use Bio::TreeIO;
ok 4
ok 5
ok 6 - pi
ok 7 - theta
ok 8 - tajimaD
ok 9 - all the mutations should be polymorphic (by definition)
ok 10 - fu and li D
ok 11 - fu and li D*
ok 12 - fu and li F
ok 13 - fu and li F
ok
t/PopGen/HtSNP.t .............................
1..8
ok 1 - use Bio::PopGen::HtSNP;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/PopGen/MK.t ................................
1..46
ok 1 - use Bio::AlignIO;
ok 2 - use Bio::PopGen::Statistics;
ok 3 - use Bio::PopGen::Utilities;
ok 4 - The object isa Bio::PopGen::Statistics
ok 5 - The object isa Bio::SimpleAlign
ok 6 - The object isa Bio::PopGen::Population
ok 7 - Marker Names
ok 8 - Number of Inds
ok 9 - number of ingroup sequences
ok 10 - number of outgroup1 sequences
ok 11 - number of outgroup2 sequences
ok 12 - NSpoly
ok 13 - NSfixed
ok 14 - Spoly
ok 15 - Sfixed
ok 16 - McDonald Kreitman
ok 17 - NSpoly
ok 18 - NSfixed
ok 19 - Spoly
ok 20 - Sfixed
ok 21 - McDonald Kreitman
ok 22 - NSpoly
ok 23 - NSfixed
ok 24 - Spoly
ok 25 - Sfixed
ok 26 - The object isa Bio::SimpleAlign
ok 27 - The object isa Bio::PopGen::Population
ok 28 - Marker Names
ok 29 - Number of Inds
ok 30 - number of ingroup sequences
ok 31 - number of outgroup1 sequences
ok 32 - number of outgroup2 sequences
ok 33 - NSpoly
ok 34 - NSfixed
ok 35 - Spoly
ok 36 - Sfixed
ok 37 - McDonald Kreitman
ok 38 - NSpoly
ok 39 - NSfixed
ok 40 - Spoly
ok 41 - Sfixed
ok 42 - McDonald Kreitman
ok 43 - NSpoly
ok 44 - NSfixed
ok 45 - Spoly
ok 46 - Sfixed
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/PopGen/PopGen.t ............................
1..100
ok 1 - use Bio::PopGen::Individual;
ok 2 - use Bio::PopGen::Genotype;
ok 3 - use Bio::PopGen::Population;
ok 4 - use Bio::PopGen::IO;
ok 5 - use Bio::PopGen::PopStats;
ok 6 - use Bio::AlignIO;
ok 7 - use Bio::PopGen::Statistics;
ok 8 - use Bio::PopGen::Utilities;
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - mrsa,mssa aflp1
ok 38 - all pops, aflp1
ok 39 - mrsa,envpop aflp1,aflp2
ok 40
ok 41
ok 42
ok 43 - mssa,mrsa all_bands
ok 44 - env,mssa mkr1
ok 45 - env,mssa,mrsa all bands
ok 46 - env,mssa,mrsa mkr2
ok 47 - mrsa,nc all_bands
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99 - Pi on 3-allele data
ok 100 - Theta on 3-allele data
ok
t/PopGen/PopGenSims.t ........................
1..23
ok 1 - use Bio::PopGen::Simulation::GeneticDrift;
ok 2 - Allele freqs should sum to 1
ok 3 - Allele freqs should sum to 1
ok 4 - Allele freqs should sum to 1
ok 5 - Allele freqs should sum to 1
ok 6 - Allele freqs should sum to 1
ok 7 - Allele freqs should sum to 1
ok 8 - Allele freqs should sum to 1
ok 9 - Allele freqs should sum to 1
ok 10 - Allele freqs should sum to 1
ok 11 - Allele freqs should sum to 1
ok 12
ok 13 - All frequencies should be <= 1
ok 14 - Allele freqs should sum to 1
ok 15 - Allele freqs should sum to 1
ok 16 - Allele freqs should sum to 1
ok 17 - Allele freqs should sum to 1
ok 18 - Allele freqs should sum to 1
ok 19 - Allele freqs should sum to 1
ok 20 - Allele freqs should sum to 1
ok 21 - Allele freqs should sum to 1
ok 22 - Allele freqs should sum to 1
ok 23 - Allele freqs should sum to 1
ok
t/PopGen/TagHaplotype.t ......................
1..3
ok 1 - use Bio::PopGen::TagHaplotype;
ok 2
ok 3
ok
t/RemoteDB/BioFetch.t ........................ skipped: Network tests have not been requested
Replacement list is longer than search list at Bio/Range.pm line 251.
t/RemoteDB/CUTG.t ............................
1..37
ok 1 - use Bio::DB::CUTG;
ok 2 - use Bio::CodonUsage::Table;
ok 3 - use Bio::CodonUsage::IO;
ok 4 - use Bio::SeqIO;
ok 5 - use Bio::Tools::SeqStats;
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24 # skip Network tests have not been requested
ok 25 # skip Network tests have not been requested
ok 26 # skip Network tests have not been requested
ok 27 # skip Network tests have not been requested
ok 28 # skip Network tests have not been requested
ok 29 # skip Network tests have not been requested
ok 30 # skip Network tests have not been requested
ok 31 # skip Network tests have not been requested
ok 32 # skip Network tests have not been requested
ok 33 # skip Network tests have not been requested
ok 34 # skip Network tests have not been requested
ok 35 # skip Network tests have not been requested
ok 36 # skip Network tests have not been requested
ok 37 # skip Network tests have not been requested
ok
t/RemoteDB/EMBL.t ............................ skipped: Network tests have not been requested
t/RemoteDB/EUtilities.t ...................... skipped: Network tests have not been requested
t/RemoteDB/EntrezGene.t ...................... skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed
t/RemoteDB/GenBank.t ......................... skipped: Network tests have not been requested
t/RemoteDB/GenPept.t ......................... skipped: Network tests have not been requested
t/RemoteDB/HIV/HIV.t .........................
1..30
ok 1 - use Bio::DB::HIV;
ok 2 - use Bio::DB::WebDBSeqI;
ok 3 - use Bio::DB::HIV::HIVAnnotProcessor;
ok 4 - The object isa Bio::DB::HIV
ok 5 - The object isa Bio::Root::Root
ok 6 - Bio::DB::HIV->can(...)
ok 7 - Bio::DB::HIV->can(...)
ok 8 - Bio::DB::HIV->can(...)
ok 9 - lanl_base set in default object
ok 10 - map_db set in default object
ok 11 - make_search_if set in default object
ok 12 - search_ set in default object
ok 13 - url_base_address set in default object
ok 14 - default sequence request format (fasta)
ok 15 - sorry till implemented
ok 16 - sorry till implemented
ok 17 - HIVQuery type exception check
ok 18 # skip Network tests have not been requested
ok 19 # skip Network tests have not been requested
ok 20 # skip Network tests have not been requested
ok 21 # skip Network tests have not been requested
ok 22 # skip Network tests have not been requested
ok 23 # skip Network tests have not been requested
ok 24 # skip Network tests have not been requested
ok 25 # skip Network tests have not been requested
ok 26 # skip Network tests have not been requested
ok 27 # skip Network tests have not been requested
ok 28 # skip Network tests have not been requested
ok 29 # skip Network tests have not been requested
ok 30 # skip Network tests have not been requested
ok
Replacement list is longer than search list at /home/fly1800/var/cpan/build/BioPerl-1.6.1-OeFNmD/blib/lib/Bio/Range.pm line 251.
t/RemoteDB/HIV/HIVAnnotProcessor.t ...........
1..11
ok 1 - use Bio::Seq;
ok 2 - use Bio::SeqIO;
ok 3 - use Bio::DB::HIV::HIVAnnotProcessor;
ok 4 - The object isa Bio::DB::HIV::HIVAnnotProcessor
ok 5 - The object isa Bio::Root::Root
ok 6 - Bio::DB::HIV::HIVAnnotProcessor->can(...)
ok 7 - Bio::DB::HIV::HIVAnnotProcessor->can('hiv_query')
ok 8 - bad type set exception
ok 9 - attach stream
ok 10 - write exception
ok 11 - access stream
ok
Use of uninitialized value $rest[0] in join or string at (eval 106) line 15.
t/RemoteDB/HIV/HIVQuery.t ....................
1..41
ok 1 - use Bio::DB::Query::HIVQuery;
ok 2 - use Bio::DB::HIV;
ok 3 - use Bio::Annotation::Collection;
ok 4 - use Bio::Annotation::Comment;
ok 5 - use Bio::Annotation::Reference;
ok 6 - use Bio::DB::HIV::HIVQueryHelper;
ok 7 - The object isa Bio::DB::Query::HIVQuery
ok 8 - The object isa Bio::Root::Root
ok 9 - Bio::DB::Query::HIVQuery->can(...)
ok 10 - Bio::DB::Query::HIVQuery->can(...)
ok 11 - Bio::DB::Query::HIVQuery->can(...)
ok 12 - _map_db_uri set in default object
ok 13 - _make_search_if_uri set in default object
ok 14 - _search_uri set in default object
ok 15 - _schema_file set in default object
ok 16 - _run_option set in default object
ok 17 - annotations container available
ok 18 - query syntax check 1
ok 19 - query syntax check 2
ok 20 - query syntax check 3
ok 21 - query parser check
ok 22 - multiquery parse check
ok 23 - use HTML::Parser;
ok 24 - help html to file
ok 25 - help html parsed
ok 26 - bad field exception check
ok 27 - bad match data exception check
ok 28 - empty field not ok exception check
ok 29 - uninitialized schema exception check
ok 30 - query not run (level 1) warning check
ok 31 - query not run (level 2) warning check
ok 32 # skip Network tests have not been requested
ok 33 # skip Network tests have not been requested
ok 34 # skip Network tests have not been requested
ok 35 # skip Network tests have not been requested
ok 36 # skip Network tests have not been requested
ok 37 # skip Network tests have not been requested
ok 38 # skip Network tests have not been requested
ok 39 # skip Network tests have not been requested
ok 40 # skip Network tests have not been requested
ok 41 # skip Network tests have not been requested
ok
t/RemoteDB/HIV/HIVQueryHelper.t ..............
1..40
ok 1 - use Bio::DB::HIV::HIVQueryHelper;
ok 2 - The object isa HIVSchema
ok 3 - The object isa QRY
ok 4 - The object isa R
ok 5 - The object isa Q
ok 6 - schema load
ok 7 - HIVSchema->can(...)
ok 8 - fields complete
ok 9 - tables complete
ok 10 - aliases complete
ok 11
ok 12 - test field syntax ok
ok 13 - test field syntax ok
ok 14 - test alias by field name
ok 15 - correct primary key for SequenceEntry
ok 16 - correct number of foreign keys for AUthor
ok 17 - correct foreign table for au_pub_id
ok 18 - correct annotation key hash
ok 19 - QRY->can(...)
ok 20 - R->can(...)
ok 21 - Q->can(...)
ok 22 - null QRY
ok 23 - null R (request object)
ok 24 - null Q (atomic query object)
ok 25 - R obj create and init (1)
ok 26 - R obj create and init (2)
ok 27 - R::In
ok 28 - !R::In
ok 29 - R::Eq
ok 30 - QRY obj create and init (1)
ok 31 - QRY obj create and init (2)
ok 32 - QRY obj create and init (3)
ok 33 - QRY overload |
ok 34 - QRY overload &
ok 35 - QRY nontrivial &
ok 36 - parse: ('odds bodkins', a)[X] m[Y] u[Z] OR 'b'[X] {A B [C] [D]}
ok 37 - make: 2 queries returned
ok 38 - {annotation fields} parsed correctly
ok 39 - parse: ('odds bodkins', a)[X] m[Y] u[Z] AND b[X] {A B [C] [D]}
ok 40 - above query is null
ok
t/RemoteDB/MeSH.t ............................ skipped: Network tests have not been requested
t/RemoteDB/Query/GenBank.t ................... skipped: Network tests have not been requested
t/RemoteDB/RefSeq.t ..........................
1..16
ok 1 - use Bio::DB::RefSeq;
ok 2 - use Bio::DB::GenBank;
ok 3 - use Bio::DB::EMBL;
ok 4
ok 5
ok 6
ok 7 # skip Network tests have not been requested
ok 8 # skip Network tests have not been requested
ok 9 # skip Network tests have not been requested
ok 10 # skip Network tests have not been requested
ok 11 # skip Network tests have not been requested
ok 12 # skip Network tests have not been requested
ok 13 # skip Network tests have not been requested
ok 14 # skip Network tests have not been requested
ok 15 # skip Network tests have not been requested
ok 16 # skip Network tests have not been requested
ok
t/RemoteDB/SeqHound.t ........................ skipped: Network tests have not been requested
t/RemoteDB/SeqRead_fail.t .................... skipped: Network tests have not been requested
t/RemoteDB/SeqVersion.t ......................
1..10
ok 1 - use Bio::DB::SeqVersion;
ok 2
ok 3 # skip Network tests have not been requested
ok 4 # skip Network tests have not been requested
ok 5 # skip Network tests have not been requested
ok 6 # skip Network tests have not been requested
ok 7 # skip Network tests have not been requested
ok 8 # skip Network tests have not been requested
ok 9 # skip Network tests have not been requested
ok 10 # skip Network tests have not been requested
ok
t/RemoteDB/SwissProt.t ....................... skipped: Network tests have not been requested
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/RemoteDB/Taxonomy.t ........................
1..103
ok 1 - use Bio::DB::Taxonomy;
ok 2 - use Bio::Tree::Tree;
ok 3
ok 4
ok 5 # skip Network tests have not been requested
ok 6 # skip Network tests have not been requested
ok 7 # skip Network tests have not been requested
ok 8 # skip Network tests have not been requested
ok 9 # skip Network tests have not been requested
ok 10 # skip Network tests have not been requested
ok 11 # skip Network tests have not been requested
ok 12 # skip Network tests have not been requested
ok 13 # skip Network tests have not been requested
ok 14 # skip Network tests have not been requested
ok 15 # skip Network tests have not been requested
ok 16 # skip Network tests have not been requested
ok 17 # skip Network tests have not been requested
ok 18 # skip Network tests have not been requested
ok 19 # skip Network tests have not been requested
ok 20 # skip Network tests have not been requested
ok 21 # skip Network tests have not been requested
ok 22 # skip Network tests have not been requested
ok 23 # skip Network tests have not been requested
ok 24 # skip Network tests have not been requested
ok 25 # skip Network tests have not been requested
ok 26 # skip Network tests have not been requested
ok 27 # skip Network tests have not been requested
ok 28 # skip Network tests have not been requested
ok 29 # skip Network tests have not been requested
ok 30 # skip Network tests have not been requested
ok 31 # skip Network tests have not been requested
ok 32 # skip Network tests have not been requested
ok 33 # skip Network tests have not been requested
ok 34 # skip Network tests have not been requested
ok 35 # skip Network tests have not been requested
ok 36 # skip Network tests have not been requested
ok 37 # skip Network tests have not been requested
ok 38 # skip Network tests have not been requested
ok 39 # skip Network tests have not been requested
ok 40 # skip Network tests have not been requested
ok 41 # skip Network tests have not been requested
ok 42 # skip Network tests have not been requested
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
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ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
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ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90 # skip Network tests have not been requested
ok 91 # skip Network tests have not been requested
ok 92 # skip Network tests have not been requested
ok 93 # skip Network tests have not been requested
ok 94 # skip Network tests have not been requested
ok 95
ok 96
ok 97
ok 98 # skip Network tests have not been requested
ok 99
ok 100
ok 101
ok 102
ok 103
ok
Replacement list is longer than search list at /home/fly1800/var/cpan/build/BioPerl-1.6.1-OeFNmD/blib/lib/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Restriction/EnzymeCollection.pm line 161.
Use of uninitialized value $opt in uc at Bio/Restriction/Analysis.pm line 369, line 4018.
Use of uninitialized value $opt in uc at Bio/Restriction/Analysis.pm line 369, line 4018.
t/Restriction/Analysis-refac.t ...............
1..29
ok 1 - use Bio::Restriction::IO;
ok 2 - use Bio::Restriction::Analysis;
ok 3 - read withrefm file
ok 4 - parse withrefm file
ok 5 - HindIII: nonambiguous intrasite cutter
ok 6 - AarI: nonambiguous extrasite cutter
ok 7 - AasI: ambiguous intrasite cutter
ok 8 - BceSI: ambiguous extrasite cutter
ok 9 - AjuI: cutter with central recog site
ok 10 - TaqII: multi-extrasite cutter
ok 11
ok 12 - HindIII plus
ok 13 - HindIII minus
ok 14 - AasI plus
ok 15 - AasI minus
ok 16 - AarI plus
ok 17 - AarI minus
ok 18 - BceSI plus
ok 19 - BceSI minus
ok 20 - AjuI plus
ok 21 - AjuI minus
ok 22 - TaqII plus
ok 23 - TaqII minus
ok 24 - build real B:R::Analysis object
ok 25 - 13 fragments
ok 26 - circularize
ok 27 - recut
ok 28 - circ: AasI
# site at origin
ok 29 - circ: still 13 fragments (cut site at origin)
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Restriction/EnzymeCollection.pm line 161.
Use of uninitialized value $opt in uc at Bio/Restriction/Analysis.pm line 369, line 1064.
Use of uninitialized value $opt in uc at Bio/Restriction/Analysis.pm line 369, line 1064.
t/Restriction/Analysis.t .....................
1..177
ok 1 - use Bio::Restriction::Enzyme;
ok 2 - use Bio::Restriction::Enzyme::MultiCut;
ok 3 - use Bio::Restriction::Enzyme::MultiSite;
ok 4 - use Bio::Restriction::EnzymeCollection;
ok 5 - use Bio::Restriction::Analysis;
ok 6 - use Bio::SeqIO;
ok 7
ok 8 - The object isa Bio::Restriction::EnzymeI
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16 - The object isa Bio::PrimarySeqI
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56 - bug 2179
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76 - The object isa Bio::Restriction::EnzymeI
ok 77 - The object isa Bio::Restriction::EnzymeI
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87 - The object isa Bio::Restriction::EnzymeI
ok 88 - The object isa Bio::Restriction::EnzymeI
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99 - The object isa Bio::Restriction::Enzyme
ok 100
ok 101
ok 102 - The object isa Bio::Restriction::Enzyme
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118 - number of unique cutters
ok 119 - number of RsaI fragments
ok 120 - number of maximum cutters
ok 121 - number of zero cutters
ok 122 - number of cutters
ok 123 - number of 3x cutters
ok 124 - 4 MseI fragments
ok 125 - 3 MseI cut sites
ok 126 - expected 2 PspEI fragments
ok 127
ok 128
ok 129 - expected 2 sizes for PspEI
ok 130
ok 131 - not circular expected 1 fragments for MwoI as it doesnt cut
ok 132
ok 133
ok 134 - number of RsaI fragments
ok 135 - 3 circular MseI fragments
ok 136 - 3 circular MseI cut sites
ok 137 - number for AciI a non-palindromic enzyme
ok 138 - 1 fragment for MwoI as it cuts across the circ point
ok 139
ok 140
ok 141
ok 142
ok 143 - 7 fragments in the multiple digest
ok 144 - 7 positions in the multiple digest
ok 145 - 7 sizes in the multiple digest
ok 146
ok 147 - expected 9 cuts for HindI
ok 148 - expect 9 fragment maps for HindI
ok 149 - sequence for GT
ok 150 - start at 40
ok 151 - end at 41
ok 152 - sequence for GGATTAAAAAAAGAGT
ok 153 - start at 42
ok 154 - end at 57
ok 155 - sequence for GTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGT
ok 156 - start at 58
ok 157 - end at 92
ok 158 - sequence for GAGTAAATTAAAATTTTATTGACTTAGGTCA
ok 159 - start at 93
ok 160 - end at 123
ok 161 - sequence for CTAAATACTTTAACCAATATAGGCATAGCGCA
ok 162 - start at 124
ok 163 - end at 155
ok 164 - sequence for CAGACAGATAAAAATTACAGAGTACA
ok 165 - start at 156
ok 166 - end at 181
ok 167 - sequence for CAACATCCATGAAACGCATTAGCA
ok 168 - start at 182
ok 169 - end at 205
ok 170 - sequence for CCA
ok 171 - start at 206
ok 172 - end at 208
ok 173 - sequence for CCAGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGT
ok 174 - start at 209
ok 175 - end at 39
ok 176
ok 177 - bug 2139
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Restriction/EnzymeCollection.pm line 161.
Use of uninitialized value $opt in uc at Bio/Restriction/Analysis.pm line 369, line 532.
t/Restriction/Gel.t ..........................
1..9
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::Restriction::Analysis;
ok 3 - use Bio::Tools::Gel;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Restriction/EnzymeCollection.pm line 161.
t/Restriction/IO.t ...........................
1..18
ok 1 - use Bio::Restriction::IO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
not ok 8 # TODO writing to a file doesn't seem to work? prints to STDOUT!
# Failed (TODO) test at t/Restriction/IO.t line 31.
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16 # skip Network tests have not been requested
ok 17 # skip Network tests have not been requested
ok 18 # skip Network tests have not been requested
ok
t/Root/Exception.t ...........................
1..8
ok 1 - use TestObject;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Root/RootI.t ...............................
1..56
ok 1 - use Bio::Root::Root;
ok 2 - use Bio::Seq;
ok 3
ok 4 - The object isa Bio::Root::RootI
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15 - simple
ok 16 - simple
ok 17 - warns for versions below current version 1.006001
ok 18 - warns for versions below current version 1.006001
ok 19 - throws for versions above 1.006001
ok 20 - throws for versions above 1.006001
ok 21 - throws for versions equal to 1.006001
ok 22 - simple
ok 23 - simple
ok 24 - warns for versions below current version 1.006001
ok 25 - warns for versions below current version 1.006001
ok 26 - throws for versions above 1.006001
ok 27 - throws for versions above 1.006001
ok 28 - arg callable since method was created
ok 29 - mal-formed arg callable since method was created with good name
ok 30 - Bio::Foo2->can('t3')
ok 31 - Methods don't pollute original Bio::Root::Root namespace
ok 32 - Bio::Foo2->can('test_4')
ok 33 - Methods don't pollute original Bio::Root::Root namespace
ok 34 - Bio::Foo3->can('t5')
ok 35 - arg not in method list not created
ok 36 - Bio::Foo3->can('t5')
ok 37 - Methods don't pollute original Bio::Root::Root namespace
ok 38 - verbose was set correctly
ok 39 - synonym was set correctly
ok 40 - real method of synonym was set correctly
ok 41 - mal-formed arg correctly resolved to created method
ok 42 - synonym of set method was set correctly
ok 43 - Bio::Foo4->can('t7')
ok 44 - Methods don't pollute original Bio::Root::Root namespace
ok 45 - Bio::Foo4->can('test7')
ok 46 - Methods don't pollute original Bio::Root::Root namespace
ok 47 - Bio::Foo4->can('test_8')
ok 48 - Methods don't pollute original Bio::Root::Root namespace
ok 49 - Bio::Foo4->can('t8')
ok 50 - Methods don't pollute original Bio::Root::Root namespace
ok 51 - must use proper versioning scheme
ok 52 - warns for versions >= 1.006001
ok 53 - warns for versions >= 1.006001
ok 54 - throws for versions >= 1.006001
ok 55 - throws for versions >= 1.006001
ok 56 - No warnings/exceptions below 1.006001
ok
t/Root/RootIO.t ..............................
1..31
ok 1 - use Bio::Root::IO;
ok 2
ok 3 - throw()
ok 4 - throw() verbose(-1)
ok 5 - warn()
ok 6 - throw() verbose(1)
ok 7 - stack_trace()
ok 8 - set verbosity to 1
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14 - filename, read
ok 15
ok 16 - filename, write
ok 17
ok 18
ok 19
ok 20 - handle, read
ok 21
ok 22 - handle, write
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30 # skip Network tests have not been requested
ok 31 # skip Network tests have not been requested
ok
t/Root/Storable.t ............................
1..35
ok 1 - use Bio::Root::Storable;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok
t/Root/Tempfile.t ............................
1..18
ok 1 - use Bio::Root::IO;
ok 2
ok 3 - The object isa Bio::Root::IO
ok 4
ok 5
ok 6 - auto UNLINK => 1
ok 7
ok 8
ok 9 - tempfile deleted
ok 10
ok 11 - UNLINK => 0
ok 12
ok 13
ok 14
ok 15 - tempfile suffix
ok 16
ok 17 - tempfile() in scalar context
ok 18
ok
--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gzip' found. Using /usr/bin/gzip.
