PATH=/usr/bin:/bin
Start 2011-04-28T14:12:54
ActivePerl-1400 CPAN-1.9402
Going to read '/home/fly1400/var/cpan/Metadata'
  Database was generated on Wed, 27 Apr 2011 22:27:21 GMT
Running make for C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz
Checksum for /net/nas/data/cpan/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz ok
BioPerl-1.6.0/
BioPerl-1.6.0/AUTHORS
BioPerl-1.6.0/Bio/
BioPerl-1.6.0/Bio/Align/
BioPerl-1.6.0/Bio/Align/AlignI.pm
BioPerl-1.6.0/Bio/Align/DNAStatistics.pm
BioPerl-1.6.0/Bio/Align/PairwiseStatistics.pm
BioPerl-1.6.0/Bio/Align/ProteinStatistics.pm
BioPerl-1.6.0/Bio/Align/StatisticsI.pm
BioPerl-1.6.0/Bio/Align/Utilities.pm
BioPerl-1.6.0/Bio/AlignIO/
BioPerl-1.6.0/Bio/AlignIO/arp.pm
BioPerl-1.6.0/Bio/AlignIO/bl2seq.pm
BioPerl-1.6.0/Bio/AlignIO/clustalw.pm
BioPerl-1.6.0/Bio/AlignIO/emboss.pm
BioPerl-1.6.0/Bio/AlignIO/fasta.pm
BioPerl-1.6.0/Bio/AlignIO/Handler/
BioPerl-1.6.0/Bio/AlignIO/Handler/GenericAlignHandler.pm
BioPerl-1.6.0/Bio/AlignIO/largemultifasta.pm
BioPerl-1.6.0/Bio/AlignIO/maf.pm
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BioPerl-1.6.0/Bio/AlignIO/metafasta.pm
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BioPerl-1.6.0/Bio/AnnotatableI.pm
BioPerl-1.6.0/Bio/Annotation/
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BioPerl-1.6.0/Bio/Annotation/TagTree.pm
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BioPerl-1.6.0/Bio/Annotation/Tree.pm
BioPerl-1.6.0/Bio/Annotation/TypeManager.pm
BioPerl-1.6.0/Bio/AnnotationCollectionI.pm
BioPerl-1.6.0/Bio/AnnotationI.pm
BioPerl-1.6.0/Bio/Assembly/
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BioPerl-1.6.0/Bio/Assembly/IO/
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BioPerl-1.6.0/Bio/Assembly/ScaffoldI.pm
BioPerl-1.6.0/Bio/Assembly/Singlet.pm
BioPerl-1.6.0/Bio/Assembly/Tools/
BioPerl-1.6.0/Bio/Assembly/Tools/ContigSpectrum.pm
BioPerl-1.6.0/Bio/Biblio/
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BioPerl-1.6.0/Bio/Biblio/IO/pubmed2ref.pm
BioPerl-1.6.0/Bio/Biblio/IO/pubmedxml.pm
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BioPerl-1.6.0/Bio/Biblio/Provider.pm
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BioPerl-1.6.0/Bio/Cluster/SequenceFamily.pm
BioPerl-1.6.0/Bio/Cluster/UniGene.pm
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BioPerl-1.6.0/Bio/ClusterI.pm
BioPerl-1.6.0/Bio/ClusterIO/
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BioPerl-1.6.0/Bio/Coordinate/ResultI.pm
BioPerl-1.6.0/Bio/Coordinate/Utils.pm
BioPerl-1.6.0/Bio/Das/
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BioPerl-1.6.0/Bio/Das/SegmentI.pm
BioPerl-1.6.0/Bio/DasI.pm
BioPerl-1.6.0/Bio/DB/
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BioPerl-1.6.0/Bio/DB/EMBL.pm
BioPerl-1.6.0/Bio/DB/EntrezGene.pm
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BioPerl-1.6.0/Bio/DB/Expression/
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BioPerl-1.6.0/Bio/DB/Fasta.pm
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BioPerl-1.6.0/Bio/DB/Flat/
BioPerl-1.6.0/Bio/DB/Flat/BDB/
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BioPerl-1.6.0/Bio/DB/Flat/BDB/fasta.pm
BioPerl-1.6.0/Bio/DB/Flat/BDB/genbank.pm