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gzip' found. Using /usr/bin/gzip.
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gunzip' found. Using /usr/bin/gunzip.
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gzip' found. Using /usr/bin/gzip.
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gunzip' found. Using /usr/bin/gunzip.
---------------------------------------------------
t/Root/Utilities.t ...........................
1..56
ok 1 - use Bio::Root::Utilities;
ok 2 - The object isa Bio::Root::Utilities
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - file_date()
ok 38 - unix (\n or 012 or ^J)
ok 39 - date format
ok 40 - date format
ok 41 - date format
ok 42 - date format
ok 43 - date format
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok
t/SearchDist.t ............................... skipped: The optional module Bio::Ext::Align (or dependencies thereof) was not installed
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/CigarString.t .....................
1..4
ok 1 - use Bio::SearchIO;
ok 2
ok 3
ok 4
ok
t/SearchIO/SearchIO.t ........................
1..19
ok 1 - use Bio::SearchIO;
ok 2 - blast for filename.bls
ok 3 - fasta for f.m9
ok 4 - blast for f.blx
ok 5 - blast for filename.blast
ok 6 - fasta for f.fy
ok 7 - blast for f.tblx
ok 8 - exonerate for f.exon
ok 9 - blastxml for f.xml
ok 10 - fasta for f.fasta
ok 11 - fasta for f.ssearch
ok 12 - blastxml for f.blastxml
ok 13 - fasta for f.SSEARCH.m9
ok 14 - fasta for f.fa
ok 15 - fasta for f.fx
ok 16 - exonerate for f.exonerate
ok 17 - fasta for f.psearch
ok 18 - blast for fast.bls
ok 19 - fasta for f.osearch
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/SimilarityPair.t ..................
1..12
ok 1 - use Bio::SearchIO;
ok 2 - use Bio::SeqIO;
ok 3
ok 4 - The object isa Bio::SeqI
ok 5
ok 6 - The object isa Bio::SearchIO
ok 7
ok 8 - The object isa Bio::Search::Hit::HitI
ok 9
ok 10 - The object isa Bio::SeqFeatureI
ok 11
ok 12
ok
"my" variable $type masks earlier declaration in same statement at t/SearchIO/Tiling.t line 302.
"my" variable $est masks earlier declaration in same scope at t/SearchIO/Tiling.t line 307.
"my" variable $fast masks earlier declaration in same scope at t/SearchIO/Tiling.t line 307.
"my" variable $type masks earlier declaration in same scope at t/SearchIO/Tiling.t line 307.
"my" variable $est masks earlier declaration in same statement at t/SearchIO/Tiling.t line 307.
"my" variable $fast masks earlier declaration in same statement at t/SearchIO/Tiling.t line 307.
"my" variable $dpct masks earlier declaration in same scope at t/SearchIO/Tiling.t line 308.
"my" variable $est masks earlier declaration in same scope at t/SearchIO/Tiling.t line 308.
"my" variable $fast masks earlier declaration in same scope at t/SearchIO/Tiling.t line 308.
"my" variable $tiling masks earlier declaration in same scope at t/SearchIO/Tiling.t line 308.
"my" variable $type masks earlier declaration in same scope at t/SearchIO/Tiling.t line 308.
"my" variable $context masks earlier declaration in same scope at t/SearchIO/Tiling.t line 308.
"my" variable $est masks earlier declaration in same scope at t/SearchIO/Tiling.t line 309.
"my" variable $fast masks earlier declaration in same scope at t/SearchIO/Tiling.t line 309.
"my" variable $type masks earlier declaration in same scope at t/SearchIO/Tiling.t line 309.
"my" variable $est masks earlier declaration in same statement at t/SearchIO/Tiling.t line 309.
"my" variable $fast masks earlier declaration in same statement at t/SearchIO/Tiling.t line 309.
"my" variable $dpct masks earlier declaration in same scope at t/SearchIO/Tiling.t line 316.
"my" variable $tiling masks earlier declaration in same scope at t/SearchIO/Tiling.t line 316.
"my" variable $type masks earlier declaration in same scope at t/SearchIO/Tiling.t line 316.
"my" variable $context masks earlier declaration in same scope at t/SearchIO/Tiling.t line 316.
"my" variable $exact masks earlier declaration in same scope at t/SearchIO/Tiling.t line 317.
"my" variable $est masks earlier declaration in same scope at t/SearchIO/Tiling.t line 317.
"my" variable $exact masks earlier declaration in same statement at t/SearchIO/Tiling.t line 317.
"my" variable $type masks earlier declaration in same scope at t/SearchIO/Tiling.t line 318.
"my" variable $exact masks earlier declaration in same statement at t/SearchIO/Tiling.t line 318.
"my" variable $est masks earlier declaration in same statement at t/SearchIO/Tiling.t line 318.
"my" variable $exact masks earlier declaration in same scope at t/SearchIO/Tiling.t line 319.
"my" variable $max masks earlier declaration in same scope at t/SearchIO/Tiling.t line 319.
"my" variable $type masks earlier declaration in same scope at t/SearchIO/Tiling.t line 320.
"my" variable $exact masks earlier declaration in same statement at t/SearchIO/Tiling.t line 320.
"my" variable $max masks earlier declaration in same statement at t/SearchIO/Tiling.t line 320.
"my" variable $dpct masks earlier declaration in same scope at t/SearchIO/Tiling.t line 322.
"my" variable $est masks earlier declaration in same scope at t/SearchIO/Tiling.t line 322.
"my" variable $fast masks earlier declaration in same scope at t/SearchIO/Tiling.t line 322.
"my" variable $tiling masks earlier declaration in same scope at t/SearchIO/Tiling.t line 322.
"my" variable $type masks earlier declaration in same scope at t/SearchIO/Tiling.t line 322.
"my" variable $context masks earlier declaration in same scope at t/SearchIO/Tiling.t line 322.
"my" variable $dpct masks earlier declaration in same scope at t/SearchIO/Tiling.t line 325.
"my" variable $exact masks earlier declaration in same scope at t/SearchIO/Tiling.t line 325.
"my" variable $max masks earlier declaration in same scope at t/SearchIO/Tiling.t line 325.
"my" variable $tiling masks earlier declaration in same scope at t/SearchIO/Tiling.t line 325.
"my" variable $type masks earlier declaration in same scope at t/SearchIO/Tiling.t line 325.
"my" variable $context masks earlier declaration in same scope at t/SearchIO/Tiling.t line 325.
"my" variable $exact masks earlier declaration in same scope at t/SearchIO/Tiling.t line 326.
"my" variable $est masks earlier declaration in same scope at t/SearchIO/Tiling.t line 326.
"my" variable $exact masks earlier declaration in same statement at t/SearchIO/Tiling.t line 326.
"my" variable $tol masks earlier declaration in same scope at t/SearchIO/Tiling.t line 326.
"my" variable $type masks earlier declaration in same scope at t/SearchIO/Tiling.t line 327.
"my" variable $exact masks earlier declaration in same statement at t/SearchIO/Tiling.t line 327.
"my" variable $est masks earlier declaration in same statement at t/SearchIO/Tiling.t line 327.
"my" variable $exact masks earlier declaration in same scope at t/SearchIO/Tiling.t line 328.
"my" variable $max masks earlier declaration in same scope at t/SearchIO/Tiling.t line 328.
"my" variable $type masks earlier declaration in same scope at t/SearchIO/Tiling.t line 329.
"my" variable $exact masks earlier declaration in same statement at t/SearchIO/Tiling.t line 329.
"my" variable $max masks earlier declaration in same statement at t/SearchIO/Tiling.t line 329.
syntax error at t/SearchIO/Tiling.t line 301, near "$type qw( query hit )"
syntax error at t/SearchIO/Tiling.t line 334, near "}"
Execution of t/SearchIO/Tiling.t aborted due to compilation errors.
# Looks like your test exited with 255 before it could output anything.
t/SearchIO/Tiling.t ..........................
1..1093
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 1093/1093 subtests
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/Writer/GbrowseGFF.t ...............
1..4
ok 1 - use Bio::SearchIO;
ok 2
ok 3
ok 4
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Use of uninitialized value within @col_spec in lc at Bio/SearchIO/Writer/ResultTableWriter.pm line 211, line 353.
t/SearchIO/Writer/HSPTableWriter.t ...........
1..8
ok 1 - use Bio::SearchIO;
ok 2 - use Bio::SearchIO::Writer::HSPTableWriter;
ok 3 - The object isa Bio::Search::Result::ResultI
ok 4
ok 5
ok 6
ok 7 - The object isa Bio::Align::AlignI
ok 8
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/Writer/HTMLWriter.t ...............
1..8
ok 1 - use Bio::SearchIO;
ok 2 - use Bio::SearchIO::Writer::HTMLResultWriter;
ok 3 - The object isa Bio::Search::Result::ResultI
ok 4
ok 5
ok 6
ok 7 - The object isa Bio::Align::AlignI
ok 8
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Use of uninitialized value within @col_spec in lc at Bio/SearchIO/Writer/ResultTableWriter.pm line 211, line 353.
t/SearchIO/Writer/HitTableWriter.t ...........
1..8
ok 1 - use Bio::SearchIO;
ok 2 - use Bio::SearchIO::Writer::HitTableWriter;
ok 3 - The object isa Bio::Search::Result::ResultI
ok 4
ok 5
ok 6
ok 7 - The object isa Bio::Align::AlignI
ok 8
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/blast.t ...........................
1..1093
ok 1 - use Bio::SearchIO;
ok 2 - database_name()
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok 176
ok 177
ok 178
ok 179
ok 180
ok 181
ok 182
ok 183
ok 184
ok 185
ok 186
ok 187
ok 188
ok 189
ok 190
ok 191
ok 192
ok 193
ok 194
ok 195
ok 196
ok 197
ok 198
ok 199
ok 200
ok 201
ok 202
ok 203
ok 204
ok 205
ok 206
ok 207
ok 208
ok 209
ok 210
ok 211
ok 212
ok 213
ok 214
ok 215
ok 216
ok 217
ok 218
ok 219
ok 220
ok 221
ok 222
ok 223
ok 224
ok 225
ok 226
ok 227
ok 228
ok 229
ok 230
ok 231
ok 232
ok 233
ok 234
ok 235
ok 236
ok 237
ok 238
ok 239
ok 240
ok 241
ok 242
ok 243
ok 244
ok 245
ok 246
ok 247
ok 248
ok 249
ok 250
ok 251
ok 252
ok 253
ok 254
ok 255
ok 256
ok 257
ok 258
ok 259
ok 260
ok 261
ok 262
ok 263
ok 264
ok 265
ok 266
ok 267
ok 268
ok 269
ok 270
ok 271
ok 272
ok 273
ok 274
ok 275
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ok 277
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ok 280
ok 281
ok 282
ok 283
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ok 285
ok 286
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ok 289
ok 290
ok 291
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ok 293
ok 294
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ok 296
ok 297
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ok 299
ok 300
ok 301
ok 302
ok 303
ok 304
ok 305
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ok 321
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ok 324
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ok 332
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ok 335
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ok 341
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not ok 387 # TODO frac_identical & frac_conserved are still too wrong
# Failed (TODO) test at t/SearchIO/blast.t line 543.
# '0.852'
# >
# '0.9'
not ok 388 # TODO frac_identical & frac_conserved are still too wrong
# Failed (TODO) test at t/SearchIO/blast.t line 544.
# '1.599'
# <=
# '1'
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ok 561 - Multiblast query test
ok 562 - Multiblast query test
ok 563 - Multiblast query test
ok 564 - Multiblast query test
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ok 814 - The object isa Bio::Search::Result::ResultI
ok 815
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ok 820
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ok 829 - The object isa Bio::Search::Result::ResultI
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ok 848
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ok 865 - The object isa Bio::Search::Result::ResultI
ok 866
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ok 873
ok 874
ok 875
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ok 885 - The object isa Bio::Search::Result::ResultI
ok 886
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ok 896
ok 897
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ok 902
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ok 907 - The object isa Bio::Search::Result::ResultI
ok 908
ok 909
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ok 911
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ok 930 - The object isa Bio::Search::Result::ResultI
ok 931
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ok 941
ok 942
ok 943 - blast for filename.bls
ok 944 - blast for f.blx
ok 945 - blast for filename.blast
ok 946 - exonerate for f.exonerate
ok 947 - blastxml for f.xml
ok 948 - blastxml for f.blastxml
ok 949 - fasta for f.psearch
ok 950 - fasta for f.fa
ok 951 - fasta for f.osearch
ok 952 - blast for f.tblx
ok 953 - fasta for f.ssearch
ok 954 - fasta for f.fx
ok 955 - fasta for f.SSEARCH.m9
ok 956 - fasta for f.m9
ok 957 - fasta for f.fasta
ok 958 - exonerate for f.exon
ok 959 - fasta for f.fy
ok 960 - blast for fast.bls
ok 961
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ok 968
ok 969
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ok 971
ok 972
ok 973
ok 974 - full hit name
ok 975 - hit accession
ok 976
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ok 978 - query start
ok 979 - query start
ok 980
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Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/blast_pull.t ......................
1..289
ok 1 - use Bio::SearchIO;
ok 2
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not ok 191 # TODO frac_identical failing!
# Failed (TODO) test at t/SearchIO/blast_pull.t line 260.
# got: '0.946'
# expected: '0.943'
ok 192
ok 193
ok 194
ok 195
ok 196 - Multiblast query test
ok 197 - Multiblast query test
ok 198 - Multiblast query test
ok 199 - Multiblast query test
ok 200
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ok 203 - full hit name
ok 204 - hit accession
ok 205
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ok 207 - query start
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ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/blasttable.t ......................
1..163
ok 1 - use Bio::SearchIO;
ok 2 - use Bio::Search::SearchUtils;
ok 3 - The object isa Bio::Search::Result::ResultI
ok 4
ok 5
ok 6 - hit1_bits
ok 7 - hit1_name
ok 8 - hsp1_bits
ok 9 - hsp1_gaps
ok 10 - hsp1_he
ok 11 - hsp1_hs
ok 12 - hsp1_hstr
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ok 20 - hsp2_hstr
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ok 24 - hsp3_bits
ok 25 - hsp3_gaps
ok 26 - hsp3_he
ok 27 - hsp3_hs
ok 28 - hsp3_hstr
ok 29 - hsp3_qe
ok 30 - hsp3_qs
ok 31 - hsp3_qstr
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ok 33 - hsp4_gaps
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ok 36 - hsp4_hstr
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ok 38 - hsp4_qs
ok 39 - hsp4_qstr
ok 40 - hsp5_bits
ok 41 - hsp5_gaps
ok 42 - hsp5_he
ok 43 - hsp5_hs
ok 44 - hsp5_hstr
ok 45 - hsp5_qe
ok 46 - hsp5_qs
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ok 49 - hsp6_gaps
ok 50 - hsp6_he
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ok 52 - hsp6_hstr
ok 53 - hsp6_qe
ok 54 - hsp6_qs
ok 55 - hsp6_qstr
ok 56 - hsp7_bits
ok 57 - hsp7_gaps
ok 58 - hsp7_he
ok 59 - hsp7_hs
ok 60 - hsp7_hstr
ok 61 - hsp7_qe
ok 62 - hsp7_qs
ok 63 - hsp7_qstr
ok 64 - hsp8_bits
ok 65 - hsp8_gaps
ok 66 - hsp8_he
ok 67 - hsp8_hs
ok 68 - hsp8_hstr
ok 69 - hsp8_qe
ok 70 - hsp8_qs
ok 71 - hsp8_qstr
ok 72 - query_name
ok 73 - The object isa Bio::Search::Result::ResultI
ok 74
ok 75
ok 76 - hit1_bits
ok 77 - hit1_name
ok 78 - hsp1_bits
ok 79 - hsp1_gaps
ok 80 - hsp1_he
ok 81 - hsp1_hs
ok 82 - hsp1_hstr
ok 83 - hsp1_qe
ok 84 - hsp1_qs
ok 85 - hsp1_qstr
ok 86 - hsp2_bits
ok 87 - hsp2_gaps
ok 88 - hsp2_he
ok 89 - hsp2_hs
ok 90 - hsp2_hstr
ok 91 - hsp2_qe
ok 92 - hsp2_qs
ok 93 - hsp2_qstr
ok 94 - hsp3_bits
ok 95 - hsp3_gaps
ok 96 - hsp3_he
ok 97 - hsp3_hs
ok 98 - hsp3_hstr
ok 99 - hsp3_qe
ok 100 - hsp3_qs
ok 101 - hsp3_qstr
ok 102 - hsp4_bits
ok 103 - hsp4_gaps
ok 104 - hsp4_he
ok 105 - hsp4_hs
ok 106 - hsp4_hstr
ok 107 - hsp4_qe
ok 108 - hsp4_qs
ok 109 - hsp4_qstr
ok 110 - hsp5_bits
ok 111 - hsp5_gaps
ok 112 - hsp5_he
ok 113 - hsp5_hs
ok 114 - hsp5_hstr
ok 115 - hsp5_qe
ok 116 - hsp5_qs
ok 117 - hsp5_qstr
ok 118 - hsp6_bits
ok 119 - hsp6_gaps
ok 120 - hsp6_he
ok 121 - hsp6_hs
ok 122 - hsp6_hstr
ok 123 - hsp6_qe
ok 124 - hsp6_qs
ok 125 - hsp6_qstr
ok 126 - hsp7_bits
ok 127 - hsp7_gaps
ok 128 - hsp7_he
ok 129 - hsp7_hs
ok 130 - hsp7_hstr
ok 131 - hsp7_qe
ok 132 - hsp7_qs
ok 133 - hsp7_qstr
ok 134 - hsp8_bits
ok 135 - hsp8_gaps
ok 136 - hsp8_he
ok 137 - hsp8_hs
ok 138 - hsp8_hstr
ok 139 - hsp8_qe
ok 140 - hsp8_qs
ok 141 - hsp8_qstr
ok 142 - query_name
ok 143
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ok 146
ok 147 - The object isa Bio::SeqFeatureI
ok 148
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ok 161
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ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/blastxml.t ........................
1..391
ok 1 - use Bio::SearchIO;
ok 2
ok 3 - The object isa Bio::Search::Result::ResultI
ok 4 - database_name()
ok 5 - query_name()
ok 6
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ok 29 - database_name()
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ok 60 - query name on HSP
ok 61 - query desc on HSP
ok 62 - hitname
ok 63 - hitdesc
ok 64
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ok 90 - The object isa Bio::Search::Hit::HitI
ok 91
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ok 168 - query name on HSP
ok 169 - query desc on HSP
ok 170 - hitname
ok 171 - hitdesc
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ok 214 - query name on HSP
ok 215 - query desc on HSP
ok 216 - hitname
ok 217 - hitdesc
ok 218
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Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/cross_match.t .....................
1..15
ok 1 - use Bio::SearchIO;
ok 2
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ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/erpin.t ...........................
1..91
ok 1 - use Bio::SearchIO;
ok 2 - The object isa Bio::Search::Result::ResultI
ok 3 - Result ERPIN
ok 4 - Result ERPIN reference
ok 5 - Result ERPIN version
ok 6 - Result parameters
ok 7 - Result statistics
ok 8 - Result entries
ok 9 - Result letters
ok 10 - Result database_name
ok 11 - Result num_hits
ok 12 - Result program_reference
ok 13 - Result query_accession
ok 14 - Result query_description
ok 15 - Result query_name
ok 16 - The object isa Bio::Search::Hit::HitI
ok 17 - Hit accession
ok 18 - Hit GI
ok 19 - Hit algorithm
ok 20 - Hit bits
ok 21 - Hit description
ok 22 - Hit length
ok 23 - Hit locus
ok 24 - Hit n
ok 25 - Hit name
ok 26 - Hit num_hsps
ok 27 - Hit overlap
ok 28 - Hit query_length
ok 29 - Hit rank
ok 30 - Hit raw_score
ok 31 - Hit score
ok 32
ok 33 - The object isa Bio::Search::HSP::HSPI
ok 34 - HSP algorithm
ok 35
ok 36 - The object isa Bio::SeqFeature::Similarity
ok 37 - The object isa Bio::SeqFeature::Similarity
ok 38 - HSP frame
ok 39 - HSP gaps
ok 40 - HSP hit isa Bio::SeqFeature::Similarity
ok 41 - HSP hit_string
ok 42 - HSP homology_string
ok 43 - HSP hsp_group
ok 44 - HSP hsp_length
ok 45 - HSP length
ok 46 - HSP links
ok 47 - HSP query isa Bio::SeqFeature::Similarity
ok 48 - HSP query_string
ok 49 - HSP range
ok 50 - HSP rank
ok 51
ok 52 - HSP expect
ok 53 - The object isa Bio::LocatableSeq
ok 54 - HSP seq_str
ok 55 - HSP start
ok 56 - HSP custom_score
ok 57 - HSP meta
ok 58
ok 59
ok 60 - HSP strand
ok 61
ok 62
ok 63 - ERPIN get_aln warning
ok 64 - The object isa Bio::Search::HSP::HSPI
ok 65 - HSP algorithm
ok 66
ok 67 - The object isa Bio::SeqFeature::Similarity
ok 68 - The object isa Bio::SeqFeature::Similarity
ok 69 - HSP frame
ok 70 - HSP gaps
ok 71 - HSP hit isa Bio::SeqFeature::Similarity
ok 72 - HSP hit_string
ok 73 - HSP homology_string
ok 74 - HSP query_string
ok 75 - HSP hsp_group
ok 76 - HSP hsp_length
ok 77 - HSP length
ok 78 - HSP links
ok 79 - The object isa Bio::SeqFeature::Similarity
ok 80 - HSP range
ok 81 - HSP rank
ok 82
ok 83 - HSP end
ok 84 - HSP expect
ok 85 - The object isa Bio::LocatableSeq
ok 86 - HSP seq_str
ok 87 - HSP start
ok 88 - HSP custom_score
ok 89
ok 90
ok 91 - HSP strand
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/exonerate.t .......................
1..49
ok 1 - use Bio::SearchIO;
ok 2
ok 3 # skip no query length available in default output
ok 4
ok 5 # skip no hit length available in default output
ok 6
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ok 25 # skip no query length available in default output
ok 26
ok 27 # skip no hit length available in default output
ok 28
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ok 45
ok 46 - query_name
ok 47
ok 48 - query_name
ok 49
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/fasta.t ...........................
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ok 1 - use Bio::SearchIO;
ok 2
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ok 288 - num_identical()
ok 289 - num_conserved()
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/gmap_f9.t .........................
1..47
ok 1 - use Bio::SearchIO;
ok 2 - Did we get a Result? isa Bio::Search::Result::GenericResult
ok 3 - Did we get the expected number of hits?
ok 4 - Did we get the expected algorithm?
ok 5 - Did we get the expected query_name?
ok 6 - Did we get a Hit? isa Bio::Search::Hit::GenericHit
ok 7 - The object isa Bio::Search::Hit::HitI
ok 8 - Check the name
ok 9 - Check the hit length
ok 10 - Check the number of hsps
ok 11 - The object isa Bio::Search::HSP::HSPI
ok 12 - Check the algorithm
ok 13 - Count gaps in the query
ok 14 - Count gaps in the hit
ok 15 - Length of the query
ok 16 - Length of the hit
ok 17 - Query sequence
ok 18 - Hit sequence
ok 19 - Check query start
ok 20 - Check query end
ok 21 - Check query end
ok 22 - Check hit start
ok 23 - Check hit end
ok 24 - Check hit end
ok 25 - Did we get a Result? isa Bio::Search::Result::GenericResult
ok 26 - Did we get the expected number of hits?
ok 27 - Did we get the expected algorithm?
ok 28 - Did we get the expected query_name?
ok 29 - The object isa Bio::Search::Hit::HitI
ok 30 - Check the name
ok 31 - Check the hit length
ok 32 - Check the number of hsps
ok 33 - The object isa Bio::Search::HSP::HSPI
ok 34 - Check the algorithm
ok 35 - Count gaps in the query
ok 36 - Count gaps in the hit
ok 37 - Length of the query
ok 38 - Length of the hit
ok 39 - Query sequence
ok 40 - Hit sequence
ok 41 - Check query start
ok 42 - Check query end
ok 43 - Check query end
ok 44 - Check hit start
ok 45 - Check hit end
ok 46 - Check hit end
ok 47 - Can we loop over multiple results properly (expecting 58)?
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/hmmer.t ...........................
1..116
ok 1 - use Bio::SearchIO;
ok 2
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ok 4
ok 5
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ok 7
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ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/hmmer_pull.t ......................
1..290
ok 1 - use Bio::SearchIO;
ok 2
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ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/infernal.t ........................
1..412
ok 1 - use Bio::SearchIO;
ok 2 - The object isa Bio::Search::Result::ResultI
ok 3 - Result
ok 4 - Result reference
ok 5 - Result version
ok 6 - Result parameters
ok 7 - Result statistics
ok 8 - Result entries
ok 9 - Result letters
ok 10 - Result database_name
ok 11 - Result num_hits
ok 12 - Result program_reference
ok 13 - Result query_accession
ok 14 - Result query_description
ok 15 - Result query_length
ok 16 - Result query_name
ok 17 - The object isa Bio::Search::Hit::HitI
ok 18 - Hit GI
ok 19 - Hit accession
ok 20 - Hit algorithm
ok 21 - Hit bits
ok 22 - Hit description
ok 23 - Hit locus
ok 24 - Hit n
ok 25 - Hit name
ok 26 - Hit num_hsps
ok 27 - Hit length_aln() not implemented
ok 28 - Hit num_unaligned_hit() not implemented
ok 29 - Hit num_unaligned_query() not implemented
ok 30 - Hit num_unaligned_sbjct() not implemented
ok 31 - Hit start not implemented
ok 32 - Hit end not implemented
ok 33 - Hit strand not implemented
ok 34 - Hit logical_length not implemented
ok 35 - Hit frac_aligned_hit not implemented
ok 36 - Hit frac_aligned_query not implemented
ok 37 - Hit frac_conserved not implemented
ok 38 - Hit frac_identical not implemented
ok 39 - Hit matches not implemented
ok 40 - Hit gaps not implemented
ok 41 - Hit frame not implemented
ok 42 - Hit range not implemented
ok 43 - Hit seq_inds not implemented
ok 44 - Hit length
ok 45 - Hit overlap
ok 46 - Hit query_length
ok 47 - Hit rank
ok 48 - Hit raw_score
ok 49 - Hit score
ok 50 - Hit p
ok 51
ok 52 - The object isa Bio::Search::HSP::HSPI
ok 53 - HSP algorithm
ok 54
ok 55 - The object isa Bio::SeqFeature::Similarity
ok 56 - The object isa Bio::SeqFeature::Similarity
ok 57
ok 58
ok 59 - HSP frame
ok 60 - HSP gaps
ok 61 - Hit length
ok 62 - The object isa Bio::Align::AlignI
ok 63 - HSP hit isa Bio::SeqFeature::Similarity
ok 64 - HSP hit_string
ok 65 - HSP homology_string
ok 66 - HSP hsp_group
ok 67 - HSP hsp_length
ok 68 - HSP length
ok 69 - HSP links
ok 70 - HSP n
ok 71 - HSP pvalue
ok 72 - HSP query isa Bio::SeqFeature::Similarity
ok 73 - HSP query_string
ok 74 - HSP range
ok 75 - HSP rank
ok 76
ok 77 - HSP end
ok 78 - HSP expect
ok 79 - HSP seq_inds not implemented
ok 80 - HSP matches not implemented
ok 81 - HSP frac_conserved not implemented
ok 82 - HSP frac_identical not implemented
ok 83 - HSP num_conserved not implemented
ok 84 - HSP num_identical not implemented
ok 85 - HSP percent_identity not implemented
ok 86 - HSP cigar_string not implemented
ok 87 - HSP cigar_string not implemented
ok 88 - The object isa Bio::LocatableSeq
ok 89 - HSP seq_str
ok 90 - HSP start
ok 91 - HSP custom_score
ok 92 - HSP meta
ok 93 - HSP strand
ok 94 - The object isa Bio::Search::HSP::HSPI
ok 95 - HSP algorithm
ok 96
ok 97 - The object isa Bio::SeqFeature::Similarity
ok 98 - The object isa Bio::SeqFeature::Similarity
ok 99 - HSP frame
ok 100 - HSP gaps
ok 101 - The object isa Bio::Align::AlignI
ok 102 - HSP hit isa Bio::SeqFeature::Similarity
ok 103 - HSP hit_string
ok 104 - HSP homology_string
ok 105 - HSP hsp_group
ok 106 - HSP hsp_length
ok 107 - HSP length
ok 108 - HSP links
ok 109 - HSP n
ok 110 - HSP pvalue
ok 111 - HSP query isa Bio::SeqFeature::Similarity
ok 112 - HSP query_string
ok 113 - HSP range
ok 114 - HSP rank
ok 115
ok 116 - HSP end
ok 117 - HSP expect
ok 118 - The object isa Bio::LocatableSeq
ok 119 - HSP seq_str
ok 120 - HSP start
ok 121 - HSP custom_score
ok 122 - HSP meta
ok 123 - HSP strand
ok 124 - The object isa Bio::Search::Result::ResultI
ok 125 - Result CMSEARCH
ok 126 - Result CMSEARCH reference
ok 127 - Result CMSEARCH version
ok 128 - Result parameters
ok 129 - Result statistics
ok 130 - Result entries
ok 131 - Result letters
ok 132 - Result database_name
ok 133 - Result num_hits
ok 134 - Result program_reference
ok 135 - Result query_accession
ok 136 - Result query_description
ok 137 - Result query_length
ok 138 - Result query_name
ok 139 - The object isa Bio::Search::Hit::HitI
ok 140 - Hit GI
ok 141 - Hit accession
ok 142 - Hit algorithm
ok 143 - Hit bits
ok 144 - Hit description
ok 145 - Hit locus
ok 146 - Hit n
ok 147 - Hit name
ok 148 - Hit num_hsps
ok 149 - No p values
ok 150 - Hit length
ok 151 - Hit overlap
ok 152 - Hit query_length
ok 153 - Hit rank
ok 154 - Hit raw_score
ok 155 - Hit score
ok 156
ok 157 - The object isa Bio::Search::HSP::HSPI
ok 158 - HSP algorithm
ok 159
ok 160 - The object isa Bio::SeqFeature::Similarity
ok 161 - The object isa Bio::SeqFeature::Similarity
ok 162
ok 163
ok 164 - HSP frame
ok 165 - HSP gaps
ok 166 - Hit length
ok 167 - The object isa Bio::Align::AlignI
ok 168 - HSP hit isa Bio::SeqFeature::Similarity
ok 169 - HSP hit_string
ok 170 - HSP homology_string
ok 171 - HSP hsp_group
ok 172 - HSP hsp_length
ok 173 - HSP length
ok 174 - HSP links
ok 175 - HSP n
ok 176 - HSP pvalue
ok 177 - HSP query isa Bio::SeqFeature::Similarity
ok 178 - HSP query_string
ok 179 - HSP range
ok 180 - HSP rank
ok 181
ok 182 - HSP end
ok 183 - HSP expect
ok 184 - The object isa Bio::LocatableSeq
ok 185 - HSP seq_str
ok 186 - HSP start
ok 187 - HSP custom_score
ok 188 - HSP meta
ok 189 - HSP strand
ok 190 - The object isa Bio::Search::HSP::HSPI
ok 191 - HSP algorithm
ok 192
ok 193 - The object isa Bio::SeqFeature::Similarity
ok 194 - The object isa Bio::SeqFeature::Similarity
ok 195 - HSP frame
ok 196 - HSP gaps
ok 197 - The object isa Bio::Align::AlignI
ok 198 - HSP hit isa Bio::SeqFeature::Similarity
ok 199 - HSP hit_string
ok 200 - HSP homology_string
ok 201 - HSP hsp_group
ok 202 - HSP hsp_length
ok 203 - HSP length
ok 204 - HSP links
ok 205 - HSP n
ok 206 - HSP pvalue
ok 207 - HSP query isa Bio::SeqFeature::Similarity
ok 208 - HSP query_string
ok 209 - HSP range
ok 210 - HSP rank
ok 211
ok 212 - HSP end
ok 213 - HSP expect
ok 214 - The object isa Bio::LocatableSeq
ok 215 - HSP seq_str
ok 216 - HSP start
ok 217 - HSP custom_score
ok 218 - HSP meta
ok 219 - HSP strand
ok 220 - The object isa Bio::Search::Hit::HitI
ok 221 - Hit accession
ok 222 - Hit GI
ok 223 - Hit algorithm
ok 224 - Hit bits
ok 225 - Hit description
ok 226 - Hit length
ok 227 - Hit locus
ok 228 - Hit n
ok 229 - Hit name
ok 230 - Hit num_hsps
ok 231 - Hit overlap
ok 232 - Hit query_length
ok 233 - Hit rank
ok 234 - Hit raw_score
ok 235 - Hit score
ok 236
ok 237 - The object isa Bio::Search::HSP::HSPI
ok 238 - HSP algorithm
ok 239
ok 240 - The object isa Bio::SeqFeature::Similarity
ok 241 - The object isa Bio::SeqFeature::Similarity
ok 242 - HSP frame
ok 243 - HSP gaps
ok 244 - The object isa Bio::Align::AlignI
ok 245 - HSP hit isa Bio::SeqFeature::Similarity
ok 246 - HSP hit_string
ok 247 - HSP homology_string
ok 248 - HSP hsp_group
ok 249 - HSP hsp_length
ok 250 - HSP length
ok 251 - HSP links
ok 252 - HSP n
ok 253 - HSP query isa Bio::SeqFeature::Similarity
ok 254 - HSP query_string
ok 255 - HSP range
ok 256 - HSP rank
ok 257
ok 258 - HSP end
ok 259 - HSP expect
ok 260 - The object isa Bio::LocatableSeq
ok 261 - HSP seq_str
ok 262 - HSP start
ok 263 - HSP custom_score
ok 264 - HSP meta
ok 265 - HSP strand
ok 266 - HSP meta gap bug
ok 267 - HSP meta
ok 268 - HSP meta
ok 269
ok 270
ok 271 - The object isa Bio::Search::Result::ResultI
ok 272 - Result CMSEARCH
ok 273 - Result CMSEARCH reference
ok 274 - Result CMSEARCH version
ok 275 - Result parameters
ok 276 - Result statistics
ok 277 - Result entries
ok 278 - Result letters
ok 279 - Result database_name
ok 280 - Result num_hits
ok 281 - Result program_reference
ok 282 - Result query_accession
ok 283 - Result query_description
ok 284 - Result query_length
ok 285 - Result query_name
ok 286 - The object isa Bio::Search::Hit::HitI
ok 287 - Hit GI
ok 288 - Hit accession
ok 289 - Hit algorithm
ok 290 - Hit bits
ok 291 - Hit description
ok 292 - Hit locus
ok 293 - Hit n
ok 294 - Hit name
ok 295 - Hit num_hsps
ok 296 - No p values
ok 297 - Hit length
ok 298 - Hit overlap
ok 299 - Hit query_length
ok 300 - Hit rank
ok 301 - Hit raw_score
ok 302 - Hit score
ok 303
ok 304 - The object isa Bio::Search::HSP::HSPI
ok 305 - HSP algorithm
ok 306
ok 307 - The object isa Bio::SeqFeature::Similarity
ok 308 - The object isa Bio::SeqFeature::Similarity
ok 309
ok 310
ok 311 - HSP frame
ok 312 - HSP gaps
ok 313 - Hit length
ok 314 - The object isa Bio::Align::AlignI
ok 315 - HSP hit isa Bio::SeqFeature::Similarity
ok 316 - HSP hit_string
ok 317 - HSP homology_string
ok 318 - HSP hsp_group
ok 319 - HSP hsp_length
ok 320 - HSP length
ok 321 - HSP links
ok 322 - HSP n
ok 323 - HSP pvalue
ok 324 - HSP query isa Bio::SeqFeature::Similarity
ok 325 - HSP query_string
ok 326 - HSP range
ok 327 - HSP rank
ok 328
ok 329 - HSP end
ok 330 - HSP expect
ok 331 - The object isa Bio::LocatableSeq
ok 332 - HSP seq_str
ok 333 - HSP start
ok 334 - HSP custom_score
ok 335 - HSP meta
ok 336 - HSP strand
ok 337 - The object isa Bio::Search::HSP::HSPI
ok 338 - HSP algorithm
ok 339
ok 340 - The object isa Bio::SeqFeature::Similarity
ok 341 - The object isa Bio::SeqFeature::Similarity
ok 342 - HSP frame
ok 343 - HSP gaps
ok 344 - The object isa Bio::Align::AlignI
ok 345 - HSP hit isa Bio::SeqFeature::Similarity
ok 346 - HSP hit_string
ok 347 - HSP homology_string
ok 348 - HSP hsp_group
ok 349 - HSP hsp_length
ok 350 - HSP length
ok 351 - HSP links
ok 352 - HSP n
ok 353 - HSP pvalue
ok 354 - HSP query isa Bio::SeqFeature::Similarity
ok 355 - HSP query_string
ok 356 - HSP range
ok 357 - HSP rank
ok 358
ok 359 - HSP end
ok 360 - HSP expect
ok 361 - The object isa Bio::LocatableSeq
ok 362 - HSP seq_str
ok 363 - HSP start
ok 364 - HSP custom_score
ok 365 - HSP meta
ok 366 - HSP strand
ok 367 - The object isa Bio::Search::Hit::HitI
ok 368 - Hit accession
ok 369 - Hit GI
ok 370 - Hit algorithm
ok 371 - Hit bits
ok 372 - Hit description
ok 373 - Hit length
ok 374 - Hit locus
ok 375 - Hit n
ok 376 - Hit name
ok 377 - Hit num_hsps
ok 378 - Hit overlap
ok 379 - Hit query_length
ok 380 - Hit rank
ok 381 - Hit raw_score
ok 382 - Hit score
ok 383
ok 384 - The object isa Bio::Search::HSP::HSPI
ok 385 - HSP algorithm
ok 386
ok 387 - The object isa Bio::SeqFeature::Similarity
ok 388 - The object isa Bio::SeqFeature::Similarity
ok 389 - HSP frame
ok 390 - HSP gaps
ok 391 - The object isa Bio::Align::AlignI
ok 392 - HSP hit isa Bio::SeqFeature::Similarity
ok 393 - HSP hit_string
ok 394 - HSP homology_string
ok 395 - HSP hsp_group
ok 396 - HSP hsp_length
ok 397 - HSP length
ok 398 - HSP links
ok 399 - HSP n
ok 400 - HSP query isa Bio::SeqFeature::Similarity
ok 401 - HSP query_string
ok 402 - HSP range
ok 403 - HSP rank
ok 404
ok 405 - HSP end
ok 406 - HSP expect
ok 407 - The object isa Bio::LocatableSeq
ok 408 - HSP seq_str
ok 409 - HSP start
ok 410 - HSP custom_score
ok 411 - HSP meta
ok 412 - HSP strand
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/megablast.t .......................
1..31
ok 1 - use Bio::SearchIO;
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/psl.t .............................
1..53
ok 1 - use Bio::SearchIO;
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 - next_hsp should be undef
ok 51 - next_hit should be undef
not ok 52 - next_result should be undef # TODO next_result should really return undef, not empty string
# Failed (TODO) test 'next_result should be undef'
# at t/SearchIO/psl.t line 97.
# got: ''
# expected: undef
ok 53
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/rnamotif.t ........................
1..60
ok 1 - use Bio::SearchIO;
ok 2 - The object isa Bio::Search::Result::ResultI
ok 3 - Result RNAMOTIF
ok 4 - Result RNAMOTIF reference
ok 5 - Result RNAMOTIF version
ok 6 - Result entries
ok 7 - Result letters
ok 8 - Result database_name
ok 9 - Result num_hits
ok 10 - Result program_reference
ok 11 - Result query_accession
ok 12 - Result query_description
ok 13 - Result query_length
ok 14 - Result query_name
ok 15 - The object isa Bio::Search::Hit::HitI
ok 16 - Hit accession
ok 17 - Hit GI
ok 18 - Hit algorithm
ok 19 - Hit description
ok 20 - Hit length
ok 21 - Hit locus
ok 22 - Hit n
ok 23 - Hit name
ok 24 - Hit num_hsps
ok 25 - Hit overlap
ok 26 - Hit rank
ok 27 - Hit raw_score
ok 28 - Hit score
ok 29
ok 30 - The object isa Bio::Search::HSP::HSPI
ok 31 - HSP algorithm
ok 32
ok 33 - The object isa Bio::SeqFeature::Similarity
ok 34 - The object isa Bio::SeqFeature::Similarity
ok 35 - HSP frame
ok 36 - HSP gaps
ok 37 - RNAMotif get_aln warning
ok 38 - HSP hit isa Bio::SeqFeature::Similarity
ok 39 - HSP hit_string
ok 40 - HSP homology_string
ok 41 - HSP hsp_group
ok 42 - HSP hsp_length
ok 43 - HSP length
ok 44 - HSP links
ok 45 - HSP n
ok 46 - HSP query isa Bio::SeqFeature::Similarity
ok 47 - HSP query_string
ok 48 - HSP range
ok 49 - HSP rank
ok 50
ok 51 - HSP end
ok 52 - HSP expect
ok 53 - The object isa Bio::LocatableSeq
ok 54 - HSP seq_str
ok 55 - HSP start
ok 56 - HSP custom_score
ok 57 - HSP meta
ok 58 - HSP strand
ok 59
ok 60
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/sim4.t ............................
1..102
ok 1 - use Bio::SearchIO;
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
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ok 31
ok 32
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ok 51
ok 52
ok 53
ok 54
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ok 56
ok 57
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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
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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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/waba.t ............................
1..64
ok 1 - use Bio::SearchIO;
ok 2 - The object isa Bio::SearchIO
ok 3 - query_name
ok 4 - query database
ok 5 - database name
ok 6 - name
ok 7 - hsps
ok 8 - total length
ok 9 - start
ok 10 - end
ok 11 - strand
ok 12 - start
ok 13 - end
ok 14 - strand
ok 15 - query string
ok 16 - hit_string
ok 17 - hmmstate string
ok 18
ok 19
ok 20
ok 21 - total length
ok 22 - start
ok 23 - end
ok 24 - strand
ok 25 - start
ok 26 - end
ok 27 - strand
ok 28 - query string
ok 29 - hit_string
ok 30 - hmmstate string
ok 31
ok 32
ok 33
ok 34 - total length
ok 35 - start
ok 36 - end
ok 37 - strand
ok 38 - start
ok 39 - end
ok 40 - strand
ok 41 - query string
ok 42 - hit_string
ok 43 - hmmstate string
ok 44
ok 45
ok 46
ok 47 - query_name
ok 48 - query database
ok 49 - database name
ok 50 - name
ok 51 - hsps
ok 52 - total length
ok 53 - start
ok 54 - end
ok 55 - strand
ok 56 - start
ok 57 - end
ok 58 - strand
ok 59 - query string
ok 60 - hit_string
ok 61 - hmmstate string
ok 62
ok 63
ok 64
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SearchIO/wise.t ............................
1..20
ok 1 - use Bio::SearchIO;
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
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Seq/DBLink.t ...............................
1..131
ok 1 - use Bio::SeqIO;
ok 2 - "swissprot:K1C9_HUMAN"
ok 3 - no double colon
ok 4 - no trailing colon
ok 5 - no double space
ok 6 - dblink value is splittable
ok 7 - "GenBank:Z29074.1"
ok 8 - no double colon
ok 9 - no trailing colon
ok 10 - no double space
ok 11 - dblink value is splittable
ok 12 - "GenPept:CAA82315.1"
ok 13 - no double colon
ok 14 - no trailing colon
ok 15 - no double space
ok 16 - dblink value is splittable
ok 17 - "GenBank:S69510.1"
ok 18 - no double colon
ok 19 - no trailing colon
ok 20 - no double space
ok 21 - dblink value is splittable
ok 22 - "GenPept:AAC60619.1"
ok 23 - no double colon
ok 24 - no trailing colon
ok 25 - no double space
ok 26 - dblink value is splittable
ok 27 - "GenBank:X75015.1"
ok 28 - no double colon
ok 29 - no trailing colon
ok 30 - no double space
ok 31 - dblink value is splittable
ok 32 - "GenPept:CAA52924.1"
ok 33 - no double colon
ok 34 - no trailing colon
ok 35 - no double space
ok 36 - dblink value is splittable
ok 37 - "GenBank:AB001594.1"
ok 38 - no double colon
ok 39 - no trailing colon
ok 40 - no double space
ok 41 - dblink value is splittable
ok 42 - "GenPept:BAA19418.1"
ok 43 - no double colon
ok 44 - no trailing colon
ok 45 - no double space
ok 46 - dblink value is splittable
ok 47 - "GenBank:I37984"
ok 48 - no double colon
ok 49 - no trailing colon
ok 50 - no double space
ok 51 - dblink value is splittable
ok 52 - "HSSP:P08670"
ok 53 - no double colon
ok 54 - no trailing colon
ok 55 - no double space
ok 56 - dblink value is splittable
ok 57 - "IntAct:P35527"
ok 58 - no double colon
ok 59 - no trailing colon
ok 60 - no double space
ok 61 - dblink value is splittable
ok 62 - "Ensembl:ENSG00000171403"
ok 63 - no double colon
ok 64 - no trailing colon
ok 65 - no double space
ok 66 - dblink value is splittable
ok 67 - "KEGG:hsa:3857"
ok 68 - no double colon
ok 69 - no trailing colon
ok 70 - no double space
ok 71 - dblink value is splittable
ok 72 - "HGNC:6447"
ok 73 - no double colon
ok 74 - no trailing colon
ok 75 - no double space
ok 76 - dblink value is splittable
ok 77 - "MIM:144200"
ok 78 - no double colon
ok 79 - no trailing colon
ok 80 - no double space
ok 81 - dblink value is splittable
ok 82 - "MIM:607606"
ok 83 - no double colon
ok 84 - no trailing colon
ok 85 - no double space
ok 86 - dblink value is splittable
ok 87 - "ArrayExpress:P35527"
ok 88 - no double colon
ok 89 - no trailing colon
ok 90 - no double space
ok 91 - dblink value is splittable
ok 92 - "GO:0005200"
ok 93 - no double colon
ok 94 - no trailing colon
ok 95 - no double space
ok 96 - dblink value is splittable
ok 97 - "GO:0008544"
ok 98 - no double colon
ok 99 - no trailing colon
ok 100 - no double space
ok 101 - dblink value is splittable
ok 102 - "InterPro:IPR011000"
ok 103 - no double colon
ok 104 - no trailing colon
ok 105 - no double space
ok 106 - dblink value is splittable
ok 107 - "InterPro:IPR001664"
ok 108 - no double colon
ok 109 - no trailing colon
ok 110 - no double space
ok 111 - dblink value is splittable
ok 112 - "InterPro:IPR002957"
ok 113 - no double colon
ok 114 - no trailing colon
ok 115 - no double space
ok 116 - dblink value is splittable
ok 117 - "Pfam:PF00038"
ok 118 - no double colon
ok 119 - no trailing colon
ok 120 - no double space
ok 121 - dblink value is splittable
ok 122 - "PRINTS:PR01248"
ok 123 - no double colon
ok 124 - no trailing colon
ok 125 - no double space
ok 126 - dblink value is splittable
ok 127 - "PROSITE:PS00226"
ok 128 - no double colon
ok 129 - no trailing colon
ok 130 - no double space
ok 131 - dblink value is splittable
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Seq/EncodedSeq.t ...........................
1..37
ok 1 - use Bio::Seq::EncodedSeq;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11 - The object isa Bio::Location::Simple
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Seq/LargeLocatableSeq.t ....................
1..8
ok 1 - use Bio::Seq::LargeLocatableSeq;
ok 2
ok 3 - The object isa Bio::Seq::LargeSeqI
ok 4
ok 5
ok 6
ok 7
ok 8
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
t/Seq/LargePSeq.t ............................
1..30
ok 1 - use Bio::Seq::LargePrimarySeq;
ok 2 - use Bio::Seq::LargeSeq;
ok 3 - use Bio::Location::Simple;
ok 4 - use Bio::Location::Fuzzy;
ok 5 - use Bio::Location::Split;
ok 6 - use Bio::SeqIO;
ok 7
ok 8
ok 9 - Sequence is ATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAATGTTTGGGGTTAAACCCCTTTGGGGGGT
ok 10 - Subseq is GGGGT
ok 11
ok 12
ok 13
ok 14 - trunc seq was GGGGTGAA
ok 15
ok 16
ok 17
ok 18 - Sequence is ATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAATGTTTGGGGTTAAACCCCTTTGGGGGGT
ok 19
ok 20 - output via Bio::SeqIO::fasta
ok 21 - Subseq is GGGGT
ok 22 - trunc seq was GGGGTGAA
ok 23
ok 24
ok 25
ok 26 - Sequence is ATGGGGTGGGGT
ok 27 - Subseq is GGGGT
ok 28 - trunc seq was GGGGT
ok 29
ok 30
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Seq/LocatableSeq.t .........................