BioPerl-1.6.0/Bio/DB/Flat/BDB/swiss.pm
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BioPerl-1.6.0/Bio/DB/Flat/BinarySearch.pm
BioPerl-1.6.0/Bio/DB/Flat.pm
BioPerl-1.6.0/Bio/DB/GenBank.pm
BioPerl-1.6.0/Bio/DB/GenericWebAgent.pm
BioPerl-1.6.0/Bio/DB/GenPept.pm
BioPerl-1.6.0/Bio/DB/GFF/
BioPerl-1.6.0/Bio/DB/GFF/Adaptor/
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BioPerl-1.6.0/Bio/DB/GFF/Adaptor/berkeleydb/
BioPerl-1.6.0/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
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BioPerl-1.6.0/Bio/DB/GFF/Adaptor/dbi/
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BioPerl-1.6.0/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm
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BioPerl-1.6.0/Bio/DB/GFF/Adaptor/dbi.pm
BioPerl-1.6.0/Bio/DB/GFF/Adaptor/memory/
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BioPerl-1.6.0/Bio/DB/GFF/Adaptor/memory.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/
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BioPerl-1.6.0/Bio/DB/GFF/Aggregator/clone.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/coding.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/gene.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/match.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/none.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/orf.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/processed_transcript.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/so_transcript.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/transcript.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/ucsc_acembly.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/ucsc_genscan.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/ucsc_refgene.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/ucsc_softberry.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator/ucsc_unigene.pm
BioPerl-1.6.0/Bio/DB/GFF/Aggregator.pm
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BioPerl-1.6.0/Bio/DB/GFF/Feature.pm
BioPerl-1.6.0/Bio/DB/GFF/Homol.pm
BioPerl-1.6.0/Bio/DB/GFF/RelSegment.pm
BioPerl-1.6.0/Bio/DB/GFF/Segment.pm
BioPerl-1.6.0/Bio/DB/GFF/Typename.pm
BioPerl-1.6.0/Bio/DB/GFF/Util/
BioPerl-1.6.0/Bio/DB/GFF/Util/Binning.pm
BioPerl-1.6.0/Bio/DB/GFF/Util/Rearrange.pm
BioPerl-1.6.0/Bio/DB/GFF.pm
BioPerl-1.6.0/Bio/DB/HIV/
BioPerl-1.6.0/Bio/DB/HIV/HIVAnnotProcessor.pm
BioPerl-1.6.0/Bio/DB/HIV/HIVQueryHelper.pm
BioPerl-1.6.0/Bio/DB/HIV/lanl-schema.xml
BioPerl-1.6.0/Bio/DB/HIV.pm
BioPerl-1.6.0/Bio/DB/InMemoryCache.pm
BioPerl-1.6.0/Bio/DB/LocationI.pm
BioPerl-1.6.0/Bio/DB/MeSH.pm
BioPerl-1.6.0/Bio/DB/NCBIHelper.pm
BioPerl-1.6.0/Bio/DB/Qual.pm
BioPerl-1.6.0/Bio/DB/Query/
BioPerl-1.6.0/Bio/DB/Query/GenBank.pm
BioPerl-1.6.0/Bio/DB/Query/HIVQuery.pm
BioPerl-1.6.0/Bio/DB/Query/WebQuery.pm
BioPerl-1.6.0/Bio/DB/QueryI.pm
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BioPerl-1.6.0/Bio/DB/ReferenceI.pm
BioPerl-1.6.0/Bio/DB/RefSeq.pm
BioPerl-1.6.0/Bio/DB/Registry.pm
BioPerl-1.6.0/Bio/DB/SeqFeature/
BioPerl-1.6.0/Bio/DB/SeqFeature/NormalizedFeature.pm
BioPerl-1.6.0/Bio/DB/SeqFeature/NormalizedFeatureI.pm