1..118
ok 1 - use Bio::LocatableSeq;
ok 2 - use Bio::AlignIO;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12 - The object isa Bio::Location::Simple
ok 13
ok 14
ok 15 - The object isa Bio::Location::Simple
ok 16
ok 17
ok 18
ok 19
not ok 20 # TODO Need to fix columns before start of seq w/ start > 1
# Failed (TODO) test at t/Seq/LocatableSeq.t line 45.
# got: 'Bio::Location::Simple=HASH(0x114312a8)'
# expected: undef
ok 21
ok 22 - The object isa Bio::AlignIO
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 - The object isa Bio::Location::Simple
ok 50
ok 51
ok 52 - The object isa Bio::Location::Simple
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 - * is counted in length
ok 106 - * is counted in length, but end is wrong
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
not ok 117 # TODO Bio::LocatableSeq global variables have scoping issues
# Failed (TODO) test at t/Seq/LocatableSeq.t line 301.
# got: '\-\.=~'
# expected: '-\?'
not ok 118 # TODO Bio::LocatableSeq global variables have scoping issues
# Failed (TODO) test at t/Seq/LocatableSeq.t line 303.
# got: '19'
# expected: anything else
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Seq/MetaSeq.t ..............................
1..128
ok 1 - use Bio::Seq::Meta;
ok 2 - use Bio::Seq::Meta::Array;
ok 3 - use Bio::SeqIO;
ok 4 - use Bio::AlignIO;
ok 5 - use Bio::Seq::Quality;
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 - aa-bb bb
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Seq/PrimaryQual.t ..........................
1..35
ok 1 - use Bio::SeqIO;
ok 2 - use Bio::Seq::Quality;
ok 3 - use Bio::Seq::PrimaryQual;
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
Replacement list is longer than search list at Bio/Range.pm line 251.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
t/Seq/PrimarySeq.t ...........................
1..62
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::Location::Simple;
ok 3 - use Bio::Location::Fuzzy;
ok 4 - use Bio::Location::Split;
ok 5
ok 6 - The object isa Bio::PrimarySeqI
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14 - The object isa Bio::IdentifiableI
ok 15 - The object isa Bio::DescribableI
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 - The object isa Bio::PrimarySeqI
ok 30
ok 31 - The object isa Bio::PrimarySeqI
ok 32
ok 33 - The object isa Bio::PrimarySeqI
ok 34
ok 35 - The object isa Bio::PrimarySeqI
ok 36
ok 37
ok 38 - alphabet copied through revcom
not ok 39 - namespace copied through revcom # TODO all attributes of primaryseqs are not currently copied through revcoms
# Failed (TODO) test 'namespace copied through revcom'
# at t/Seq/PrimarySeq.t line 109.
# got: ''
# expected: 't'
not ok 40 - namespace_string copied through revcom # TODO all attributes of primaryseqs are not currently copied through revcoms
# Failed (TODO) test 'namespace_string copied through revcom'
# at t/Seq/PrimarySeq.t line 110.
# got: ':X677667'
# expected: 't:X677667.47'
not ok 41 - is_circular copied through revcom # TODO all attributes of primaryseqs are not currently copied through revcoms
# Failed (TODO) test 'is_circular copied through revcom'
# at t/Seq/PrimarySeq.t line 112.
# got: undef
# expected: '0'
ok 42 - Translation: LVAST
ok 43 - Translation: MVAST
ok 44 - Translation: MVAST
ok 45 - Translation: MVAST*
ok 46 - Translation: M*
ok 47 - Translation: M
ok 48
ok 49 - Translation: MWP
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 - Bug \#2864
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Seq/PrimedSeq.t ............................
1..10
ok 1 - use Bio::SeqIO;
ok 2 - use Bio::Seq::PrimedSeq;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Seq/Quality.t ..............................
1..61
ok 1 - use Bio::Seq::Quality;
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
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Seq/Seq.t ..................................
1..62
ok 1 - use Bio::Seq;
ok 2 - use Bio::Seq::RichSeq;
ok 3 - use Bio::SeqFeature::Generic;
ok 4 - use Bio::Species;
ok 5 - use Bio::Annotation::SimpleValue;
ok 6
ok 7
ok 8
ok 9
ok 10 - truncated sequence length
ok 11 - truncated sequence string
ok 12
ok 13
ok 14 - alphabet
ok 15 - id
ok 16 - accession number
ok 17 - subseq
ok 18 - The object isa Bio::IdentifiableI
ok 19 - The object isa Bio::DescribableI
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 - translated sequence
ok 34 - translated sequence with unambiguous codons
ok 35 - translated sequence with unambiguous codons
ok 36 - translated sequence with unambiguous codons
ok 37 - translated sequence with unambiguous codons
ok 38 - translated sequence with unambiguous codons
ok 39 - translated sequence with unambigious 2 char codon
ok 40 - translated sequence with stop
ok 41 - translated sequence
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 - Bug \#2864
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Seq/WithQuality.t ..........................
1..22
ok 1 - use Bio::Seq::SeqWithQuality;
ok 2 - use Bio::PrimarySeq;
ok 3 - use Bio::Seq::PrimaryQual;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19 - The object isa Bio::Seq::PrimaryQual
ok 20 - The object isa Bio::PrimarySeq
ok 21
ok 22
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqEvolution.t .............................
1..39
ok 1 - use Bio::SeqEvolution::Factory;
ok 2 - use Bio::PrimarySeq;
ok 3
ok 4 - The object isa Bio::SeqEvolution::DNAPoint
ok 5
ok 6 - The object isa Bio::SeqEvolution::DNAPoint
ok 7
ok 8 - The object isa Bio::SeqEvolution::DNAPoint
ok 9
ok 10
ok 11 - get rate()
ok 12 - get and set rate()
ok 13 - identity()
ok 14 - identity()
ok 15 - pam()
ok 16 - pam()
ok 17 - mutation_count()
ok 18 - mutation_count()
ok 19 - seq_type()
ok 20 - seq_type()
ok 21 - next_seq()
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27 - each_mutation()
ok 28
ok 29
ok 30 - get_alignment_identity()
ok 31
ok 32
ok 33 - get_mutation_counter()
ok 34 - get_sequence_counter()
ok 35 - reset_sequence_counter()
ok 36 - get_sequence_counter() == 0
ok 37
ok 38
ok 39 - The object isa Bio::SimpleAlign
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
defined(@array) is deprecated at Bio/FeatureIO/gff.pm line 810.
(Maybe you should just omit the defined()?)
t/SeqFeature/FeatureIO.t .....................
1..35
ok 1 - use Bio::FeatureIO;
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 - vecscreen_simple gets the correct features
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
t/SeqFeature/Location.t ......................
1..103
ok 1 - use Bio::Location::Simple;
ok 2 - use Bio::Location::Split;
ok 3 - use Bio::Location::Fuzzy;
ok 4 - use Bio::SeqFeature::Generic;
ok 5 - use Bio::SeqFeature::SimilarityPair;
ok 6 - use Bio::SeqFeature::FeaturePair;
ok 7 - The object isa Bio::LocationI
ok 8 - The object isa Bio::RangeI
ok 9 - Bio::Location::Simple tests
ok 10
ok 11
ok 12
ok 13
ok 14 - Bio::SeqFeature::Generic isa Bio::SeqFeatureI
ok 15 - The object isa Bio::RangeI
ok 16
ok 17
ok 18 - Bio::SeqFeature::FeaturePair tests
ok 19
ok 20
ok 21
ok 22 - Bio::SeqFeature::Generic tests
ok 23
ok 24 - Bio::Location::Fuzzy tests
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 - Bio::Location::Split tests
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 - Bugfix 1074
ok 56
ok 57
ok 58
ok 59 - Positive length
ok 60
ok 61 - seq_id() on Bio::Location::Split
ok 62
ok 63
ok 64 - The object isa Bio::LocationI
ok 65 - The object isa Bio::RangeI
ok 66 - Bio::Location::Simple EXACT
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72 - Bio::Location::Simple IN-BETWEEN
ok 73
ok 74
ok 75
ok 76
ok 77 - Testing error handling
ok 78
ok 79
ok 80
ok 81 - use Bio::Location::WidestCoordPolicy;
ok 82 - use Bio::Location::NarrowestCoordPolicy;
ok 83 - use Bio::Location::AvWithinCoordPolicy;
ok 84 - Default coodinate policy
ok 85
ok 86
ok 87
ok 88 - The object isa Bio::Location::WidestCoordPolicy
ok 89 - Narrowest coodinate policy
ok 90
ok 91
ok 92
ok 93 - The object isa Bio::Location::NarrowestCoordPolicy
ok 94 - Average coodinate policy
ok 95
ok 96
ok 97
ok 98 - The object isa Bio::Location::AvWithinCoordPolicy
ok 99 - Widest coodinate policy
ok 100
ok 101
ok 102
ok 103 - The object isa Bio::Location::WidestCoordPolicy
ok
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
t/SeqFeature/LocationFactory.t ...............
1..272
ok 1 - use Bio::Factory::FTLocationFactory;
ok 2 - The object isa Bio::Factory::LocationFactoryI
ok 3 - Bio::Location::Fuzzy
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12 - Location String: <1..888
ok 13
ok 14 - Bio::Location::Fuzzy
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23 - Location String: complement(34..(122.126))
ok 24
ok 25 - Bio::Location::Fuzzy
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34 - Location String: 1..?
ok 35
ok 36 - Bio::Location::Fuzzy
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45 - Location String: (102.110)
ok 46
ok 47 - Bio::Location::Fuzzy
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56 - Location String: 145^177
ok 57
ok 58 - Bio::Location::Simple
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67 - Location String: 340..565
ok 68
ok 69 - Bio::Location::Fuzzy
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78 - Location String: <1..?
ok 79
ok 80 - Bio::Location::Simple
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89 - Location String: J00194:100..202
ok 90
ok 91 - Bio::Location::Split
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100 - Location String: complement(join(4918..5163,2691..4571))
ok 101
ok 102 - Bio::Location::Simple
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111 - Location String: 467
ok 112
ok 113 - Bio::Location::Fuzzy
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122 - Location String: ?..>393
ok 123
ok 124 - Bio::Location::Fuzzy
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133 - Location String: ?2465..2774
ok 134
ok 135 - Bio::Location::Fuzzy
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144 - Location String: <345..500
ok 145
ok 146 - Bio::Location::Simple
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155 - Location String: J00194:100..202
ok 156
ok 157 - Bio::Location::Split
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166 - Location String: join(AY016290.1:108..185,AY016291.1:1546..1599)
ok 167
ok 168 - Bio::Location::Split
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok 176
ok 177 - Location String: join(12..78,134..202)
ok 178
ok 179 - Bio::Location::Fuzzy
ok 180
ok 181
ok 182
ok 183
ok 184
ok 185
ok 186
ok 187
ok 188 - Location String: ?22..?64
ok 189
ok 190 - Bio::Location::Fuzzy
ok 191
ok 192
ok 193
ok 194
ok 195
ok 196
ok 197
ok 198
ok 199 - Location String: ?..?
ok 200
ok 201 - Bio::Location::Fuzzy
ok 202
ok 203
ok 204
ok 205
ok 206
ok 207
ok 208
ok 209
ok 210 - Location String: 22..?64
ok 211
ok 212 - Bio::Location::Fuzzy
ok 213
ok 214
ok 215
ok 216
ok 217
ok 218
ok 219
ok 220
ok 221 - Location String: (122.133)..(204.221)
ok 222
ok 223 - Bio::Location::Simple
ok 224
ok 225
ok 226
ok 227
ok 228
ok 229
ok 230
ok 231
ok 232 - Location String: 123^124
ok 233
ok 234 - Bio::Location::Fuzzy
ok 235
ok 236
ok 237
ok 238
ok 239
ok 240
ok 241
ok 242
ok 243 - Location String: (23.45)..600
ok 244
ok 245 - Bio::Location::Fuzzy
ok 246
ok 247
ok 248
ok 249
ok 250
ok 251
ok 252
ok 253
ok 254 - Location String: ?..536
ok 255
ok 256 - Bio::Location::Fuzzy
ok 257
ok 258
ok 259
ok 260
ok 261
ok 262
ok 263
ok 264
ok 265 - Location String: (122.133)..(204.221)
ok 266
ok 267 - join(11025..11049,join(complement(239890..240081),complement(241499..241580),complement(251354..251412),complement(315036..315294)))
ok 268 - join(11025..11049,complement(join(315036..315294,251354..251412,241499..241580,239890..240081)))
ok 269 - join(20464..20694,21548..22763,complement(join(314652..314672,232596..232990,231520..231669)))
ok 270 - join(20464..20694,21548..22763,join(complement(231520..231669),complement(232596..232990),complement(314652..314672)))
ok 271 - join(1000..2000,join(3000..4000,join(5000..6000,7000..8000)),9000..10000)
ok 272 - order(S67862.1:72..75,join(S67863.1:1..788,1..19))
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqFeature/Primer.t ........................
1..18
ok 1 - use Bio::SeqFeature::Primer;
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqFeature/Range.t .........................
1..49
ok 1 - use Bio::Range;
ok 2 - BioRange object isa Bio::Range
ok 3
ok 4 - BioRange object isa Bio::Range
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15 - BioRange object isa Bio::Range
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25 - BioRange object isa Bio::Range
ok 26 - BioRange object isa Bio::Range
ok 27 - BioRange object isa Bio::Range
ok 28 - 1 & -1
ok 29 - 1 & 1 true
ok 30 - 1 & 0 true
ok 31 - 1 & -1 false
ok 32 - 1 & 1 true
ok 33 - 1 & 0 false
ok 34 - 1 & -1 false
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45 - Bio::Range object isa Bio::Range
ok 46
ok 47
ok 48
ok 49
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqFeature/RangeI.t ........................
1..38
ok 1 - use Bio::SeqFeature::Generic;
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqFeature/SeqAnalysisParser.t .............
1..14
ok 1 - use Bio::Factory::SeqAnalysisParserFactory;
ok 2 - use Bio::SeqIO;
ok 3 - The object isa Bio::SeqIO
ok 4 - The object isa Bio::PrimarySeqI
ok 5 - The object isa Bio::SeqAnalysisParserI
ok 6
ok 7
ok 8
ok 9 - The object isa Bio::PrimarySeqI
ok 10 - The object isa Bio::SeqAnalysisParserI
ok 11
ok 12
ok 13 - The object isa Bio::SeqAnalysisParserI
ok 14
ok
t/SeqFeature/SeqFeatAnnotated.t .............. skipped: Network tests have not been requested
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/SeqFeature/SeqFeatCollection.t .............
1..24
ok 1 - use Bio::SeqFeature::Collection;
ok 2 - use Bio::Location::Simple;
ok 3 - use Bio::Tools::GFF;
ok 4 - use Bio::SeqIO;
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
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/SeqFeature/SeqFeature.t ....................
1..222
ok 1 - use Bio::Seq;
ok 2 - use Bio::SeqIO;
ok 3 - use Bio::SeqFeature::Generic;
ok 4 - use Bio::SeqFeature::FeaturePair;
ok 5 - use Bio::SeqFeature::Computation;
ok 6 - use Bio::SeqFeature::Gene::Transcript;
ok 7 - use Bio::SeqFeature::Gene::UTR;
ok 8 - use Bio::SeqFeature::Gene::Exon;
ok 9 - use Bio::SeqFeature::Gene::Poly_A_site;
ok 10 - use Bio::SeqFeature::Gene::GeneStructure;
ok 11 - use Bio::Location::Fuzzy;
ok 12 - start of feature location
ok 13 - end of feature location
ok 14 - primary tag
ok 15 - source tag
ok 16
ok 17
ok 18 - feature1 of pair stored
ok 19 - feature2 of pair stored
ok 20 - feature start
ok 21 - feature end
ok 22 - primary tag
ok 23 - source tag
ok 24 - hstart
ok 25 - hend
ok 26 - hprimary tag
ok 27 - hsource tag
ok 28 - inverted end
ok 29
ok 30 - seq string
ok 31 - sf1 end
ok 32 - sf1 start
ok 33
ok 34 - sf2
ok 35
ok 36 - computation id
ok 37 - score value
ok 38
ok 39
ok 40 - sft[0] is exon
ok 41
ok 42 - computation id
ok 43
ok 44 - score value
ok 45 - sfeat start for EXPAND-ED feature (bug \#947)
ok 46 - sfeat end for EXPAND-ED feature (bug \#947)
ok 47
ok 48 - can create feature starting and ending at 0
ok 49
ok 50 - can create feature starting and ending at 0
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 - mRNA spliced length
ok 71 - has 2 UTRs
ok 72
ok 73
ok 74
ok 75
ok 76 - The object isa Bio::SeqIO
ok 77 - The object isa Bio::Seq
ok 78 # skip Network tests have not been requested
ok 79 # skip Network tests have not been requested
ok 80 # skip Network tests have not been requested
ok 81 # skip Network tests have not been requested
ok 82 # skip Network tests have not been requested
ok 83 - The object isa Bio::SeqIO
ok 84 - The object isa Bio::Seq
ok 85 # skip Network tests have not been requested
ok 86 # skip Network tests have not been requested
ok 87 - The object isa Bio::SeqIO
ok 88 - spliced seq translation matches expected
ok 89 - spliced seq translation matches expected
ok 90 - spliced seq translation matches expected
ok 91 - spliced seq translation matches expected
ok 92 - spliced seq translation matches expected
ok 93 - spliced seq translation matches expected
ok 94 - spliced seq translation matches expected
ok 95 - spliced seq translation matches expected
ok 96 - spliced seq translation matches expected
ok 97 - spliced seq translation matches expected
ok 98 - spliced seq translation matches expected
ok 99 - spliced seq translation matches expected
ok 100 - spliced seq translation matches expected
ok 101 - spliced seq translation matches expected
ok 102 - spliced seq translation matches expected
ok 103 - spliced seq translation matches expected
ok 104 - spliced seq translation matches expected
ok 105 - spliced seq translation matches expected
ok 106 - spliced seq translation matches expected
ok 107 - spliced seq translation matches expected
ok 108 - spliced seq translation matches expected
ok 109 - spliced seq translation matches expected
ok 110 - spliced seq translation matches expected
ok 111 - spliced seq translation matches expected
ok 112 - spliced seq translation matches expected
ok 113 - spliced seq translation matches expected
ok 114 - spliced seq translation matches expected
ok 115 - spliced seq translation matches expected
ok 116 - spliced seq translation matches expected
ok 117 - spliced seq translation matches expected
ok 118 - spliced seq translation matches expected
ok 119 - spliced seq translation matches expected
ok 120 - spliced seq translation matches expected
ok 121 - spliced seq translation matches expected
ok 122 - spliced seq translation matches expected
ok 123 - spliced seq translation matches expected
ok 124 - spliced seq translation matches expected
ok 125 - spliced seq translation matches expected
ok 126 - spliced seq translation matches expected
ok 127 - spliced seq translation matches expected
ok 128 - spliced seq translation matches expected
ok 129 - spliced seq translation matches expected
ok 130 - spliced seq translation matches expected
ok 131 - spliced seq translation matches expected
ok 132 - spliced seq translation matches expected
ok 133 - spliced seq translation matches expected
ok 134 - spliced seq translation matches expected
ok 135 - spliced seq translation matches expected
ok 136 - spliced seq translation matches expected
ok 137 - spliced seq translation matches expected
ok 138 - spliced seq translation matches expected
ok 139 - spliced seq translation matches expected
ok 140 - spliced seq translation matches expected
ok 141 - spliced seq translation matches expected
ok 142 - spliced seq translation matches expected
ok 143 - spliced seq translation matches expected
ok 144 - spliced seq translation matches expected
ok 145 - spliced seq translation matches expected
ok 146 - spliced seq translation matches expected
ok 147 - spliced seq translation matches expected
ok 148 - spliced seq translation matches expected
ok 149 - spliced seq translation matches expected
ok 150 - spliced seq translation matches expected
ok 151 - spliced seq translation matches expected
ok 152 - spliced seq translation matches expected
ok 153 - spliced seq translation matches expected
ok 154 - spliced seq translation matches expected
ok 155 - spliced seq translation matches expected
ok 156 - spliced seq translation matches expected
ok 157 - spliced seq translation matches expected
ok 158 - spliced seq translation matches expected
ok 159 - spliced seq translation matches expected
ok 160 - spliced seq translation matches expected
ok 161 - spliced seq translation matches expected
ok 162 - spliced seq translation matches expected
ok 163 - spliced seq translation matches expected
ok 164 - spliced seq translation matches expected
ok 165 - spliced seq translation matches expected
ok 166 - spliced seq translation matches expected
ok 167 - spliced seq translation matches expected
ok 168 - spliced seq translation matches expected
ok 169 - spliced seq translation matches expected
ok 170 - spliced seq translation matches expected
ok 171 - spliced seq translation matches expected
ok 172 - spliced seq translation matches expected
ok 173 - spliced seq translation matches expected
ok 174 - spliced seq translation matches expected
ok 175 - spliced seq translation matches expected
ok 176 - spliced seq translation matches expected
ok 177 - spliced seq translation matches expected
ok 178 - spliced seq translation matches expected
ok 179 - spliced seq translation matches expected
ok 180 - spliced seq translation matches expected
ok 181 - spliced seq translation matches expected
ok 182 - spliced seq translation matches expected
ok 183 - spliced seq translation matches expected
ok 184 - spliced seq translation matches expected
ok 185 - spliced seq translation matches expected
ok 186 - spliced seq translation matches expected
ok 187 - spliced seq translation matches expected
ok 188 - spliced seq translation matches expected
ok 189 - spliced seq translation matches expected
ok 190 - spliced seq translation matches expected
ok 191 - spliced seq translation matches expected
ok 192 - spliced seq translation matches expected
ok 193 - spliced seq translation matches expected
ok 194 - spliced seq translation matches expected
ok 195 - spliced seq translation matches expected
ok 196 - spliced seq translation matches expected
ok 197 - spliced seq translation matches expected
ok 198 - spliced seq translation matches expected
ok 199 - spliced seq translation matches expected
ok 200 - spliced seq translation matches expected
ok 201 - spliced seq translation matches expected
ok 202 - spliced seq translation matches expected
ok 203 - spliced seq translation matches expected
ok 204 - spliced seq translation matches expected
ok 205
ok 206 - phase check
ok 207
ok 208 - phase check
ok 209
ok 210 - phase check
ok 211
ok 212 - phase check
ok 213
ok 214 - phase check
ok 215 - tags found
ok 216 - get_tagset_values tag values found
ok 217 - get_tagset_values tag values for multiple tags found
ok 218 - get_tag_values tag values found
ok 219 - get_tag_values lives with tag
ok 220 - get_tagset_values no tag values found
ok 221 - get_tagset_values lives with no tag
ok 222 - get_tag_values throws with no tag
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqFeature/SeqFeaturePrimer.t ..............
1..8
ok 1 - use Bio::SeqFeature::Primer;
ok 2 - The object isa Bio::SeqFeature::Primer
ok 3 - The object isa Bio::SeqFeature::Primer
ok 4 - The object isa Bio::Seq
ok 5
ok 6
ok 7
ok 8
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/SeqFeature/Unflattener.t ...................
1..9
ok 1 - use Bio::SeqIO;
ok 2 - use Bio::SeqFeature::Tools::Unflattener;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
t/SeqFeature/Unflattener2.t ..................
1..12
ok 1 - use Bio::SeqIO;
ok 2 - use Bio::SeqFeature::Tools::Unflattener;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqIO.t ....................................
1..41
ok 1 - use Bio::SeqIO;
ok 2
ok 3 - ID for format gcg
ok 4
ok 5
ok 6
ok 7
ok 8 - ID for format fasta
ok 9
ok 10
ok 11
ok 12 - accession.version
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19 - ID for format pir
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25 - ID for format tab
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31 - ID for format ace
ok 32
ok 33
ok 34
ok 35
ok 36 - use Algorithm::Diff;
ok 37 - use IO::ScalarArray;
ok 38 - use IO::String;
ok 39
ok 40
ok 41
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/SeqIO/Handler.t ............................
1..561
ok 1 - use Bio::SeqIO;
ok 2 - AI129902
ok 3
ok 4
ok 5
ok 6 - NT_021877
ok 7
ok 8
ok 9
ok 10
ok 11 - BAB68554
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21 - operator overloading in AnnotationI is deprecated
ok 22 - NC_006346
ok 23
ok 24
ok 25 - U71225
ok 26
ok 27 - AB077698
ok 28
ok 29 - DQ018368
ok 30 - D10483
ok 31
ok 32
ok 33
ok 34 - bug 1487
ok 35
ok 36 - bug 1647
ok 37
ok 38
ok 39 - bug 1673
ok 40
ok 41
ok 42
ok 43 - AF165282
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52 - species parsing incorrect for genbank
ok 53 - genus duplicated in genbank parsing
ok 54
ok 55
ok 56 - species parsing incorrect for genbank
ok 57 - genus duplicated in genbank parsing
ok 58
ok 59
ok 60 - species parsing incorrect for genbank
ok 61 - genus duplicated in genbank parsing
ok 62
ok 63 - streaming
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69 - Total number of sequences in test file
ok 70
ok 71 - Fuzzy in
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83 - Fuzzy out
ok 84 - BK000016
ok 85
ok 86 - BK000016
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 - BK000016
ok 102 - roundtrip
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 - revcomp split location
ok 121 - Bug 1925
ok 122
ok 123
ok 124 - wgs
ok 125
ok 126 - wgs_scafld
ok 127
ok 128 - wgs_scafld
ok 129
ok 130
ok 131 - BC000007
ok 132 - BK000016-tpa.gbk
ok 133 - ay116458.gb
ok 134 - ay149291.gb
ok 135 - NC_006346.gb
ok 136 - ay007676.gb
ok 137 - dq519393.gb
ok 138
ok 139 - swissprot:K1C9_HUMAN
ok 140
ok 141 - swissprot
ok 142
ok 143 - GenBank:Z29074.1
ok 144
ok 145 - GenBank
ok 146
ok 147 - GenPept:CAA82315.1
ok 148
ok 149 - GenPept
ok 150
ok 151 - GenBank:S69510.1
ok 152
ok 153 - GenBank
ok 154
ok 155 - GenPept:AAC60619.1
ok 156
ok 157 - GenPept
ok 158
ok 159 - GenBank:X75015.1
ok 160
ok 161 - GenBank
ok 162
ok 163 - GenPept:CAA52924.1
ok 164
ok 165 - GenPept
ok 166
ok 167 - GenBank:AB001594.1
ok 168
ok 169 - GenBank
ok 170
ok 171 - GenPept:BAA19418.1
ok 172
ok 173 - GenPept
ok 174
ok 175 - GenBank:I37984
ok 176
ok 177 - GenBank
ok 178
ok 179 - HSSP:P08670
ok 180
ok 181 - HSSP
ok 182
ok 183 - IntAct:P35527
ok 184
ok 185 - IntAct
ok 186
ok 187 - Ensembl:ENSG00000171403
ok 188
ok 189 - Ensembl
ok 190
ok 191 - KEGG:hsa:3857
ok 192
ok 193 - KEGG
ok 194
ok 195 - HGNC:6447
ok 196
ok 197 - HGNC
ok 198
ok 199 - MIM:144200
ok 200
ok 201 - MIM
ok 202
ok 203 - MIM:607606
ok 204
ok 205 - MIM
ok 206
ok 207 - ArrayExpress:P35527
ok 208
ok 209 - ArrayExpress
ok 210
ok 211 - GO:0005200
ok 212
ok 213 - GO
ok 214
ok 215 - GO:0008544
ok 216
ok 217 - GO
ok 218
ok 219 - InterPro:IPR011000
ok 220
ok 221 - InterPro
ok 222
ok 223 - InterPro:IPR001664
ok 224
ok 225 - InterPro
ok 226
ok 227 - InterPro:IPR002957
ok 228
ok 229 - InterPro
ok 230
ok 231 - Pfam:PF00038
ok 232
ok 233 - Pfam
ok 234
ok 235 - PRINTS:PR01248
ok 236
ok 237 - PRINTS
ok 238
ok 239 - PROSITE:PS00226
ok 240
ok 241 - PROSITE
ok 242
ok 243 - Bug 2195
ok 244 - Bug 2195
ok 245 - The object isa Bio::Annotation::SimpleValue
ok 246
ok 247 - The object isa Bio::Annotation::SimpleValue
ok 248
ok 249
ok 250
ok 251
ok 252
ok 253
ok 254
ok 255
ok 256
ok 257
ok 258
ok 259
ok 260
ok 261
ok 262
ok 263
ok 264
ok 265
ok 266
ok 267
ok 268
ok 269
ok 270
ok 271
ok 272
ok 273 - success reading Embl with ^ location and badly split double quotes
ok 274
ok 275
ok 276 - success writing Embl format with ^ < and > locations
ok 277
ok 278
ok 279
ok 280
ok 281
ok 282
ok 283
ok 284
ok 285
ok 286
ok 287
ok 288
ok 289
ok 290
ok 291
ok 292
ok 293
ok 294
ok 295
ok 296
ok 297
ok 298
ok 299
ok 300
ok 301
ok 302
ok 303
ok 304
ok 305
ok 306
ok 307
ok 308
ok 309 - genus duplication test
ok 310
ok 311
ok 312 - The object isa Bio::SeqIO
ok 313 - The object isa Bio::Taxon
ok 314
ok 315
ok 316 - operator overloading in AnnotationI is deprecated
ok 317
ok 318 - dates
ok 319 - dates
ok 320 - dates
ok 321
ok 322 - The object isa Bio::Seq::RichSeqI
ok 323
ok 324
ok 325
ok 326 - operator overloading in AnnotationI is deprecated
ok 327
ok 328
ok 329
ok 330
ok 331 - id is ROA1_HUMAN
ok 332
ok 333
ok 334
ok 335
ok 336
ok 337
ok 338
ok 339 - operator overloading in AnnotationI is deprecated
ok 340
ok 341
ok 342
ok 343 - The object isa Bio::Seq::RichSeqI
ok 344
ok 345
ok 346
ok 347
ok 348
ok 349
ok 350
ok 351
ok 352
ok 353 - operator overloading in AnnotationI is deprecated
ok 354
ok 355
ok 356
ok 357 - GC1QBP
ok 358 - HABP1
ok 359 - SF2P32
ok 360 - C1QBP
ok 361
ok 362 - The object isa Bio::Seq::RichSeqI
ok 363
ok 364
ok 365
ok 366
ok 367
ok 368
ok 369 - F54H12.1
ok 370 - The object isa Bio::Seq::RichSeqI
ok 371
ok 372
ok 373
ok 374
ok 375
ok 376
ok 377
ok 378
ok 379
ok 380
ok 381
ok 382 - The object isa Bio::Seq::RichSeqI
ok 383
ok 384
ok 385
ok 386
ok 387 - The object isa Bio::Seq::RichSeqI
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 - The object isa Bio::Seq::RichSeqI
ok 402
ok 403
ok 404
ok 405
ok 406
ok 407
ok 408
ok 409
ok 410
ok 411
ok 412
ok 413
ok 414
ok 415
ok 416
ok 417
ok 418
ok 419
ok 420
ok 421
ok 422
ok 423
ok 424
ok 425
ok 426
ok 427
ok 428
ok 429
ok 430
ok 431
ok 432
ok 433
ok 434
ok 435
ok 436
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 - The object isa Bio::Taxon
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
ok 516
ok 517 - The object isa Bio::Taxon
ok 518
ok 519
ok 520 - operator overloading in AnnotationI is deprecated
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 - P39765
ok 552
ok 553
ok 554
ok 555
ok 556
ok 557
ok 558
ok 559
ok 560
ok 561 - operator overloading in AnnotationI is deprecated
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqIO/MultiFile.t ..........................
1..3
ok 1 - use Bio::SeqIO::MultiFile;
ok 2
ok 3
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqIO/Multiple_fasta.t .....................
1..9
ok 1 - use Bio::SeqIO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9 - all sequences in the file
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/SeqIO/SeqBuilder.t .........................
1..101
ok 1 - use Bio::SeqIO;
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 - The object isa Bio::Factory::ObjectBuilderI
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
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/SeqIO/Splicedseq.t .........................
1..14
ok 1 - use Bio::SeqIO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11 - get_SeqFeatures()
ok 12 - protein sequence
ok 13 - nucleotide sequence - correct CDS range
ok 14 - nucleotide length
ok
t/SeqIO/abi.t ................................ skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqIO/ace.t ................................
1..7
ok 1 - use Bio::SeqIO;
ok 2 - number of sequence objects
ok 3 - unescaping of characters, Name; 4% strewn with \ various / escaped characters
ok 4 - alphabets detected
ok 5 - alphabets detected
ok 6 - writing sequence
ok 7 - test output
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/SeqIO/agave.t ..............................
1..8
ok 1 - use Bio::SeqIO::agave;
not ok 2 # TODO & SKIP No tests for agave format -- no sample file to test against
not ok 3 # TODO & SKIP No tests for agave format -- no sample file to test against
not ok 4 # TODO & SKIP No tests for agave format -- no sample file to test against
not ok 5 # TODO & SKIP No tests for agave format -- no sample file to test against
not ok 6 # TODO & SKIP No tests for agave format -- no sample file to test against
not ok 7 # TODO & SKIP No tests for agave format -- no sample file to test against
not ok 8 # TODO & SKIP No tests for agave format -- no sample file to test against
ok
t/SeqIO/alf.t ................................ skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/SeqIO/asciitree.t ..........................
1..2
ok 1 - use Bio::SeqIO;
not ok 2 # TODO Output doesn't exists on linux
# Failed (TODO) test at t/SeqIO/asciitree.t line 39.
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/SeqIO/bsml.t ...............................
1..16
ok 1 - use XML::DOM;
ok 2 - use Bio::SeqIO::bsml;
ok 3 - The object isa Bio::Seq::RichSeqI
ok 4 - got correct number of refs
ok 5 - display_id
ok 6 - molecule
ok 7 - is_circular
ok 8 - dates
ok 9 - accession_number
ok 10 - seq_version
ok 11 - got correct number of SeqFeatures
ok 12 - feature start
ok 13 - feature end
ok 14 - get_tag_values db_xref
ok 15 - get_Annotations reference
ok 16 - get_Annotations dblink
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/SeqIO/bsml_sax.t ...........................
1..15
ok 1 - use Bio::SeqIO;
ok 2 - The object isa Bio::Seq::RichSeqI
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
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
defined(@array) is deprecated at Bio/SeqIO/chadoxml.pm line 1674.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at Bio/SeqIO/chadoxml.pm line 1699.
(Maybe you should just omit the defined()?)
t/SeqIO/chadoxml.t ...........................
1..8
ok 1 - use Bio::SeqIO::chadoxml;
not ok 2 # TODO & SKIP No tests for chadoxml format -- no sample file to test against
not ok 3 # TODO & SKIP No tests for chadoxml format -- no sample file to test against
not ok 4 # TODO & SKIP No tests for chadoxml format -- no sample file to test against
not ok 5 # TODO & SKIP No tests for chadoxml format -- no sample file to test against
not ok 6 # TODO & SKIP No tests for chadoxml format -- no sample file to test against
not ok 7 # TODO & SKIP No tests for chadoxml format -- no sample file to test against
not ok 8 # TODO & SKIP No tests for chadoxml format -- no sample file to test against
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/SeqIO/chaos.t ..............................
1..8
ok 1 - use Bio::SeqIO::chaos;
not ok 2 # TODO & SKIP No tests for chaos format -- no sample file to test against
not ok 3 # TODO & SKIP No tests for chaos format -- no sample file to test against
not ok 4 # TODO & SKIP No tests for chaos format -- no sample file to test against
not ok 5 # TODO & SKIP No tests for chaos format -- no sample file to test against
not ok 6 # TODO & SKIP No tests for chaos format -- no sample file to test against
not ok 7 # TODO & SKIP No tests for chaos format -- no sample file to test against
not ok 8 # TODO & SKIP No tests for chaos format -- no sample file to test against
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/SeqIO/chaosxml.t ...........................
1..2
ok 1 - use Bio::SeqIO;
ok 2
ok
t/SeqIO/ctf.t ................................ skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/SeqIO/embl.t ...............................
1..69
ok 1 - use Bio::SeqIO::embl;
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 - success reading Embl with ^ location and badly split double quotes
ok 25
ok 26 - success writing Embl format with ^ < and > locations
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 - genus duplication test
ok 55
ok 56
ok 57
ok 58
ok 59 - CDS - accession on PA line
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67 - CDS - OX tagname
ok 68 - CDS - OX database
ok 69 - CDS - OX primary_id
ok
t/SeqIO/entrezgene.t ......................... skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqIO/excel.t ..............................
1..4
ok 1 - use Bio::SeqIO::excel;
ok 2 - The object isa Bio::SeqIO
ok 3 - Bio::SeqIO::excel->can('next_seq')
ok 4 - Bio::SeqIO::excel->can('write_seq')
ok
t/SeqIO/exp.t ................................ skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqIO/fasta.t ..............................
1..22
ok 1 - use Bio::SeqIO::fasta;
ok 2 - The object isa Bio::SeqIO
ok 3 - Bio::SeqIO::fasta->can('next_seq')
ok 4 - Bio::SeqIO::fasta->can('write_seq')
ok 5 - The object isa Bio::Seq
ok 6 - sequence
ok 7 - length
ok 8 - primary_id
ok 9 - description
ok 10 - The object isa Bio::Seq
ok 11 - sequence
ok 12 - length
ok 13 - primary_id
ok 14 - description
ok 15 - use Algorithm::Diff;
ok 16 - use IO::ScalarArray;
ok 17 - use IO::String;
ok 18 - fasta format can round-trip
ok 19 - dies with roa1.genbank
ok 20 - dies with test.gcg
ok 21 - dies with test.ace
ok 22 - dies with test.raw
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqIO/fastq.t ..............................
1..127
ok 1 - use Bio::SeqIO::fastq;
ok 2 - use Bio::Seq::Quality;
ok 3 - bug2335 parses
ok 4 - correct num. seqs in bug2335
ok 5 - sample sequence obtained
ok 6 - The object isa Bio::Seq::Quality
ok 7 - seq() matches bug2335
ok 8 - desc() matches bug2335
ok 9 - display_id() matches bug2335
ok 10 - qual() matches bug2335
ok 11 - evil_wrapping parses
ok 12 - correct num. seqs in evil_wrapping
ok 13 - sample sequence obtained
ok 14 - The object isa Bio::Seq::Quality
ok 15 - seq() matches evil_wrapping
ok 16 - desc() matches evil_wrapping
ok 17 - display_id() matches evil_wrapping
ok 18 - qual() matches evil_wrapping
ok 19 - example parses
ok 20 - correct num. seqs in example
ok 21 - sample sequence obtained
ok 22 - The object isa Bio::Seq::Quality
ok 23 - seq() matches example
ok 24 - desc() matches example
ok 25 - display_id() matches example
ok 26 - qual() matches example
ok 27 - illumina_faked parses
ok 28 - correct num. seqs in illumina_faked
ok 29 - sample sequence obtained
ok 30 - The object isa Bio::Seq::Quality
ok 31 - seq() matches illumina_faked
ok 32 - desc() matches illumina_faked
ok 33 - display_id() matches illumina_faked
ok 34 - qual() matches illumina_faked
ok 35 - sanger_93 parses
ok 36 - correct num. seqs in sanger_93
ok 37 - sample sequence obtained
ok 38 - The object isa Bio::Seq::Quality
ok 39 - seq() matches sanger_93
ok 40 - desc() matches sanger_93
ok 41 - display_id() matches sanger_93
ok 42 - qual() matches sanger_93
ok 43 - sanger_faked parses
ok 44 - correct num. seqs in sanger_faked
ok 45 - sample sequence obtained
ok 46 - The object isa Bio::Seq::Quality
ok 47 - seq() matches sanger_faked
ok 48 - desc() matches sanger_faked
ok 49 - display_id() matches sanger_faked
ok 50 - qual() matches sanger_faked
ok 51 - solexa_example parses
ok 52 - correct num. seqs in solexa_example
ok 53 - sample sequence obtained
ok 54 - The object isa Bio::Seq::Quality
ok 55 - seq() matches solexa_example
ok 56 - desc() matches solexa_example
ok 57 - display_id() matches solexa_example
ok 58 - qual() matches solexa_example
ok 59 - solexa_faked parses
ok 60 - correct num. seqs in solexa_faked
ok 61 - sample sequence obtained
ok 62 - The object isa Bio::Seq::Quality
ok 63 - seq() matches solexa_faked
ok 64 - desc() matches solexa_faked
ok 65 - display_id() matches solexa_faked
ok 66 - qual() matches solexa_faked
ok 67 - test1_sanger parses
ok 68 - correct num. seqs in test1_sanger
ok 69 - sample sequence obtained
ok 70 - The object isa Bio::Seq::Quality
ok 71 - seq() matches test1_sanger
ok 72 - desc() matches test1_sanger
ok 73 - display_id() matches test1_sanger
ok 74 - qual() matches test1_sanger
ok 75 - test2_solexa parses
ok 76 - correct num. seqs in test2_solexa
ok 77 - sample sequence obtained
ok 78 - The object isa Bio::Seq::Quality
ok 79 - seq() matches test2_solexa
ok 80 - desc() matches test2_solexa
ok 81 - display_id() matches test2_solexa
ok 82 - qual() matches test2_solexa
ok 83 - test3_illumina parses
ok 84 - correct num. seqs in test3_illumina
ok 85 - sample sequence obtained
ok 86 - The object isa Bio::Seq::Quality
ok 87 - seq() matches test3_illumina
ok 88 - desc() matches test3_illumina
ok 89 - display_id() matches test3_illumina
ok 90 - qual() matches test3_illumina
ok 91 - tricky parses
ok 92 - correct num. seqs in tricky
ok 93 - sample sequence obtained
ok 94 - The object isa Bio::Seq::Quality
ok 95 - seq() matches tricky
ok 96 - desc() matches tricky
ok 97 - display_id() matches tricky
ok 98 - qual() matches tricky
ok 99 - Conversion from illumina to sanger
ok 100 - Conversion from illumina to illumina
ok 101 - Conversion from illumina to solexa
ok 102 - Conversion from sanger to sanger
ok 103 - Conversion from sanger to illumina
ok 104 - Conversion from sanger to solexa
ok 105 - Conversion from solexa to sanger
ok 106 - Conversion from solexa to illumina
ok 107 - Conversion from solexa to solexa
ok 108 - Exception caught for error_diff_ids
ok 109 - Exception caught for error_long_qual
ok 110 - Exception caught for error_no_qual
ok 111 - Exception caught for error_qual_del
ok 112 - Exception caught for error_qual_escape
ok 113 - Exception caught for error_qual_null
ok 114 - Exception caught for error_qual_space
ok 115 - Exception caught for error_qual_tab
ok 116 - Exception caught for error_qual_unit_sep
ok 117 - Exception caught for error_qual_vtab
ok 118 - Exception caught for error_short_qual
ok 119 - Exception caught for error_spaces
ok 120 - Exception caught for error_tabs
ok 121 - Exception caught for error_trunc_at_plus
ok 122 - Exception caught for error_trunc_at_qual
ok 123 - Exception caught for error_trunc_at_seq
ok 124 - Exception caught for error_trunc_in_plus
ok 125 - Exception caught for error_trunc_in_qual
ok 126 - Exception caught for error_trunc_in_seq
ok 127 - Exception caught for error_trunc_in_title
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
defined(@array) is deprecated at Bio/SeqIO/chadoxml.pm line 1674.
(Maybe you should just omit the defined()?)
defined(@array) is deprecated at Bio/SeqIO/chadoxml.pm line 1699.
(Maybe you should just omit the defined()?)
t/SeqIO/flybase_chadoxml.t ...................
1..8
ok 1 - use Bio::SeqIO::flybase_chadoxml;
not ok 2 # TODO & SKIP No tests for flybase_chadoxml format -- no sample file to test against
not ok 3 # TODO & SKIP No tests for flybase_chadoxml format -- no sample file to test against
not ok 4 # TODO & SKIP No tests for flybase_chadoxml format -- no sample file to test against
not ok 5 # TODO & SKIP No tests for flybase_chadoxml format -- no sample file to test against
not ok 6 # TODO & SKIP No tests for flybase_chadoxml format -- no sample file to test against
not ok 7 # TODO & SKIP No tests for flybase_chadoxml format -- no sample file to test against
not ok 8 # TODO & SKIP No tests for flybase_chadoxml format -- no sample file to test against
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118, line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118, line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118, line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118, line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118, line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118, line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118, line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118, line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118, line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118, line 880.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118, line 880.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118, line 880.
t/SeqIO/game.t ...............................
1..24
ok 1 - use Bio::SeqIO::game;
ok 2 - The object isa Bio::SeqIO
ok 3 - The object isa Bio::Seq::RichSeq
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqIO/gcg.t ................................
1..17
ok 1 - use Bio::SeqIO::gcg;
ok 2 - The object isa Bio::SeqIO
ok 3 - Bio::SeqIO::gcg->can('next_seq')
ok 4 - Bio::SeqIO::gcg->can('write_seq')
ok 5 - The object isa Bio::Seq
ok 6 - The object isa Bio::Seq::RichSeq
ok 7 - sequence
ok 8 - length
not ok 9 - primary_id # TODO possible bug: RichSeq not setting primary_id?
# Failed (TODO) test 'primary_id'
# at t/SeqIO/gcg.t line 54.
# got: 'Bio::PrimarySeq=HASH(0x203b1a28)'
# expected: 'roa1_drome'
ok 10 - description
ok 11
ok 12 - The object isa Bio::SeqI
ok 13
ok 14 - use Algorithm::Diff;
ok 15 - use IO::ScalarArray;
ok 16 - use IO::String;
ok 17 - gcg format can round-trip
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/SeqIO/genbank.t ............................
1..260
ok 1 - use Bio::SeqIO::genbank;
ok 2 - The object isa Bio::SeqIO
ok 3 - AI129902
ok 4
ok 5
ok 6
ok 7 - NT_021877
ok 8
ok 9
ok 10
ok 11
ok 12 - BAB68554
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22 - operator overloading in AnnotationI is deprecated
ok 23 - NC_006346
ok 24
ok 25
ok 26 - U71225
ok 27
ok 28 - AB077698
ok 29
ok 30 - DQ018368
ok 31 - D10483
ok 32
ok 33
ok 34
ok 35 - bug 1487
ok 36
ok 37 - bug 1647
ok 38
ok 39
ok 40 - bug 1673
ok 41
ok 42
ok 43
ok 44 - AF165282
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53 - species parsing incorrect for genbank
ok 54 - genus duplicated in genbank parsing
ok 55
ok 56
ok 57 - species parsing incorrect for genbank
ok 58 - genus duplicated in genbank parsing
ok 59
ok 60
ok 61 - species parsing incorrect for genbank
ok 62 - genus duplicated in genbank parsing
ok 63
ok 64 - streaming
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70 - Total number of sequences in test file
ok 71
ok 72 - Fuzzy in
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84 - Fuzzy out
ok 85 - BK000016
ok 86
ok 87 - BK000016
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 - BK000016
ok 103 - roundtrip
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 - revcomp split location
ok 122 - Bug 1925
ok 123
ok 124
ok 125 - wgs
ok 126
ok 127 - wgs_scafld
ok 128
ok 129 - wgs_scafld
ok 130
ok 131
ok 132 - BC000007
ok 133 - BK000016-tpa.gbk
ok 134 - ay116458.gb
ok 135 - ay149291.gb
ok 136 - NC_006346.gb
ok 137 - ay007676.gb
ok 138 - dq519393.gb
ok 139
ok 140 - swissprot:K1C9_HUMAN
ok 141
ok 142 - swissprot
ok 143
ok 144 - GenBank:Z29074.1
ok 145
ok 146 - GenBank
ok 147
ok 148 - GenPept:CAA82315.1
ok 149
ok 150 - GenPept
ok 151
ok 152 - GenBank:S69510.1
ok 153
ok 154 - GenBank
ok 155
ok 156 - GenPept:AAC60619.1
ok 157
ok 158 - GenPept
ok 159
ok 160 - GenBank:X75015.1
ok 161
ok 162 - GenBank
ok 163
ok 164 - GenPept:CAA52924.1
ok 165
ok 166 - GenPept
ok 167
ok 168 - GenBank:AB001594.1
ok 169
ok 170 - GenBank
ok 171
ok 172 - GenPept:BAA19418.1
ok 173
ok 174 - GenPept
ok 175
ok 176 - GenBank:I37984
ok 177
ok 178 - GenBank
ok 179
ok 180 - HSSP:P08670
ok 181
ok 182 - HSSP
ok 183
ok 184 - IntAct:P35527
ok 185
ok 186 - IntAct
ok 187
ok 188 - Ensembl:ENSG00000171403
ok 189
ok 190 - Ensembl
ok 191
ok 192 - KEGG:hsa:3857
ok 193
ok 194 - KEGG
ok 195
ok 196 - HGNC:6447
ok 197
ok 198 - HGNC
ok 199
ok 200 - MIM:144200
ok 201
ok 202 - MIM
ok 203
ok 204 - MIM:607606
ok 205
ok 206 - MIM
ok 207
ok 208 - ArrayExpress:P35527
ok 209
ok 210 - ArrayExpress
ok 211
ok 212 - GO:0005200
ok 213
ok 214 - GO
ok 215
ok 216 - GO:0008544
ok 217
ok 218 - GO
ok 219
ok 220 - InterPro:IPR011000
ok 221
ok 222 - InterPro
ok 223
ok 224 - InterPro:IPR001664
ok 225
ok 226 - InterPro
ok 227
ok 228 - InterPro:IPR002957
ok 229
ok 230 - InterPro
ok 231
ok 232 - Pfam:PF00038
ok 233
ok 234 - Pfam
ok 235
ok 236 - PRINTS:PR01248
ok 237
ok 238 - PRINTS
ok 239
ok 240 - PROSITE:PS00226
ok 241
ok 242 - PROSITE
ok 243
ok 244 - Bug 2195
ok 245 - Bug 2195
ok 246 - The object isa Bio::Annotation::SimpleValue
ok 247
ok 248 - The object isa Bio::Annotation::SimpleValue
ok 249
ok 250 - P39765
ok 251
ok 252
ok 253
ok 254
ok 255
ok 256
ok 257
ok 258
ok 259
ok 260 - operator overloading in AnnotationI is deprecated
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqIO/interpro.t ...........................