BioPerl-1.6.0/Bio/DB/SeqFeature/NormalizedTableFeatureI.pm
BioPerl-1.6.0/Bio/DB/SeqFeature/Segment.pm
BioPerl-1.6.0/Bio/DB/SeqFeature/Store/
BioPerl-1.6.0/Bio/DB/SeqFeature/Store/bdb.pm
BioPerl-1.6.0/Bio/DB/SeqFeature/Store/berkeleydb.pm
BioPerl-1.6.0/Bio/DB/SeqFeature/Store/DBI/
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BioPerl-1.6.0/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm
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BioPerl-1.6.0/Bio/DB/SeqFeature/Store/GFF3Loader.pm
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BioPerl-1.6.0/Bio/DB/SeqFeature/Store/LoadHelper.pm
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BioPerl-1.6.0/Bio/DB/SeqVersion/
BioPerl-1.6.0/Bio/DB/SeqVersion/gi.pm
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BioPerl-1.6.0/Bio/DB/Taxonomy/
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BioPerl-1.6.0/Bio/DB/Taxonomy/flatfile.pm
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BioPerl-1.6.0/Bio/DB/TFBS/
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BioPerl-1.6.0/Bio/DB/TFBS.pm
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BioPerl-1.6.0/Bio/Expression/
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BioPerl-1.6.0/Bio/Expression/FeatureGroup/
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BioPerl-1.6.0/Bio/Expression/FeatureI.pm
BioPerl-1.6.0/Bio/Expression/FeatureSet/
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BioPerl-1.6.0/Bio/Expression/Platform.pm
BioPerl-1.6.0/Bio/Expression/ProbeI.pm
BioPerl-1.6.0/Bio/Expression/Sample.pm
BioPerl-1.6.0/Bio/Factory/
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BioPerl-1.6.0/Bio/Factory/DriverFactory.pm
BioPerl-1.6.0/Bio/Factory/FTLocationFactory.pm
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BioPerl-1.6.0/Bio/Factory/SequenceFactoryI.pm
BioPerl-1.6.0/Bio/Factory/SequenceProcessorI.pm
BioPerl-1.6.0/Bio/Factory/SequenceStreamI.pm
BioPerl-1.6.0/Bio/Factory/TreeFactoryI.pm
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BioPerl-1.6.0/Bio/FeatureIO/
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BioPerl-1.6.0/Bio/LiveSeq/Translation.pm
BioPerl-1.6.0/Bio/LocatableSeq.pm
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BioPerl-1.6.0/Bio/Map/
BioPerl-1.6.0/Bio/Map/Clone.pm
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BioPerl-1.6.0/examples/tools/standaloneblast.pl
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BioPerl-1.6.0/scripts/biblio/biblio.PLS
BioPerl-1.6.0/scripts/biblio/TAG
BioPerl-1.6.0/scripts/Bio-DB-GFF/
BioPerl-1.6.0/scripts/Bio-DB-GFF/bulk_load_gff.PLS
BioPerl-1.6.0/scripts/Bio-DB-GFF/fast_load_gff.PLS
BioPerl-1.6.0/scripts/Bio-DB-GFF/genbank2gff.PLS
BioPerl-1.6.0/scripts/Bio-DB-GFF/genbank2gff3.PLS
BioPerl-1.6.0/scripts/Bio-DB-GFF/generate_histogram.PLS
BioPerl-1.6.0/scripts/Bio-DB-GFF/load_gff.PLS
BioPerl-1.6.0/scripts/Bio-DB-GFF/meta_gff.PLS
BioPerl-1.6.0/scripts/Bio-DB-GFF/process_gadfly.PLS
BioPerl-1.6.0/scripts/Bio-DB-GFF/process_sgd.PLS
BioPerl-1.6.0/scripts/Bio-DB-GFF/process_wormbase.PLS
BioPerl-1.6.0/scripts/Bio-DB-GFF/README
BioPerl-1.6.0/scripts/Bio-SeqFeature-Store/
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BioPerl-1.6.0/scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