1..20
ok 1 - use Bio::SeqIO::interpro;
ok 2 - The object isa Bio::SeqIO
ok 3 - seq obj is defined
ok 4 - The object isa Bio::Seq::RichSeq
ok 5 - right number of SeqFeatures
ok 6 - The object isa Bio::SeqFeature::Generic
ok 7 - display_name()
ok 8 - seq object is defined
ok 9 - right number of SeqFeatures
ok 10 - there is no next_seq (correctly)
ok 11 - bug 1908
ok 12 - right number of SeqFeatures
ok 13 - primary_tag()
ok 14 - display_name()
ok 15 - location->end()
ok 16 - right number of dblinks
ok 17 - first primary_id
ok 18 - second primary_id
ok 19 - right number of dblinks
ok 20 - primary_id via dblinks
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/SeqIO/kegg.t ...............................
1..16
ok 1 - use Bio::SeqIO::kegg;
ok 2 - The object isa Bio::SeqIO
ok 3
ok 4 - The object isa Bio::Seq::RichSeq
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqIO/largefasta.t .........................
1..16
ok 1 - use Bio::SeqIO::largefasta;
ok 2 - The object isa Bio::SeqIO
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqIO/lasergene.t ..........................
1..13
ok 1 - use Bio::SeqIO::lasergene;
ok 2
ok 3 - The object isa Bio::SeqIO
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqIO/locuslink.t ..........................
1..26
ok 1 - use Bio::SeqIO::locuslink;
ok 2 - use Bio::SeqFeature::Generic;
ok 3 - use Bio::SeqFeature::AnnotationAdaptor;
ok 4
ok 5 - The object isa Bio::SeqIO
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqIO/metafasta.t ..........................
1..6
ok 1 - use Bio::SeqIO::metafasta;
ok 2 - The object isa Bio::SeqIO
ok 3
ok 4 - The object isa Bio::Seq::Meta
ok 5
ok 6
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqIO/phd.t ................................
1..17
ok 1 - use Bio::SeqIO::phd;
ok 2 - The object isa Bio::SeqIO::phd
ok 3 - Did you get the 'QUALITY_LEVELS' comment?
ok 4 - The object isa Bio::Seq::Quality
ok 5 - The object isa Bio::SeqIO::phd
ok 6
ok 7 - $seq->subseq()
ok 8 - $seq->subqual_tex()
ok 9 - $seq->subqual_tex()
ok 10 - $phd->chromat_file()
ok 11 - $phd->chromat_file()
ok 12 - $seq->subseq()
ok 13 - $seq->subqual_tex()
ok 14 - $seq->subqual_tex()
ok 15 - $seq->subseq()
ok 16 - $seq->subqual_tex()
ok 17 - $seq->subqual_tex()
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqIO/pir.t ................................
1..9
ok 1 - use Bio::SeqIO::pir;
ok 2 - new instance is defined
ok 3 - The object isa Bio::SeqIO
ok 4 - checked length
ok 5 - checked length
ok 6 - checked length
ok 7 - checked length
ok 8 - checked length
ok 9 - checked length
ok
t/SeqIO/pln.t ................................ skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/qual.t ...............................
1..18
ok 1 - use Bio::SeqIO;
ok 2 - use Bio::Seq::PrimaryQual;
ok 3
ok 4 - The object isa Bio::Seq::PrimaryQual
ok 5
ok 6 - The object isa Bio::Seq::PrimaryQual
ok 7 - The object isa Bio::Seq::PrimaryQual
ok 8 - The object isa Bio::Seq::PrimaryQual
ok 9 - The object isa Bio::Seq::PrimaryQual
ok 10 - The object isa Bio::Seq::PrimaryQual
ok 11 - The object isa Bio::Seq::PrimaryQual
ok 12 - The object isa Bio::Seq::PrimaryQual
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqIO/raw.t ................................
1..25
ok 1 - use Bio::SeqIO::raw;
ok 2 - The object isa Bio::SeqIO
ok 3
ok 4 - Bio::SeqIO::raw->can('next_seq')
ok 5 - Bio::SeqIO::raw->can('write_seq')
ok 6 - The object isa Bio::Seq
ok 7 - sequence
ok 8 - length
ok 9 - The object isa Bio::Seq
ok 10 - sequence
ok 11 - length
ok 12 - use Algorithm::Diff;
ok 13 - raw format can round-trip
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqIO/scf.t ................................
1..78
ok 1 - use Bio::SeqIO::scf;
ok 2 - use Bio::Seq::SequenceTrace;
ok 3
ok 4 - The object isa Bio::Seq::SequenceTrace
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13 - The object isa Bio::Seq::Quality
ok 14 - The object isa Bio::Seq::Quality
ok 15 - alphabet
ok 16 - display_id
ok 17 - primary_id is the stringified memory position
ok 18 - set primary_id
ok 19 - accession_number
ok 20 - desc
ok 21 - desc
ok 22 - id
ok 23 - id
ok 24 - seq
ok 25 - subseq
ok 26 - baseat
ok 27 - qualat
ok 28 - trace_value_at
not ok 29 - accuracies # TODO documentation and code for accuracies() do not match
# Failed (TODO) test 'accuracies'
# at t/SeqIO/scf.t line 78.
# got: 'ARRAY(0xf636160)'
# expected: '482'
ok 30
ok 31 - sub_peak_index
ok 32 - peak_index_at
ok 33
ok 34
ok 35 - The object isa Bio::Seq::SequenceTrace
ok 36 - accuracy_at
ok 37 - The object isa Bio::Seq::SequenceTrace
ok 38
ok 39
ok 40
ok 41 - The object isa Bio::Annotation::Collection
ok 42
ok 43 - The object isa Bio::Annotation::Collection
ok 44
ok 45
ok 46 - The object isa Bio::Annotation::Collection
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54 - The object isa Bio::Seq::SequenceTrace
ok 55 - The object isa Bio::Annotation::Collection
ok 56
ok 57
ok 58
ok 59
ok 60 - The object isa Bio::Seq::SequenceTrace
ok 61
ok 62 - The object isa Bio::Seq::SequenceTrace
ok 63 - qual scores match
ok 64 - The object isa Bio::Seq::SequenceTrace
ok 65
ok 66 - The object isa Bio::Seq::SequenceTrace
not ok 67 - display_id matches # TODO display_id doesn't round trip yet
# Failed (TODO) test 'display_id matches'
# at t/SeqIO/scf.t line 285.
# got: 'ML4942R'
# expected: undef
ok 68 - qual scores match
ok 69 - The object isa Bio::Seq::SequenceTrace
ok 70
ok 71 - The object isa Bio::Seq::SequenceTrace
not ok 72 - display_id matches # TODO display_id doesn't round trip yet
# Failed (TODO) test 'display_id matches'
# at t/SeqIO/scf.t line 285.
# got: 'IIABP1D4373'
# expected: undef
ok 73 - qual scores match
ok 74 - The object isa Bio::Seq::SequenceTrace
ok 75
ok 76 - The object isa Bio::Seq::SequenceTrace
not ok 77 - display_id matches # TODO display_id doesn't round trip yet
# Failed (TODO) test 'display_id matches'
# at t/SeqIO/scf.t line 285.
# got: 'IIABP1D4373'
# expected: undef
ok 78 - qual scores match
ok
t/SeqIO/strider.t ............................ skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/SeqIO/swiss.t ..............................
1..240
ok 1 - use Bio::SeqIO::swiss;
ok 2 - The object isa Bio::SeqIO
ok 3 - The object isa Bio::Taxon
ok 4
ok 5
ok 6 - operator overloading in AnnotationI is deprecated
ok 7 - dates
ok 8 - dates
ok 9 - dates
ok 10
ok 11 - The object isa Bio::Seq::RichSeqI
ok 12
ok 13
ok 14
ok 15 - operator overloading in AnnotationI is deprecated
ok 16
ok 17
ok 18
ok 19
ok 20 - id is ROA1_HUMAN
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28 - operator overloading in AnnotationI is deprecated
ok 29
ok 30
ok 31
ok 32
ok 33 - The object isa Bio::Seq::RichSeqI
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43 - operator overloading in AnnotationI is deprecated
ok 44
ok 45
ok 46
ok 47 - GC1QBP
ok 48 - HABP1
ok 49 - SF2P32
ok 50 - C1QBP
ok 51
ok 52 - The object isa Bio::Seq::RichSeqI
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59 - F54H12.1
ok 60 - The object isa Bio::Seq::RichSeqI
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72 - The object isa Bio::Seq::RichSeqI
ok 73
ok 74
ok 75
ok 76
ok 77 - The object isa Bio::Seq::RichSeqI
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 - The object isa Bio::Seq::RichSeqI
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175 - The object isa Bio::Taxon
ok 176
ok 177
ok 178 - operator overloading in AnnotationI is deprecated
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 - The object isa Bio::Taxon
ok 208
ok 209
ok 210 - operator overloading in AnnotationI is deprecated
ok 211
ok 212
ok 213
ok 214
ok 215
ok 216
ok 217
ok 218
ok 219
ok 220
ok 221
ok 222
ok 223
ok 224
ok 225
ok 226
ok 227
ok 228
ok 229
ok 230
ok 231
ok 232
ok 233
ok 234
ok 235
ok 236
ok 237
ok 238
ok 239
ok 240
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqIO/tab.t ................................
1..8
ok 1 - use Bio::SeqIO::tab;
ok 2 - The object isa Bio::SeqIO
ok 3 - seq is defined
ok 4 - check seq length
ok 5 - check matching
ok 6 - seq is defined
ok 7 - check seq length
ok 8 - check matching
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/SeqIO/table.t ..............................
1..450
ok 1 - use Bio::Tools::CodonTable;
ok 2 - use Bio::SeqIO::table;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139
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ok 142
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ok 144
ok 145
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ok 155
ok 156
ok 157
ok 158
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ok 160
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ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/SeqIO/tigr.t ...............................
1..8
ok 1 - use Bio::SeqIO::tigr;
not ok 2 # TODO & SKIP No tests for tigr format -- no sample file to test against
not ok 3 # TODO & SKIP No tests for tigr format -- no sample file to test against
not ok 4 # TODO & SKIP No tests for tigr format -- no sample file to test against
not ok 5 # TODO & SKIP No tests for tigr format -- no sample file to test against
not ok 6 # TODO & SKIP No tests for tigr format -- no sample file to test against
not ok 7 # TODO & SKIP No tests for tigr format -- no sample file to test against
not ok 8 # TODO & SKIP No tests for tigr format -- no sample file to test against
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqIO/tigrxml.t ............................
1..49
ok 1 - use Bio::SeqIO::tigrxml;
ok 2 - The object isa Bio::SeqIO
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
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ok 44
ok 45
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ok 47
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ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/SeqIO/tinyseq.t ............................
1..16
ok 1 - use Bio::SeqIO::tinyseq;
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/SeqIO/ztr.t ................................ skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
Replacement list is longer than search list at /home/fly1800/var/cpan/build/BioPerl-1.6.1-OeFNmD/blib/lib/Bio/Range.pm line 251.
t/SeqTools/Backtranslate.t ...................
1..8
ok 1 - use Bio::Tools::SeqPattern::Backtranslate;
ok 2 - Bio::Tools::SeqPattern::Backtranslate->can('_reverse_translate_motif')
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8 - threw Regexp ((?^:syntax token))
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqTools/CodonTable.t ......................
1..56
ok 1 - use Bio::Tools::CodonTable;
ok 2 - use Bio::CodonUsage::IO;
ok 3
ok 4 - The object isa Bio::Tools::CodonTable
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
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ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok
t/SeqTools/ECnumber.t ........................
1..27
ok 1 - use Bio::Tools::ECnumber;
ok 2 - The object isa Bio::Tools::ECnumber
ok 3 - The object isa Bio::Tools::ECnumber
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
Replacement list is longer than search list at Bio/Range.pm line 251.
Use of uninitialized value $format in lc at Bio/SeqIO.pm line 382.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118, line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118, line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118, line 934.
t/SeqTools/GuessSeqFormat.t ..................
1..49
ok 1 - use Bio::SeqIO;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::Tools::GuessSeqFormat;
ok 4
ok 5
ok 6
ok 7 - Guessed:ace
ok 8 - The object isa Bio::PrimarySeqI
ok 9 - Guessed:embl
ok 10 - The object isa Bio::SeqI
ok 11 - Guessed:fasta
ok 12 - The object isa Bio::SeqI
ok 13 - Guessed:gcg
ok 14 - The object isa Bio::SeqI
ok 15 - Guessed:genbank
ok 16 - The object isa Bio::SeqI
ok 17 - Guessed:mase
ok 18 - Guessed:pfam
ok 19 - Guessed:pir
ok 20 - The object isa Bio::SeqI
ok 21 - Guessed:raw
ok 22 - The object isa Bio::SeqI
ok 23 - Guessed:swiss
ok 24 - The object isa Bio::SeqI
ok 25 - Guessed:tab
ok 26 - The object isa Bio::SeqI
ok 27 - Guessed:game
ok 28 - The object isa Bio::SeqI
ok 29 - clustalw
ok 30 - The object isa Bio::Align::AlignI
ok 31 - fasta
ok 32 - The object isa Bio::Align::AlignI
ok 33 - mase
ok 34 - The object isa Bio::Align::AlignI
ok 35 - msf
ok 36 - The object isa Bio::Align::AlignI
ok 37 - nexus
ok 38 - The object isa Bio::Align::AlignI
ok 39 - pfam
ok 40 - The object isa Bio::Align::AlignI
ok 41 - phylip
ok 42 - The object isa Bio::Align::AlignI
ok 43 - prodom
ok 44 - The object isa Bio::Align::AlignI
ok 45 - stockholm
ok 46 - The object isa Bio::Align::AlignI
ok 47
ok 48
ok 49 - fasta
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqTools/OddCodes.t ........................
1..11
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::Tools::OddCodes;
ok 3 - The object isa Bio::Tools::OddCodes
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqTools/SeqPattern.t ......................
1..28
ok 1 - use Bio::Tools::SeqPattern;
ok 2
ok 3 - The object isa Bio::Tools::SeqPattern
ok 4
ok 5
ok 6
ok 7 - The object isa Bio::Tools::SeqPattern
ok 8
ok 9
ok 10 - The object isa Bio::Tools::SeqPattern
ok 11
ok 12 - threw Regexp ((?^:revcom for .+ sequence types))
ok 13 - threw Regexp ((?^:backtranslate for .+ sequence types))
ok 14 - The object isa Bio::Tools::SeqPattern
ok 15 - The object isa Bio::Tools::SeqPattern
ok 16
ok 17 - The object isa Bio::Tools::SeqPattern
ok 18 - The object isa Bio::Tools::SeqPattern
ok 19
ok 20 - The object isa Bio::Tools::SeqPattern
ok 21 - The object isa Bio::Tools::SeqPattern
ok 22
ok 23 - The object isa Bio::Tools::SeqPattern
ok 24 - The object isa Bio::Tools::SeqPattern
ok 25
ok 26 - The object isa Bio::Tools::SeqPattern
ok 27 - The object isa Bio::Tools::SeqPattern
ok 28
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqTools/SeqStats.t ........................
1..44
ok 1 - use Bio::SeqIO;
ok 2 - use Bio::Tools::SeqStats;
ok 3 - new Bio::Root::IO object
ok 4 - new Bio::Tools:SeqStats object
ok 5 - count_monomers()
ok 6 - count_codons()
ok 7 - get_mol_wt()
ok 8
ok 9 - The object isa Bio::Tools::SeqStats
ok 10
ok 11
ok 12
ok 13
ok 14
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ok 40
ok 41
ok 42
ok 43
ok 44
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqTools/SeqUtils.t ........................
1..51
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::SeqUtils;
ok 3 - use Bio::LiveSeq::Mutation;
ok 4 - use Bio::SeqFeature::Generic;
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 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34 - cat - has expected tags
ok 35 - cat - has expected tag values
ok 36 - cat - note tag transfered (no throw)
ok 37 - cat - note tag values transfered (correct count)
ok 38 - different alphabets
ok 39
ok 40
ok 41
ok 42
ok 43 - trunc_with_features - has expected tags
ok 44 - trunc_with_features - has expected tag values
ok 45
ok 46
ok 47
ok 48 - revcom_with_features - has expected tags
ok 49 - revcom_with_features - has expected tag values
ok 50 - still not circular
ok 51 - still circular
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/SeqTools/SeqWords.t ........................
1..22
ok 1 - use Bio::SeqIO;
ok 2 - use Bio::Tools::SeqWords;
ok 3 - new Bio::Root::IO object
ok 4 - new Bio::Tools::SeqWords object
ok 5 - count_words
ok 6
ok 7 - The object isa Bio::Tools::SeqWords
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16 - The object isa Bio::Tools::SeqWords
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Species.t ..................................
1..21
ok 1 - use Bio::Species;
ok 2 - use Bio::DB::Taxonomy;
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 # skip Network tests have not been requested
ok 18 # skip Network tests have not been requested
ok 19 # skip Network tests have not been requested
ok 20 # skip Network tests have not been requested
ok 21 # skip Network tests have not been requested
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Structure/IO.t .............................
1..14
ok 1 - use Bio::Structure::IO;
ok 2
ok 3
ok 4 - The object isa Bio::Structure::Entry
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok
t/Structure/Structure.t ......................
1..51
ok 1 - use Bio::Structure::Entry;
ok 2 - use Bio::Structure::Model;
ok 3 - use Bio::Structure::Chain;
ok 4 - use Bio::Structure::Residue;
ok 5 - use Bio::Structure::Atom;
ok 6
ok 7 - The object isa Bio::Structure::Entry
ok 8
ok 9 - The object isa Bio::Structure::Model
ok 10
ok 11 - The object isa Bio::Structure::Chain
ok 12
ok 13 - The object isa Bio::Structure::Residue
ok 14
ok 15 - The object isa Bio::Structure::Atom
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23 - The object isa Bio::Structure::Model
ok 24
ok 25
ok 26
ok 27 - The object isa Bio::Structure::Chain
ok 28
ok 29
ok 30
ok 31
ok 32 - The object isa Bio::Structure::Residue
ok 33
ok 34
ok 35
ok 36
ok 37
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ok 44
ok 45
ok 46
ok 47
ok 48
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ok 51
ok
t/Symbol.t ...................................
1..9
ok 1 - use Bio::Symbol::Symbol;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok
t/TaxonTree.t ................................ skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated
t/Tools/Alignment/Consed.t ...................
1..15
ok 1 - use Bio::Tools::Alignment::Consed;
ok 2 - new CSM::Consed object was created
ok 3 - The object isa Bio::Tools::Alignment::Consed
ok 4 - singlets can be successfully set
ok 5 - singlets can be retrieved
ok 6 - doublets can be set
ok 7 - doublets can be retreived
ok 8 - doublets can be retrieved
ok 9 - pairs can be retrieved
ok 10 - multiplets can be retrieved
ok 11 - singletons can be retrieved
ok 12 - how many sequences there are in the acefile _and_ in the singlets file
ok 13 - statistics from the Bio::Tools::Alignment::Consed object to compare the total number of sequences accounted for there to the number of sequences found via grep
ok 14
ok 15
ok
t/Tools/Analysis/DNA/ESEfinder.t ............. skipped: Network tests have not been requested
t/Tools/Analysis/Protein/Domcut.t ............ skipped: Network tests have not been requested
t/Tools/Analysis/Protein/ELM.t ............... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/GOR4.t .............. skipped: Network tests have not been requested
t/Tools/Analysis/Protein/HNN.t ............... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/Mitoprot.t .......... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/NetPhos.t ........... skipped: Network tests have not been requested
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Tools/Analysis/Protein/Scansite.t ..........
1..14
ok 1 - use Bio::Tools::Analysis::Protein::Scansite;
ok 2 - use Bio::SeqIO;
ok 3 - use Bio::WebAgent;
ok 4
ok 5
ok 6
ok 7
ok 8
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Analysis/Protein/Sopma.t .............
1..16
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::Tools::Analysis::Protein::Sopma;
ok 3
ok 4
ok 5 # skip Network tests have not been requested
ok 6 # skip Network tests have not been requested
ok 7 # skip Network tests have not been requested
ok 8 # skip Network tests have not been requested
ok 9 # skip Network tests have not been requested
ok 10 # skip Network tests have not been requested
ok 11 # skip Network tests have not been requested
ok 12 # skip Network tests have not been requested
ok 13 # skip Network tests have not been requested
ok 14 # skip Network tests have not been requested
ok 15 # skip Network tests have not been requested
ok 16 # skip Network tests have not been requested
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/EMBOSS/Palindrome.t ..................
1..13
ok 1 - use Bio::Tools::EMBOSS::Palindrome;
ok 2 - use Bio::Tools::GFF;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok
t/Tools/EUtilities/EUtilParameters.t .........
1..13
ok 1 - use Bio::Tools::EUtilities::EUtilParameters;
ok 2
ok 3 - The object isa HTTP::Request
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10 - available_parameters
ok 11 - available_parameters
ok 12 - get_parameters
ok 13 - get_parameters
ok
t/Tools/EUtilities/egquery.t .................
1..19
ok 1 - use Bio::Tools::EUtilities;
ok 2 - get_db
ok 3 - get_database
ok 4 - get_databases
ok 5 - get_term
ok 6 - get_count
ok 7 - get_count
ok 8 - get_count
ok 9 - get_GlobalQueries
ok 10 - get_term
ok 11 - get_term
ok 12 - get_term
ok 13 - get_term
ok 14 - get_term
ok 15 - get_term
ok 16 - get_term
ok 17 - get_term
ok 18 - get_term
ok 19 - get_term
ok
t/Tools/EUtilities/einfo.t ...................
1..51
ok 1 - use Bio::Tools::EUtilities;
ok 2 - use Bio::Tools::EUtilities::EUtilParameters;
ok 3 - get_available_databases
ok 4 - get_databases
ok 5 - get_db
ok 6 - get_record_count
ok 7 - get_menu_name
ok 8 - get_last_update
ok 9 - get_description
ok 10 - FieldInfo
ok 11 - LinkInfo
ok 12 - get_db
ok 13 - get_dbs
ok 14 - get_record_count
ok 15 - get_menu_name
ok 16 - get_last_update
ok 17 - get_description
ok 18 - FieldInfo
ok 19 - get_term_count
ok 20 - get_field_name
ok 21 - get_field_code
ok 22 - get_field_description
ok 23 - is_date
ok 24 - is_singletoken
ok 25 - is_hierarchy
ok 26 - is_hidden
ok 27 - is_numerical
ok 28 - get_term_count
ok 29 - get_field_name
ok 30 - get_field_code
ok 31 - get_field_description
ok 32 - is_date
ok 33 - is_singletoken
ok 34 - is_hierarchy
ok 35 - is_hidden
ok 36 - is_numerical
ok 37 - LinkInfo
ok 38 - get_dbto
ok 39 - get_dbfrom
ok 40 - get_link_name
ok 41 - get_link_description
ok 42 - get_priority
ok 43 - get_html_tag
ok 44 - get_url
ok 45 - get_dbto
ok 46 - get_dbfrom
ok 47 - get_link_name
ok 48 - get_link_description
ok 49 - get_priority
ok 50 - get_html_tag
ok 51 - get_url
ok
t/Tools/EUtilities/elink_acheck.t ............
1..130
ok 1 - use Bio::Tools::EUtilities;
ok 2 - use Bio::Tools::EUtilities::EUtilParameters;
ok 3 - The object isa Bio::Tools::EUtilities::Link
ok 4
ok 5 - get_ids
ok 6 - get_ids
ok 7 - uncorrelated LinkSets lump everything together
ok 8
ok 9 - The object isa Bio::Tools::EUtilities::EUtilDataI
ok 10 - The object isa Bio::Tools::EUtilities::Link::LinkSet
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 - The object isa Bio::Tools::EUtilities::Link
ok 68
ok 69 - get_ids
ok 70 - get_ids
ok 71 - correlated LinkSets separate ID data
ok 72
ok 73 - The object isa Bio::Tools::EUtilities::EUtilDataI
ok 74 - The object isa Bio::Tools::EUtilities::Link::LinkSet
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
t/Tools/EUtilities/elink_lcheck.t ............
1..64
ok 1 - use Bio::Tools::EUtilities;
ok 2 - use Bio::Tools::EUtilities::EUtilParameters;
ok 3 - The object isa Bio::Tools::EUtilities::Link
ok 4
ok 5 - get_ids
ok 6 - uncorrelated LinkSets lump everything together
ok 7
ok 8 - The object isa Bio::Tools::EUtilities::EUtilDataI
ok 9 - The object isa Bio::Tools::EUtilities::Link::LinkSet
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 - The object isa Bio::Tools::EUtilities::Link
ok 35
ok 36 - get_ids
ok 37 - correlated LinkSets separate ID data
ok 38
ok 39 - The object isa Bio::Tools::EUtilities::EUtilDataI
ok 40 - The object isa Bio::Tools::EUtilities::Link::LinkSet
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/Tools/EUtilities/elink_llinks.t ............
1..86
ok 1 - use Bio::Tools::EUtilities;
ok 2 - use Bio::Tools::EUtilities::EUtilParameters;
ok 3 - The object isa Bio::Tools::EUtilities::Link
ok 4
ok 5 - get_ids
ok 6 - uncorrelated LinkSets lump everything together
ok 7
ok 8 - The object isa Bio::Tools::EUtilities::EUtilDataI
ok 9 - The object isa Bio::Tools::EUtilities::Link::LinkSet
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 - The object isa Bio::Tools::EUtilities::Link
ok 46
ok 47 - get_ids
ok 48 - correlated LinkSets separate ID data
ok 49
ok 50 - The object isa Bio::Tools::EUtilities::EUtilDataI
ok 51 - The object isa Bio::Tools::EUtilities::Link::LinkSet
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
t/Tools/EUtilities/elink_ncheck.t ............
1..60
ok 1 - use Bio::Tools::EUtilities;
ok 2 - use Bio::Tools::EUtilities::EUtilParameters;
ok 3 - The object isa Bio::Tools::EUtilities::Link
ok 4
ok 5 - get_ids
ok 6 - uncorrelated LinkSets lump everything together
ok 7
ok 8 - The object isa Bio::Tools::EUtilities::EUtilDataI
ok 9 - The object isa Bio::Tools::EUtilities::Link::LinkSet
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::Tools::EUtilities::Link
ok 31
ok 32 - get_ids
ok 33 - correlated LinkSets separate ID data
ok 34
ok 35 - The object isa Bio::Tools::EUtilities::EUtilDataI
ok 36 - The object isa Bio::Tools::EUtilities::Link::LinkSet
ok 37
ok 38
ok 39
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ok
t/Tools/EUtilities/elink_neighbor.t ..........
1..63
ok 1 - use Bio::Tools::EUtilities;
ok 2 - use Bio::Tools::EUtilities::EUtilParameters;
ok 3 - The object isa Bio::Tools::EUtilities::Link
ok 4
ok 5 - get_ids
ok 6 - uncorrelated LinkSets lump everything together
ok 7
ok 8 - The object isa Bio::Tools::EUtilities::EUtilDataI
ok 9 - The object isa Bio::Tools::EUtilities::Link::LinkSet
ok 10
ok 11
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ok 31
ok 32
ok 33
ok 34 - The object isa Bio::Tools::EUtilities::Link
ok 35
ok 36 - get_ids
ok 37 - correlated LinkSets separate ID data
ok 38
ok 39 - The object isa Bio::Tools::EUtilities::EUtilDataI
ok 40 - The object isa Bio::Tools::EUtilities::Link::LinkSet
ok 41
ok 42
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ok 61
ok 62
ok 63
ok
t/Tools/EUtilities/elink_neighbor_history.t ..
1..65
ok 1 - use Bio::Tools::EUtilities;
ok 2 - use Bio::Tools::EUtilities::EUtilParameters;
ok 3 - The object isa Bio::Tools::EUtilities::Link
ok 4
ok 5 - get_ids
ok 6 - uncorrelated LinkSets lump everything together
ok 7
ok 8 - The object isa Bio::Tools::EUtilities::EUtilDataI
ok 9 - The object isa Bio::Tools::EUtilities::Link::LinkSet
ok 10 - The object isa Bio::Tools::EUtilities::HistoryI
ok 11
ok 12
ok 13
ok 14
ok 15
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ok 21
ok 22
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ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35 - The object isa Bio::Tools::EUtilities::Link
ok 36
ok 37 - get_ids
ok 38 - correlated LinkSets separate ID data
ok 39
ok 40 - The object isa Bio::Tools::EUtilities::EUtilDataI
ok 41 - The object isa Bio::Tools::EUtilities::Link::LinkSet
ok 42 - The object isa Bio::Tools::EUtilities::HistoryI
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
t/Tools/EUtilities/elink_scores.t ............
1..58
ok 1 - use Bio::Tools::EUtilities;
ok 2 - use Bio::Tools::EUtilities::EUtilParameters;
ok 3 - The object isa Bio::Tools::EUtilities::Link
ok 4
ok 5 - get_ids
ok 6 - uncorrelated LinkSets lump everything together
ok 7
ok 8 - The object isa Bio::Tools::EUtilities::EUtilDataI
ok 9 - The object isa Bio::Tools::EUtilities::Link::LinkSet
ok 10
ok 11
ok 12
ok 13
ok 14
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ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok
t/Tools/EUtilities/epost.t ...................
1..17
ok 1 - use Bio::Tools::EUtilities;
ok 2 - use Bio::Tools::EUtilities::EUtilParameters;
ok 3 - The object isa Bio::Tools::EUtilities::EUtilDataI
ok 4 - The object isa Bio::Tools::EUtilities::Query
ok 5 - eutil
ok 6 - datatype
ok 7 - The object isa Bio::Tools::EUtilities::HistoryI
ok 8 - The object isa Bio::Tools::EUtilities::EUtilDataI
ok 9 - eutil
ok 10 - eutil
ok 11 - get_webenv
ok 12 - get_query_key
ok 13 - history
ok 14 - get_database
ok 15 - get_ids
ok 16 - get_database
ok 17 - get_ids
ok
t/Tools/EUtilities/esearch.t .................
1..33
ok 1 - use Bio::Tools::EUtilities;
ok 2 - use Bio::Tools::EUtilities::EUtilParameters;
ok 3 - get_count
ok 4
ok 5 - get_ids
ok 6 - get_retstart
ok 7 - get_retmax
ok 8 - get_translation_from
ok 9 - get_translation_to
ok 10 - get_db
ok 11 - get_database
ok 12 - get_term
ok 13 - get_db
ok 14 - get_database
ok 15 - get_term
ok 16 - get_corrected_query
ok 17 - get_replaced_terms
ok 18 - get_count
ok 19 - The object isa Bio::Tools::EUtilities::HistoryI
ok 20 - get_webenv
ok 21 - get_query_key
ok 22 - history
ok 23 - get_ids
ok 24 - get_retstart
ok 25 - get_retmax
ok 26 - get_translation_from
ok 27 - get_translation_to
ok 28 - get_db
ok 29 - get_database
ok 30 - get_term
ok 31 - get_corrected_query
ok 32 - get_replaced_terms
ok 33 - get_GlobalQueries
ok
t/Tools/EUtilities/espell.t ..................
1..22
ok 1 - use Bio::Tools::EUtilities;
ok 2 - use Bio::Tools::EUtilities::EUtilParameters;
ok 3 - get_db
ok 4 - get_dbs
ok 5 - get_database
ok 6 - get_databases
ok 7 - get_term
ok 8 - get_corrected_query
ok 9 - get_replaced_terms
ok 10 - get_replaced_terms
ok 11 - get_count
ok 12
ok 13 - get_ids
ok 14 - get_retstart
ok 15 - get_retmax
ok 16 - get_translation_from
ok 17 - get_translation_to
ok 18 - get_db
ok 19 - get_dbs
ok 20 - get_database
ok 21 - get_databases
ok 22 - get_term
ok
t/Tools/EUtilities/esummary.t ................
1..83
ok 1 - use Bio::Tools::EUtilities;
ok 2 - use Bio::Tools::EUtilities::EUtilParameters;
ok 3 - The object isa Bio::Tools::EUtilities::Summary
ok 4
ok 5 - The object isa Bio::Tools::EUtilities::Summary
ok 6
ok 7 - get_ids
ok 8
ok 9 - The object isa Bio::Tools::EUtilities::Summary::DocSum
ok 10
ok 11
ok 12
ok 13 - The object isa Bio::Tools::EUtilities::Summary::Item
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::Tools::EUtilities::Summary::Item
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 - The object isa Bio::Tools::EUtilities::Summary
ok 53
ok 54 - The object isa Bio::Tools::EUtilities::Summary
ok 55
ok 56 - get_ids
ok 57
ok 58 - The object isa Bio::Tools::EUtilities::Summary::DocSum
ok 59
ok 60
ok 61
ok 62
ok 63 - The object isa Bio::Tools::EUtilities::Summary::Item
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Est2Genome.t .........................
1..61
ok 1 - use Bio::Tools::Est2Genome;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
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ok 14
ok 15
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ok 58
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ok 61
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/FootPrinter.t ........................
1..27
ok 1 - use Bio::Tools::FootPrinter;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
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ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/GFF.t ................................
1..34
ok 1 - use Bio::Tools::GFF;
ok 2 - use Bio::SeqFeature::Generic;
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
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ok 31
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ok 33
ok 34
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Geneid.t .............................
1..26
ok 1 - use Bio::Tools::Geneid;
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
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ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Genewise.t ...........................
1..33
ok 1 - use Bio::Tools::Genewise;
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
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ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Genomewise.t .........................
1..21
ok 1 - use Bio::Tools::Genomewise;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
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ok 14
ok 15
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ok 21
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Genpred.t ............................
1..185
ok 1 - use Bio::Tools::Fgenesh;
ok 2 - use Bio::Tools::Genscan;
ok 3 - use Bio::Tools::Genemark;
ok 4 - use Bio::Tools::Glimmer;
ok 5 - use Bio::Tools::MZEF;
ok 6 - use Bio::SeqIO;
ok 7
ok 8
ok 9
ok 10 - strand match (-1 and -1)
ok 11 - score match (1.05 and 1.05)
ok 12
ok 13 - predicted and extracted protein seqs match
ok 14 - strand match (1 and 1)
ok 15 - score match (4.46 and 4.46)
ok 16
ok 17 - predicted and extracted protein seqs match
ok 18 - initial exons 0
ok 19 - score match 1.74
ok 20
ok 21 - predicted and extracted protein seqs match
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 - Genemark tests
ok 43
ok 44
ok 45
ok 46 - The object isa Bio::Location::Fuzzy
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55 - The object isa Bio::Location::Fuzzy
ok 56
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ok 115
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ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126 - The object isa Bio::Location::SplitLocationI
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140 - The object isa Bio::Location::SplitLocationI
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 - The object isa Bio::Location::Fuzzy
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161 - The object isa Bio::Location::Fuzzy
ok 162
ok 163
ok 164
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ok 166
ok 167
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ok 169
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ok 182
ok 183
ok 184
ok 185
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Hmmer.t ..............................
1..29
ok 1 - use Bio::Tools::HMMER::Domain;
ok 2 - use Bio::Tools::HMMER::Set;
ok 3 - use Bio::Tools::HMMER::Results;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
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ok 13
ok 14
ok 15
ok 16
ok 17
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ok 24
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ok 26
ok 27
ok 28
ok 29
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/IUPAC.t ..............................
1..4
ok 1 - use Bio::Tools::IUPAC;
ok 2 - use Bio::Seq;
ok 3
ok 4
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Lucy.t ...............................
1..22
ok 1 - use Bio::Tools::Lucy;
ok 2 - The object isa Bio::Tools::Lucy
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
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ok 18
ok 19
ok 20
ok 21
ok 22
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Match.t ..............................
1..38
ok 1 - use Bio::Tools::Match;
ok 2
ok 3 - The object isa Bio::SeqFeature::Annotated
ok 4 - correct source
ok 5 - feature start correct
ok 6 - feature end correct
ok 7 - feature core score correct
ok 8 - feature matrix score correct
ok 9 - feature matrix id correct
ok 10 - The object isa Bio::SeqFeature::Annotated
ok 11 - correct source
ok 12 - feature start correct
ok 13 - feature end correct
ok 14 - feature core score correct
ok 15 - feature matrix score correct
ok 16 - feature matrix id correct
ok 17 - The object isa Bio::SeqFeature::Annotated
ok 18 - correct source
ok 19 - feature start correct
ok 20 - feature end correct
ok 21 - feature core score correct
ok 22 - feature matrix score correct
ok 23 - feature matrix id correct
ok 24 - The object isa Bio::SeqFeature::Annotated
ok 25 - correct source
ok 26 - feature start correct
ok 27 - feature end correct
ok 28 - feature core score correct
ok 29 - feature matrix score correct
ok 30 - feature matrix id correct
ok 31 - The object isa Bio::SeqFeature::Annotated
ok 32 - correct source
ok 33 - feature start correct
ok 34 - feature end correct
ok 35 - feature core score correct
ok 36 - feature matrix score correct
ok 37 - feature matrix id correct
ok 38 - correct number of results managed to get tested
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Phylo/Gerp.t .........................
1..33
ok 1 - use Bio::Tools::Phylo::Gerp;
ok 2
ok 3 - The object isa Bio::SeqFeature::Annotated
ok 4 - correct source
ok 5 - feature start correct
ok 6 - feature end correct
ok 7 - feature score correct
ok 8 - feature pvalue correct
ok 9 - The object isa Bio::SeqFeature::Annotated
ok 10 - correct source
ok 11 - feature start correct
ok 12 - feature end correct
ok 13 - feature score correct
ok 14 - feature pvalue correct
ok 15 - The object isa Bio::SeqFeature::Annotated
ok 16 - correct source
ok 17 - feature start correct
ok 18 - feature end correct
ok 19 - feature score correct
ok 20 - feature pvalue correct
ok 21 - The object isa Bio::SeqFeature::Annotated
ok 22 - correct source
ok 23 - feature start correct
ok 24 - feature end correct
ok 25 - feature score correct
ok 26 - feature pvalue correct
ok 27 - The object isa Bio::SeqFeature::Annotated
ok 28 - correct source
ok 29 - feature start correct
ok 30 - feature end correct
ok 31 - feature score correct
ok 32 - feature pvalue correct
ok 33 - correct number of results parsed out
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Tools/Phylo/Molphy.t .......................
1..18
ok 1 - use Bio::Tools::Phylo::Molphy;
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
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Phylo/PAML.t .........................
1..202
ok 1 - use Bio::Tools::Phylo::PAML;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
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ok 137
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ok 139
ok 140
ok 141
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ok 149
ok 150
ok 151
ok 152
ok 153
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ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163 - node\#8 reconstructed seq
ok 164 - ancestral AA
ok 165 - ancestral AA
ok 166 - derived AA
ok 167 - ancestral AA
ok 168 - ancestral AA
ok 169 - derived AA
ok 170 - derived AA
ok 171
ok 172
ok 173
ok 174
ok 175
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ok 196
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ok 201
ok 202
ok
t/Tools/Phylo/Phylip/ProtDist.t ..............
1..47
ok 1 - use Bio::Tools::Phylo::Phylip::ProtDist;
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
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ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
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ok 29
ok 30
ok 31
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ok 33
ok 34
ok 35
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ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Primer3.t ............................
1..14
ok 1 - use Bio::Tools::Primer3;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10 - The object isa Bio::Seq::PrimedSeq
ok 11
ok 12
ok 13
ok 14 - bug 2862
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Promoterwise.t .......................
1..7
ok 1 - use Bio::Tools::Promoterwise;
ok 2 - The object isa Bio::Tools::Promoterwise
ok 3
ok 4
ok 5
ok 6
ok 7
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Pseudowise.t .........................
1..21
ok 1 - use Bio::Tools::Pseudowise;
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/QRNA.t ...............................
1..30
ok 1 - use Bio::Tools::QRNA;
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
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ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok
t/Tools/RandDistFunctions.t ..................
1..5
ok 1 - use Bio::Tools::RandomDistFunctions;
ok 2
ok 3
ok 4
ok 5
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/RepeatMasker.t .......................
1..14
ok 1 - use Bio::Tools::RepeatMasker;
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/Tools/Run/RemoteBlast.t .................... skipped: Network tests have not been requested
t/Tools/Run/RemoteBlast_rpsblast.t ........... skipped: Network tests have not been requested
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Run/StandAloneBlast.t ................
1..45
ok 1 - use Bio::Tools::Run::StandAloneBlast;
ok 2 - use Bio::SeqIO;
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::Tools::Run::StandAloneBlast
ok 14 - The object isa Bio::Tools::Run::StandAloneNCBIBlast
ok 15 - The object isa Bio::Tools::Run::StandAloneBlast
ok 16 - The object isa Bio::Tools::Run::StandAloneWUBlast
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 # skip blastall not installed, skipping tests
ok 35 # skip blastall not installed, skipping tests
ok 36 # skip blastall not installed, skipping tests
ok 37 # skip blastall not installed, skipping tests
ok 38 # skip blastall not installed, skipping tests
ok 39 # skip blastall not installed, skipping tests
ok 40 # skip blastall not installed, skipping tests
ok 41 # skip blastall not installed, skipping tests
ok 42 # skip blastall not installed, skipping tests
ok 43 # skip blastall not installed, skipping tests
ok 44 # skip blastall not installed, skipping tests
ok 45 # skip blastall not installed, skipping tests
ok
t/Tools/Run/WrapperBase.t ....................
1..27
ok 1 - use Bio::Tools::Run::WrapperBase;
ok 2 - The object isa Bio::Tools::Run::WrapperBase
ok 3 - run() exists
ok 4 - program_dir() exists
ok 5 - program_name() exists
ok 6 - version() exists
ok 7 - error_string could be set
ok 8 - arguments could be set
ok 9 - no_param_checks could be set
ok 10 - save_tempfiles could be set
ok 11 - outfile_name could be set
ok 12 - quiet could be set
ok 13 - tempdir created a directory
ok 14 - could create file in tempdir
ok 15 - following cleanup() with save_tempfiles unset, tempdir was deleted
ok 16 - The object isa Bio::Root::IO
ok 17 - io() always returns the same instance of IO
ok 18 - program_path was correct
ok 19 - pretend program name not found as executable
ok 20 - perl found as exectuable
ok 21 - params string correct
ok 22 - params string correct
ok 23 - params string correct
ok 24 - params string correct
ok 25 - params string correct
ok 26 - params string correct
ok 27 - params string correct
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Seg.t ................................
1..15
ok 1 - use Bio::Tools::Seg;
ok 2 - parser defined
ok 3
ok 4 - seq id for seq 0 identified
ok 5 - start for seq 0 identified
ok 6 - end for seq 0 identified
ok 7 - score for seq 0 identified
ok 8 - seq id for seq 1 identified
ok 9 - start for seq 1 identified
ok 10 - end for seq 1 identified
ok 11 - score for seq 1 identified
ok 12 - seq id for seq 2 identified
ok 13 - start for seq 2 identified
ok 14 - end for seq 2 identified
ok 15 - score for seq 2 identified
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Tools/SiRNA.t ..............................
1..11
ok 1 - use Bio::Tools::SiRNA;
ok 2 - use Bio::Seq;
ok 3 - use Bio::SeqIO;
ok 4 - The object isa Bio::SeqIO
ok 5 - The object isa Bio::Tools::SiRNA
ok 6 - CDS only: got 65
ok 7
ok 8
ok 9 - The object isa Bio::Seq
ok 10
ok 11
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Sigcleave.t ..........................
1..18
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::Tools::Sigcleave;
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 - unable to get raw sigcleave results
ok 16
ok 17 - unable to get raw sigcleave results
ok 18
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Signalp.t ............................
1..11
ok 1 - use Bio::Tools::Signalp;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Signalp/ExtendedSignalp.t ............
1..185
ok 1 - use Bio::Tools::Signalp::ExtendedSignalp;
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
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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
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ok 98
ok 99
ok 100
ok 101
ok 102
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ok 104
ok 105
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ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
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ok 125
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ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
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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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Sim4.t ...............................
1..27
ok 1 - use Bio::Tools::Sim4::Results;
ok 2 - new Sim4 results instance
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11 - new Sim4 results instance
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Spidey/Spidey.t ......................
1..26
ok 1 - use Bio::Tools::Spidey::Results;
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/TandemRepeatsFinder.t ................
1..65
ok 1 - use Bio::Tools::TandemRepeatsFinder;
ok 2 - Parser created successfully
ok 3 - empty results file correctly returns no results
ok 4 - Second parser created successfully
ok 5 - seq_id for first result correctly parsed
ok 6 - start for first result correctly parsed
ok 7 - end for first result correctly parsed
ok 8 - source tag for first result correctly parsed
ok 9 - primary tag for first result correctly parsed
ok 10 - score for first result correctly parsed
ok 11 - sequence description correctly parsed.
ok 12 - correctly parsed all run parameters
ok 13 - correctly parsed period_size for first result
ok 14 - correctly parsed copy_number for first result
ok 15 - correctly parsed consensus_size for first result
ok 16 - correctly parsed percent_matches for first result
ok 17 - correctly parsed percent_indels for first result
ok 18 - correctly parsed percent_a for first result
ok 19 - correctly parsed percent_c for first result
ok 20 - correctly parsed percent_g for first result
ok 21 - correctly parsed percent_t for first result
ok 22 - correctly parsed entropy for first result
ok 23 - correctly parsed repeat_sequence for first result
ok 24 - correctly parsed consensus_sequence for first result
ok 25 - seq_id for second result correctly parsed
ok 26 - start for second result correctly parsed
ok 27 - end for second result correctly parsed
ok 28 - source tag for first result correctly parsed
ok 29 - primary tag for first result correctly parsed
ok 30 - score for first result correctly parsed
ok 31 - sequence description correctly parsed.
ok 32 - correctly reatained all run parameters for second feature
ok 33 - correctly parsed period_size for second result
ok 34 - correctly parsed copy_number for second result
ok 35 - correctly parsed consensus_size for second result
ok 36 - correctly parsed percent_matches for second result
ok 37 - correctly parsed percent_indels for second result
ok 38 - correctly parsed percent_a for second result
ok 39 - correctly parsed percent_c for second result
ok 40 - correctly parsed percent_g for second result
ok 41 - correctly parsed percent_t for second result
ok 42 - correctly parsed entropy for second result
ok 43 - correctly parsed repeat_sequence for second result
ok 44 - correctly parsed consensus_sequence for second result
ok 45 - seq_id for first result correctly parsed
ok 46 - start for first result correctly parsed
ok 47 - end for first result correctly parsed
ok 48 - source tag for first result correctly parsed
ok 49 - primary tag for first result correctly parsed
ok 50 - score for first result correctly parsed
ok 51 - sequence description correctly parsed.
ok 52 - correctly reatained all run parameters for third feature
ok 53 - correctly parsed period_size for third result
ok 54 - correctly parsed copy_number for third result
ok 55 - correctly parsed consensus_size for third result
ok 56 - correctly parsed percent_matches for third result
ok 57 - correctly parsed percent_indels for third result
ok 58 - correctly parsed percent_a for third result
ok 59 - correctly parsed percent_c for third result
ok 60 - correctly parsed percent_g for third result
ok 61 - correctly parsed percent_t for third result
ok 62 - correctly parsed entropy for third result
ok 63 - correctly parsed repeat_sequence for third result
ok 64 - correctly parsed consensus_sequence for third result
ok 65 - correctly return undef when no features are left
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/TargetP.t ............................