BioPerl-1.6.0/scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
BioPerl-1.6.0/scripts/das/
BioPerl-1.6.0/scripts/das/README
BioPerl-1.6.0/scripts/das/TAG
BioPerl-1.6.0/scripts/DB/
BioPerl-1.6.0/scripts/DB/biofetch_genbank_proxy.PLS
BioPerl-1.6.0/scripts/DB/bioflat_index.PLS
BioPerl-1.6.0/scripts/DB/biogetseq.PLS
BioPerl-1.6.0/scripts/DB/flanks.PLS
BioPerl-1.6.0/scripts/DB/TAG
BioPerl-1.6.0/scripts/index/
BioPerl-1.6.0/scripts/index/bp_fetch.PLS
BioPerl-1.6.0/scripts/index/bp_index.PLS
BioPerl-1.6.0/scripts/index/bp_seqret.PLS
BioPerl-1.6.0/scripts/index/TAG
BioPerl-1.6.0/scripts/popgen/
BioPerl-1.6.0/scripts/popgen/composite_LD.PLS
BioPerl-1.6.0/scripts/popgen/heterogeneity_test.PLS
BioPerl-1.6.0/scripts/README
BioPerl-1.6.0/scripts/searchio/
BioPerl-1.6.0/scripts/searchio/fastam9_to_table.PLS
BioPerl-1.6.0/scripts/searchio/filter_search.PLS
BioPerl-1.6.0/scripts/searchio/hmmer_to_table.PLS
BioPerl-1.6.0/scripts/searchio/parse_hmmsearch.PLS
BioPerl-1.6.0/scripts/searchio/README
BioPerl-1.6.0/scripts/searchio/search2table.PLS
BioPerl-1.6.0/scripts/searchio/TAG
BioPerl-1.6.0/scripts/seq/
BioPerl-1.6.0/scripts/seq/extract_feature_seq.PLS
BioPerl-1.6.0/scripts/seq/make_mrna_protein.PLS
BioPerl-1.6.0/scripts/seq/seqconvert.PLS
BioPerl-1.6.0/scripts/seq/seqretsplit.PLS
BioPerl-1.6.0/scripts/seq/split_seq.PLS
BioPerl-1.6.0/scripts/seq/TAG
BioPerl-1.6.0/scripts/seq/translate_seq.PLS
BioPerl-1.6.0/scripts/seq/unflatten_seq.PLS
BioPerl-1.6.0/scripts/seqstats/
BioPerl-1.6.0/scripts/seqstats/aacomp.PLS
BioPerl-1.6.0/scripts/seqstats/chaos_plot.PLS
BioPerl-1.6.0/scripts/seqstats/gccalc.PLS
BioPerl-1.6.0/scripts/seqstats/oligo_count.PLS
BioPerl-1.6.0/scripts/seqstats/TAG
BioPerl-1.6.0/scripts/taxa/
BioPerl-1.6.0/scripts/taxa/classify_hits_kingdom.PLS
BioPerl-1.6.0/scripts/taxa/local_taxonomydb_query.PLS
BioPerl-1.6.0/scripts/taxa/query_entrez_taxa.PLS
BioPerl-1.6.0/scripts/taxa/TAG
BioPerl-1.6.0/scripts/taxa/taxid4species.PLS
BioPerl-1.6.0/scripts/taxa/taxonomy2tree.PLS
BioPerl-1.6.0/scripts/tree/
BioPerl-1.6.0/scripts/tree/blast2tree.PLS
BioPerl-1.6.0/scripts/tree/nexus2nh.PLS
BioPerl-1.6.0/scripts/tree/TAG
BioPerl-1.6.0/scripts/tree/tree2pag.PLS
BioPerl-1.6.0/scripts/utilities/
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BioPerl-1.6.0/scripts/utilities/bp_nrdb.PLS
BioPerl-1.6.0/scripts/utilities/bp_sreformat.PLS
BioPerl-1.6.0/scripts/utilities/dbsplit.PLS
BioPerl-1.6.0/scripts/utilities/download_query_genbank.PLS
BioPerl-1.6.0/scripts/utilities/mask_by_search.PLS
BioPerl-1.6.0/scripts/utilities/mutate.PLS
BioPerl-1.6.0/scripts/utilities/pairwise_kaks.PLS
BioPerl-1.6.0/scripts/utilities/README
BioPerl-1.6.0/scripts/utilities/remote_blast.PLS
BioPerl-1.6.0/scripts/utilities/search2alnblocks.PLS
BioPerl-1.6.0/scripts/utilities/search2BSML.PLS
BioPerl-1.6.0/scripts/utilities/search2gff.PLS
BioPerl-1.6.0/scripts/utilities/search2tribe.PLS
BioPerl-1.6.0/scripts/utilities/seq_length.PLS
BioPerl-1.6.0/scripts/utilities/TAG
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BioPerl-1.6.0/t/Align/
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BioPerl-1.6.0/t/Biblio/biofetch.t