1..124
ok 1 - use Bio::Tools::TargetP;
ok 2
ok 3
ok 4
ok 5 - good SeqID
ok 6 - good Seqlength
ok 7 - correct Mitochondrion cutoff
ok 8 - correct signalpPeptide cutoff
ok 9 - correct other cutoff
ok 10 - correct location
ok 11 - correct Reliability class score
ok 12 - No peptide signal length reported
ok 13 - good SeqID
ok 14 - good Seqlength
ok 15 - correct Mitochondrion cutoff
ok 16 - correct signalpPeptide cutoff
ok 17 - correct other cutoff
ok 18 - correct location
ok 19 - correct Reliability class score
ok 20 - correct peptide signal length
ok 21 - good SeqID
ok 22 - good Seqlength
ok 23 - correct Mitochondrion cutoff
ok 24 - correct signalpPeptide cutoff
ok 25 - correct other cutoff
ok 26 - correct location
ok 27 - correct Reliability class score
ok 28 - correct peptide signal length
ok 29 - good SeqID
ok 30 - good Seqlength
ok 31 - correct Mitochondrion cutoff
ok 32 - correct signalpPeptide cutoff
ok 33 - correct other cutoff
ok 34 - correct location
ok 35 - correct Reliability class score
ok 36 - No peptide signal length reported
ok 37 - good SeqID
ok 38 - good Seqlength
ok 39 - correct Mitochondrion cutoff
ok 40 - correct signalpPeptide cutoff
ok 41 - correct other cutoff
ok 42 - correct location
ok 43 - correct Reliability class score
ok 44 - No peptide signal length reported
ok 45 - good SeqID
ok 46 - good Seqlength
ok 47 - correct Mitochondrion cutoff
ok 48 - correct signalpPeptide cutoff
ok 49 - correct other cutoff
ok 50 - correct location
ok 51 - correct Reliability class score
ok 52 - No peptide signal length reported
ok 53 - good SeqID
ok 54 - good Seqlength
ok 55 - correct Mitochondrion cutoff
ok 56 - correct signalpPeptide cutoff
ok 57 - correct other cutoff
ok 58 - correct location
ok 59 - correct Reliability class score
ok 60 - No peptide signal length reported
ok 61 - good SeqID
ok 62 - good Seqlength
ok 63 - correct Mitochondrion cutoff
ok 64 - correct signalpPeptide cutoff
ok 65 - correct other cutoff
ok 66 - correct location
ok 67 - correct Reliability class score
ok 68 - correct peptide signal length
ok 69 - good SeqID
ok 70 - good Seqlength
ok 71 - correct Mitochondrion cutoff
ok 72 - correct signalpPeptide cutoff
ok 73 - correct other cutoff
ok 74 - correct location
ok 75 - correct Reliability class score
ok 76 - No peptide signal length reported
ok 77 - good SeqID
ok 78 - good Seqlength
ok 79 - correct Mitochondrion cutoff
ok 80 - correct signalpPeptide cutoff
ok 81 - correct other cutoff
ok 82 - correct location
ok 83 - correct Reliability class score
ok 84 - No peptide signal length reported
ok 85 - good SeqID
ok 86 - good Seqlength
ok 87 - correct Mitochondrion cutoff
ok 88 - correct signalpPeptide cutoff
ok 89 - correct other cutoff
ok 90 - correct location
ok 91 - correct Reliability class score
ok 92 - No peptide signal length reported
ok 93 - good SeqID
ok 94 - good Seqlength
ok 95 - correct Mitochondrion cutoff
ok 96 - correct signalpPeptide cutoff
ok 97 - correct other cutoff
ok 98 - correct location
ok 99 - correct Reliability class score
ok 100 - No peptide signal length reported
ok 101 - good SeqID
ok 102 - good Seqlength
ok 103 - correct Mitochondrion cutoff
ok 104 - correct signalpPeptide cutoff
ok 105 - correct other cutoff
ok 106 - correct location
ok 107 - correct Reliability class score
ok 108 - correct peptide signal length
ok 109 - good SeqID
ok 110 - good Seqlength
ok 111 - correct Mitochondrion cutoff
ok 112 - correct signalpPeptide cutoff
ok 113 - correct other cutoff
ok 114 - correct location
ok 115 - correct Reliability class score
ok 116 - No peptide signal length reported
ok 117 - good SeqID
ok 118 - good Seqlength
ok 119 - correct Mitochondrion cutoff
ok 120 - correct signalpPeptide cutoff
ok 121 - correct other cutoff
ok 122 - correct location
ok 123 - correct Reliability class score
ok 124 - No peptide signal length reported
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/Tmhmm.t ..............................
1..12
ok 1 - use Bio::Tools::Tmhmm;
ok 2 - new()
ok 3 - got 3 feat
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/ePCR.t ...............................
1..27
ok 1 - use Bio::Tools::EPCR;
ok 2 - use Bio::SeqIO;
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 - got 3 forward strand ePCR hits
ok 27 - got 3 reverse strand ePCR hits
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/pICalculator.t .......................
1..38
ok 1 - use Bio::Seq;
ok 2 - use Bio::Tools::pICalculator;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok
t/Tools/rnamotif.t ........................... skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tools/tRNAscanSE.t .........................
1..14
ok 1 - use Bio::Tools::tRNAscanSE;
ok 2 - The object isa Bio::Tools::tRNAscanSE
ok 3
ok 4 - seq_id
ok 5 - codon
ok 6 - start
ok 7 - end
ok 8 - strand
ok 9 - exons
ok 10 - end
ok 11 - start
ok 12 - start
ok 13 - end
ok 14 - seq_id
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Tree/Compatible.t ..........................
1..5
ok 1 - use Bio::Tree::Compatible;
ok 2 - use Bio::TreeIO;
ok 3
ok 4
ok 5
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Tree/Node.t ................................
1..40
ok 1 - use Bio::Tree::Node;
ok 2 - use Bio::Tree::AlleleNode;
ok 3 - use Bio::TreeIO;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11 - retrieve the first value
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 - with fake node
ok 37 - after reroot on fake node
ok 38 - reroot on B
ok 39 - remove fake node, reroot on former B anc
ok 40 - roundtrip
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Tree/PhyloNetwork/Factory.t ................
1..70
ok 1 - use Bio::PhyloNetwork::Factory;
ok 2 - The object isa Bio::PhyloNetwork::Factory
ok 3 - factory
ok 4 - seen all the data lines
ok 5 - found
ok 6 - found
ok 7 - found
ok 8 - found
ok 9 - found
ok 10 - found
ok 11 - found
ok 12 - found
ok 13 - found
ok 14 - found
ok 15 - found
ok 16 - found
ok 17 - found
ok 18 - found
ok 19 - found
ok 20 - found
ok 21 - found
ok 22 - found
ok 23 - found
ok 24 - found
ok 25 - found
ok 26 - found
ok 27 - found
ok 28 - found
ok 29 - found
ok 30 - found
ok 31 - found
ok 32 - found
ok 33 - found
ok 34 - found
ok 35 - found
ok 36 - found
ok 37 - found
ok 38 - found
ok 39 - found
ok 40 - found
ok 41 - found
ok 42 - found
ok 43 - found
ok 44 - found
ok 45 - found
ok 46 - found
ok 47 - found
ok 48 - found
ok 49 - found
ok 50 - found
ok 51 - found
ok 52 - found
ok 53 - found
ok 54 - found
ok 55 - found
ok 56 - found
ok 57 - found
ok 58 - found
ok 59 - found
ok 60 - found
ok 61 - found
ok 62 - found
ok 63 - found
ok 64 - found
ok 65 - found
ok 66 - found
ok 67 - found
ok 68 - found
ok 69 - found
ok 70 - found
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Tree/PhyloNetwork/GraphViz.t ............... skipped: The optional module GraphViz (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/MuVector.t ...............
1..8
ok 1 - use Bio::PhyloNetwork::muVector;
ok 2 - The object isa Bio::PhyloNetwork::muVector
ok 3 - The object isa Bio::PhyloNetwork::muVector
ok 4 - arithmetic
ok 5 - display
ok 6 - is_positive
ok 7 - geq_poset
ok 8 - geq_poset
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Tree/PhyloNetwork/PhyloNetwork.t ...........
1..30
ok 1 - use Bio::PhyloNetwork;
ok 2 - The object isa Bio::PhyloNetwork
ok 3 - is_leaf
ok 4 - is_tree_node
ok 5 - is_hybrid_node
ok 6 - is_root
ok 7 - is_tree_child
ok 8 - nodes
ok 9 - leaves
ok 10 - internal_nodes
ok 11 - edges
ok 12 - tree_edges
ok 13 - hybrid_edges
ok 14 - mudata
ok 15 - build from mudata
ok 16 - heights
ok 17 - mu_distance
ok 18 - time_consistent
ok 19 - temporal_representation
ok 20 - tripartitions
ok 21 - tripartitions
ok 22 - tripartition_error
ok 23 - weight (manhattan)
ok 24 - optimal_alignment (manhattan)
ok 25 - weight (hamming)
ok 26 - optimal_alignment (hamming)
ok 27 - eNewick
ok 28 - eNewick_full
ok 29 - explode
ok 30 - The object isa Bio::Tree::Tree
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Tree/PhyloNetwork/RandomFactory.t ..........
1..70
ok 1 - use Bio::PhyloNetwork::RandomFactory;
ok 2 - The object isa Bio::PhyloNetwork::RandomFactory
ok 3 - random factory
ok 4
ok 5 - found
ok 6 - found
ok 7 - found
ok 8 - found
ok 9 - found
ok 10 - found
ok 11 - found
ok 12 - found
ok 13 - found
ok 14 - found
ok 15 - found
ok 16 - found
ok 17 - found
ok 18 - found
ok 19 - found
ok 20 - found
ok 21 - found
ok 22 - found
ok 23 - found
ok 24 - found
ok 25 - found
ok 26 - found
ok 27 - found
ok 28 - found
ok 29 - found
ok 30 - found
ok 31 - found
ok 32 - found
ok 33 - found
ok 34 - found
ok 35 - found
ok 36 - found
ok 37 - found
ok 38 - found
ok 39 - found
ok 40 - found
ok 41 - found
ok 42 - found
ok 43 - found
ok 44 - found
ok 45 - found
ok 46 - found
ok 47 - found
ok 48 - found
ok 49 - found
ok 50 - found
ok 51 - found
ok 52 - found
ok 53 - found
ok 54 - found
ok 55 - found
ok 56 - found
ok 57 - found
ok 58 - found
ok 59 - found
ok 60 - found
ok 61 - found
ok 62 - found
ok 63 - found
ok 64 - found
ok 65 - found
ok 66 - found
ok 67 - found
ok 68 - found
ok 69 - found
ok 70 - found
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Tree/PhyloNetwork/TreeFactory.t ............
1..19
ok 1 - use Bio::PhyloNetwork::TreeFactory;
ok 2 - The object isa Bio::PhyloNetwork::TreeFactory
ok 3 - tree factory
ok 4 - seen all the data lines
ok 5 - found
ok 6 - found
ok 7 - found
ok 8 - found
ok 9 - found
ok 10 - found
ok 11 - found
ok 12 - found
ok 13 - found
ok 14 - found
ok 15 - found
ok 16 - found
ok 17 - found
ok 18 - found
ok 19 - found
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Tree/RandomTreeFactory.t ...................
1..5
ok 1 - use Bio::Tree::RandomFactory;
ok 2 - use Bio::TreeIO;
ok 3 - use Bio::Tree::Statistics;
ok 4
ok 5
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
--------------------- WARNING ---------------------
MSG: Must specify a valid ARRAY reference to initialize a Node's Descendents
---------------------------------------------------
Can't use string ("id") as an ARRAY ref while "strict refs" in use at Bio/Tree/Node.pm line 143, line 3.
# Looks like you planned 62 tests but ran 34.
# Looks like your test exited with 255 just after 34.
t/Tree/Tree.t ................................
1..62
ok 1 - use Bio::TreeIO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7 - retrieve the first value
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14 - Number of nodes that have ADH2 as name
ok 15 - Test Monophyly
ok 16 - Height
ok 17 - Depth
ok 18 - non-monophyletic group
ok 19 - not a binary tree
ok 20 - 12 nodes
ok 21 - after force_binary() it is
ok 22 - and there are more nodes (17)
ok 23 - B,C are Monophyletic
ok 24 - A,B are Monophyletic
ok 25 - B,F are not Monophyletic
ok 26 - A,B are Monophyletic
ok 27 - A,B,C are not Monophyletic w D as outgroup
ok 28 - A,F,E are monophyletic with I as outgroup
ok 29 - subtree_length() without attributes is an alias to total_branch_lenght()
ok 30 - Length of the tree is larger that lenght of a subtree
ok 31 - Can re-root with A as outgroup
ok 32 - Count the number of nodes
ok 33 - same length
ok 34 - Root node is A
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 28/62 subtests
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Tree/TreeIO.t ..............................
1..74
ok 1 - use Bio::TreeIO;
ok 2
ok 3 - The object isa Bio::Tree::TreeI
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13 - The object isa Bio::Tree::TreeI
ok 14
ok 15
ok 16
ok 17
ok 18 - Saw SINFRUP0000006110 as expected
ok 19
ok 20
ok 21
ok 22 - The object isa Bio::Tree::TreeI
ok 23 - Total Nodes
ok 24
ok 25
ok 26
ok 27 - The object isa Bio::Tree::TreeI
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34 - The object isa Bio::Tree::TreeI
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42 - The object isa Bio::Tree::TreeI
ok 43 - Leaf nodes
ok 44 - All nodes
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 - bug 2356
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
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Tree/TreeIO/lintree.t ......................
1..24
ok 1 - use Bio::TreeIO;
ok 2 - The object isa Bio::Tree::TreeI
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9 - The object isa Bio::Tree::TreeI
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17 - The object isa Bio::Tree::TreeI
ok 18 - Leaf nodes
ok 19 - All nodes
ok 20
ok 21
ok 22
ok 23
ok 24
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Tree/TreeIO/newick.t .......................
1..24
ok 1 - use Bio::TreeIO;
ok 2
ok 3 - The object isa Bio::Tree::TreeI
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13 - The object isa Bio::Tree::TreeI
ok 14
ok 15
ok 16
ok 17
ok 18 - Saw SINFRUP0000006110 as expected
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Tree/TreeIO/nexus.t ........................
1..24
ok 1 - use Bio::TreeIO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10 - bug 2356
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
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Tree/TreeIO/nhx.t ..........................
1..7
ok 1 - use Bio::TreeIO;
ok 2
ok 3 - The object isa Bio::Tree::TreeI
ok 4 - Total Nodes
ok 5
ok 6
ok 7
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Tree/TreeIO/phyloxml.t .....................
1..97
ok 1 - use Bio::TreeIO;
ok 2 - use Bio::TreeIO::phyloxml;
ok 3
ok 4 - The object isa Bio::Tree::TreeI
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15 - The object isa Bio::Tree::TreeI
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23 - The object isa Bio::Tree::TreeI
ok 24
ok 25
ok 26
ok 27
ok 28 - The object isa Bio::Tree::TreeI
ok 29 - The object isa Bio::Annotation::Collection
ok 30 - The object isa Bio::Annotation::Collection
ok 31
ok 32 - The object isa Bio::Annotation::Collection
ok 33
ok 34 - The object isa Bio::SeqI
ok 35 - The object isa Bio::Annotation::Collection
ok 36
ok 37
ok 38 - The object isa Bio::Tree::TreeI
ok 39
ok 40 - The object isa Bio::SeqI
ok 41 - The object isa Bio::Annotation::Relation
ok 42
ok 43 - The object isa Bio::SeqI
ok 44 - The object isa Bio::Annotation::Relation
ok 45
ok 46 - The object isa Bio::SeqI
ok 47
ok 48 - The object isa Bio::Tree::TreeI
ok 49 - The object isa Bio::SeqI
ok 50
ok 51
ok 52
ok 53
ok 54 - The object isa Bio::Tree::TreeI
ok 55 - The object isa Bio::Annotation::Relation
ok 56
ok 57 - The object isa Bio::Tree::AnnotatableNode
ok 58
ok 59
ok 60
ok 61 - The object isa Bio::Tree::TreeI
ok 62 - The object isa Bio::Tree::AnnotatableNode
ok 63 - The object isa Bio::AnnotationCollectionI
ok 64 - The object isa Bio::Annotation::Collection
ok 65
ok 66
ok 67
ok 68 - The object isa Bio::Tree::TreeI
ok 69 - The object isa Bio::Tree::AnnotatableNode
ok 70 - The object isa Bio::AnnotationCollectionI
ok 71 - The object isa Bio::Annotation::Collection
ok 72
ok 73
ok 74
ok 75 - The object isa Bio::Tree::TreeI
ok 76
ok 77 - The object isa Bio::Tree::TreeI
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83 - The object isa Bio::Tree::TreeI
ok 84
ok 85
ok 86
ok 87
ok 88 - The object isa Bio::Tree::TreeI
ok 89
ok 90 - The object isa Bio::Tree::AnnotatableNode
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96 - The object isa Bio::Tree::TreeI
ok 97
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
Use of uninitialized value $txt[0] in join or string at /home/fly1800/var/megalib/SVG/Element.pm line 1205, line 1.
t/Tree/TreeIO/svggraph.t .....................
1..4
ok 1 - use Bio::TreeIO;
ok 2
ok 3
ok 4
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Tree/TreeIO/tabtree.t ......................
1..24
ok 1 - use Bio::TreeIO;
ok 2 - The object isa Bio::Tree::TreeI
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9 - The object isa Bio::Tree::TreeI
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17 - The object isa Bio::Tree::TreeI
ok 18 - Leaf nodes
ok 19 - All nodes
ok 20
ok 21
ok 22
ok 23
ok 24
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Tree/TreeStatistics.t ......................
1..40
ok 1 - use Bio::TreeIO;
ok 2 - use Bio::Tree::Statistics;
ok 3 - cherries
ok 4 - cherries
ok 5 - read traits
ok 6 - parsimony score
ok 7 - subtree parsimony score
ok 8 - ps value
ok 9 - fitch_down
ok 10 - ps value after fitch_down
ok 11 - persistence of a leaf
ok 12 - persistence of an internal node value
ok 13 - persistence of an internal node value
ok 14 - persistence of an internal node value
ok 15 - leaf node: number of clusters = 0
ok 16 - number of clusters
ok 17 - number of clusters
ok 18 - number of clusters
ok 19 - number of leaves in phylotype
ok 20 - number of leaves in phylotype
ok 21 - number of leaves in phylotype
ok 22 - number of leaves in phylotype
ok 23 - phylotype length
ok 24 - phylotype length
ok 25 - phylotype length
ok 26 - phylotype length
ok 27 - phylotype length
ok 28 - sum of leaf distances
ok 29 - sum of leaf distances
ok 30 - sum of leaf distances
ok 31 - sum of leaf distances
ok 32 - sum of leaf distances
ok 33 - genetic diversity
ok 34 - separation
ok 35 - association index
ok 36 - subtree association index
ok 37 - monophyletic clade size
ok 38 - monophyletic clade size
ok 39 - monophyletic clade size
ok 40 - monophyletic clade size
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Variation/AAChange.t .......................
1..27
ok 1 - use Bio::Variation::Allele;
ok 2 - use Bio::Variation::AAChange;
ok 3 - use Bio::Variation::RNAChange;
ok 4
ok 5 - The object isa Bio::Variation::AAChange
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 - Trivial name is [V3A]
ok 27
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Variation/AAReverseMutate.t ................
1..16
ok 1 - use Bio::Variation::AAReverseMutate;
ok 2
ok 3 - The object isa Bio::Variation::AAReverseMutate
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10 - The object isa Bio::Variation::RNAChange
ok 11
ok 12
ok 13
ok 14 - Codon_ori is |ttc|
ok 15
ok 16
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Variation/Allele.t .........................
1..14
ok 1 - use Bio::Variation::Allele;
ok 2 - The object isa Bio::Variation::Allele
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Variation/DNAMutation.t ....................
1..37
ok 1 - use Bio::Variation::DNAMutation;
ok 2 - use Bio::Variation::Allele;
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Variation/RNAChange.t ......................
1..31
ok 1 - use Bio::Variation::Allele;
ok 2 - use Bio::Variation::RNAChange;
ok 3 - use Bio::Variation::AAChange;
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 - label ismissense
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25 - Codon_ori is |gaa|
ok 26 - Codon_mut is |aaa|
ok 27
ok 28
ok 29
ok 30
ok 31
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Variation/SNP.t ............................
1..13
ok 1 - use Bio::Variation::SNP;
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
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Variation/SeqDiff.t ........................
1..44
ok 1 - use Bio::Variation::SeqDiff;
ok 2 - use Bio::Variation::DNAMutation;
ok 3 - use Bio::Variation::Allele;
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 - The object isa Bio::Variation::VariantI
ok 34 - The object isa Bio::Variation::VariantI
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42 - The object isa Bio::PrimarySeq
ok 43
ok 44
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Variation/Variation_IO.t ...................
1..26
ok 1 - use Bio::Variation::IO;
ok 2
ok 3
ok 4
ok 5
ok 6 - test output file compared to input
ok 7
ok 8
ok 9
ok 10
ok 11 - test output file compared to input
ok 12
ok 13
ok 14
ok 15
ok 16 - test output file compared to input
ok 17
ok 18
ok 19
ok 20
ok 21 - test output file compared to input
ok 22
ok 23
ok 24
ok 25
ok 26 - test output file compared to input
ok
Test Summary Report
-------------------
t/LocalDB/SeqFeature.t (Wstat: 256 Tests: 69 Failed: 1)
Failed test: 2
Non-zero exit status: 1
t/LocalDB/transfac_pro.t (Wstat: 65280 Tests: 4 Failed: 1)
Failed test: 4
Non-zero exit status: 255
Parse errors: Bad plan. You planned 115 tests but ran 4.
t/Map/Map.t (Wstat: 65280 Tests: 134 Failed: 3)
Failed tests: 132-134
Non-zero exit status: 255
Parse errors: Bad plan. You planned 267 tests but ran 134.
t/Map/Physical.t (Wstat: 256 Tests: 39 Failed: 1)
Failed test: 39
Non-zero exit status: 1
t/Matrix/IO/masta.t (Wstat: 6400 Tests: 1 Failed: 0)
Non-zero exit status: 25
Parse errors: Bad plan. You planned 16 tests but ran 1.
t/Matrix/IO/psm.t (Wstat: 65280 Tests: 2 Failed: 1)
Failed test: 2
Non-zero exit status: 255
Parse errors: Bad plan. You planned 63 tests but ran 2.
t/Matrix/ProtPsm.t (Wstat: 65280 Tests: 2 Failed: 1)
Failed test: 2
Non-zero exit status: 255
Parse errors: Bad plan. You planned 14 tests but ran 2.
t/Matrix/SiteMatrix.t (Wstat: 65280 Tests: 1 Failed: 1)
Failed test: 1
Non-zero exit status: 255
Parse errors: Bad plan. You planned 14 tests but ran 1.
t/Ontology/IO/obo.t (Wstat: 1792 Tests: 83 Failed: 7)
Failed tests: 14-20
Non-zero exit status: 7
t/PodSyntax.t (Wstat: 1280 Tests: 999 Failed: 5)
Failed tests: 376, 701, 734, 784, 987
Non-zero exit status: 5
t/SearchIO/Tiling.t (Wstat: 65280 Tests: 0 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 1093 tests but ran 0.
t/Tree/Tree.t (Wstat: 65280 Tests: 34 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 62 tests but ran 34.
Files=329, Tests=17250, 171 wallclock secs ( 2.57 usr 2.63 sys + 150.89 cusr 13.37 csys = 169.46 CPU)
Result: FAIL
Failed 12/329 test programs. 21/17250 subtests failed.
make: *** [test] Error 255
CJFIELDS/BioPerl-1.6.1.tar.gz
make test TEST_VERBOSE=1 -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
reports CJFIELDS/BioPerl-1.6.1.tar.gz
VmSize: 263908 kB
Finished 2013-06-21T11:06:24