BioPerl-1.6.0/t/Biblio/eutils.t
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BioPerl-1.6.0/t/ClusterIO/
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BioPerl-1.6.0/t/Tools/Run/
BioPerl-1.6.0/t/Tools/Run/RemoteBlast.t
BioPerl-1.6.0/t/Tools/Run/StandAloneBlast.t
BioPerl-1.6.0/t/Tools/Run/WrapperBase.t
BioPerl-1.6.0/t/Tools/Seg.t
BioPerl-1.6.0/t/Tools/Sigcleave.t
BioPerl-1.6.0/t/Tools/Signalp/
BioPerl-1.6.0/t/Tools/Signalp/ExtendedSignalp.t
BioPerl-1.6.0/t/Tools/Signalp.t
BioPerl-1.6.0/t/Tools/Sim4.t
BioPerl-1.6.0/t/Tools/SiRNA.t
BioPerl-1.6.0/t/Tools/Spidey/
BioPerl-1.6.0/t/Tools/Spidey/Spidey.t
BioPerl-1.6.0/t/Tools/TandemRepeatsFinder.t
BioPerl-1.6.0/t/Tools/TargetP.t
BioPerl-1.6.0/t/Tools/Tmhmm.t
BioPerl-1.6.0/t/Tools/tRNAscanSE.t
BioPerl-1.6.0/t/Tree/
BioPerl-1.6.0/t/Tree/Compatible.t
BioPerl-1.6.0/t/Tree/Node.t
BioPerl-1.6.0/t/Tree/PhyloNetwork/
BioPerl-1.6.0/t/Tree/PhyloNetwork/Factory.t
BioPerl-1.6.0/t/Tree/PhyloNetwork/GraphViz.t
BioPerl-1.6.0/t/Tree/PhyloNetwork/MuVector.t
BioPerl-1.6.0/t/Tree/PhyloNetwork/PhyloNetwork.t
BioPerl-1.6.0/t/Tree/PhyloNetwork/RandomFactory.t
BioPerl-1.6.0/t/Tree/PhyloNetwork/TreeFactory.t
BioPerl-1.6.0/t/Tree/RandomTreeFactory.t
BioPerl-1.6.0/t/Tree/Tree.t
BioPerl-1.6.0/t/Tree/TreeIO/
BioPerl-1.6.0/t/Tree/TreeIO/lintree.t
BioPerl-1.6.0/t/Tree/TreeIO/newick.t
BioPerl-1.6.0/t/Tree/TreeIO/nexus.t
BioPerl-1.6.0/t/Tree/TreeIO/nhx.t
BioPerl-1.6.0/t/Tree/TreeIO/phyloxml.t
BioPerl-1.6.0/t/Tree/TreeIO/svggraph.t
BioPerl-1.6.0/t/Tree/TreeIO/tabtree.t
BioPerl-1.6.0/t/Tree/TreeIO.t
BioPerl-1.6.0/t/Tree/TreeStatistics.t
BioPerl-1.6.0/t/Variation/
BioPerl-1.6.0/t/Variation/AAChange.t
BioPerl-1.6.0/t/Variation/AAReverseMutate.t
BioPerl-1.6.0/t/Variation/Allele.t
BioPerl-1.6.0/t/Variation/DNAMutation.t
BioPerl-1.6.0/t/Variation/RNAChange.t
BioPerl-1.6.0/t/Variation/SeqDiff.t
BioPerl-1.6.0/t/Variation/SNP.t
BioPerl-1.6.0/t/Variation/Variation_IO.t

  CPAN.pm: Going to build C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz

>>> /home/fly1400/ap1400/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 Algorithm::Munkres is not installed
   (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork)
    *  Optional prerequisite Bio::ASN1::EntrezGene is not installed
   (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!])
    *  Optional prerequisite GraphViz is not installed
   (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz)
    *  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)
    *  Optional prerequisite SVG::Graph is not installed
   (wanted for creating SVG images, used by Bio::TreeIO::svggraph)
    - DBD::mysql is not installed

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

Checking features:
  Network..................enabled
  BioDBSeqFeature_mysql....disabled
  BioDBGFF.................enabled
  BioDBSeqFeature_BDB......enabled

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

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

Do you want to run tests that require connection to servers across the internet
(likely to cause some failures)? y/n [n] Could not get valid metadata. Error is: Invalid metadata structure. Errors: 'Perl_5' for 'license' does not have a URL scheme (resources -> license) [Validation: 1.2]
 at /home/fly1400/var/megalib/Module/Build/Base.pm line 4559

Could not create MYMETA files
  - will not run internet-requiring tests
Creating new 'Build' script for 'BioPerl' version '1.006000'
>>> make
/home/fly1400/ap1400/bin/perl-static Build --makefile_env_macros 1
Building BioPerl
blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl
blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl
blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl
blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl
blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl
blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl
blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl
blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl
blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl
blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl
blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl
blib/script/flanks.PLS -> blib/script/bp_flanks.pl
blib/script/split_seq.PLS -> blib/script/bp_split_seq.pl
blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl
blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl
blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl
blib/script/mutate.PLS -> blib/script/bp_mutate.pl
blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl
blib/script/bp_index.PLS -> blib/script/bp_index.pl
blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl
blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.pl
blib/script/bp_seqfeature_load.PLS -> blib/script/bp_seqfeature_load.pl
blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.pl
blib/script/hmmer_to_table.PLS -> blib/script/bp_hmmer_to_table.pl
blib/script/fastam9_to_table.PLS -> blib/script/bp_fastam9_to_table.pl
blib/script/biofetch_genbank_proxy.PLS -> blib/script/bp_biofetch_genbank_proxy.pl
blib/script/seq_length.PLS -> blib/script/bp_seq_length.pl
blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl
blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl
blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl
blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl
blib/script/search2gff.PLS -> blib/script/bp_search2gff.pl
blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl
blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl
blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl
blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl
blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.pl
blib/script/bp_seqfeature_delete.PLS -> blib/script/bp_seqfeature_delete.pl
blib/script/query_entrez_taxa.PLS -> blib/script/bp_query_entrez_taxa.pl
blib/script/pairwise_kaks.PLS -> blib/script/bp_pairwise_kaks.pl
blib/script/fast_load_gff.PLS -> blib/script/bp_fast_load_gff.pl
blib/script/chaos_plot.PLS -> blib/script/bp_chaos_plot.pl
blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl
blib/script/bp_mrtrans.PLS -> blib/script/bp_mrtrans.pl
blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl
blib/script/download_query_genbank.PLS -> blib/script/bp_download_query_genbank.pl
blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl
blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl
blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl
blib/script/composite_LD.PLS -> blib/script/bp_composite_LD.pl
blib/script/classify_hits_kingdom.PLS -> blib/script/bp_classify_hits_kingdom.pl
blib/script/aacomp.PLS -> blib/script/bp_aacomp.pl
blib/script/process_wormbase.PLS -> blib/script/bp_process_wormbase.pl
blib/script/local_taxonomydb_query.PLS -> blib/script/bp_local_taxonomydb_query.pl
blib/script/biblio.PLS -> blib/script/bp_biblio.pl
blib/script/seqretsplit.PLS -> blib/script/bp_seqretsplit.pl
blib/script/remote_blast.PLS -> blib/script/bp_remote_blast.pl
blib/script/genbank2gff3.PLS -> blib/script/bp_genbank2gff3.pl
blib/script/search2table.PLS -> blib/script/bp_search2table.pl
blib/script/search2BSML.PLS -> blib/script/bp_search2BSML.pl
blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl
  CJFIELDS/BioPerl-1.6.0.tar.gz
  make -- OK
Running make test
>>> make test TEST_VERBOSE=1
/home/fly1400/ap1400/bin/perl-static Build --makefile_env_macros 1 test
Copying scripts/utilities/bp_sreformat.PLS -> blib/script/bp_sreformat.PLS
Changing sharpbang in blib/script/bp_sreformat.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/bp_sreformat.PLS.bak
blib/script/bp_sreformat.PLS -> blib/script/bp_sreformat.pl
Copying scripts/seq/seqconvert.PLS -> blib/script/seqconvert.PLS
Changing sharpbang in blib/script/seqconvert.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/seqconvert.PLS.bak
blib/script/seqconvert.PLS -> blib/script/bp_seqconvert.pl
Copying scripts/searchio/parse_hmmsearch.PLS -> blib/script/parse_hmmsearch.PLS
Changing sharpbang in blib/script/parse_hmmsearch.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/parse_hmmsearch.PLS.bak
blib/script/parse_hmmsearch.PLS -> blib/script/bp_parse_hmmsearch.pl
Copying scripts/index/bp_seqret.PLS -> blib/script/bp_seqret.PLS
Changing sharpbang in blib/script/bp_seqret.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/bp_seqret.PLS.bak
blib/script/bp_seqret.PLS -> blib/script/bp_seqret.pl
Copying scripts/tree/tree2pag.PLS -> blib/script/tree2pag.PLS
Changing sharpbang in blib/script/tree2pag.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/tree2pag.PLS.bak
blib/script/tree2pag.PLS -> blib/script/bp_tree2pag.pl
Copying scripts/Bio-DB-GFF/meta_gff.PLS -> blib/script/meta_gff.PLS
Changing sharpbang in blib/script/meta_gff.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/meta_gff.PLS.bak
blib/script/meta_gff.PLS -> blib/script/bp_meta_gff.pl
Copying scripts/tree/nexus2nh.PLS -> blib/script/nexus2nh.PLS
Changing sharpbang in blib/script/nexus2nh.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/nexus2nh.PLS.bak
blib/script/nexus2nh.PLS -> blib/script/bp_nexus2nh.pl
Copying scripts/searchio/filter_search.PLS -> blib/script/filter_search.PLS
Changing sharpbang in blib/script/filter_search.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/filter_search.PLS.bak
blib/script/filter_search.PLS -> blib/script/bp_filter_search.pl
Copying scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.PLS
blib/script/bp_seqfeature_gff3.PLS -> blib/script/bp_seqfeature_gff3.pl
Copying scripts/Bio-DB-GFF/generate_histogram.PLS -> blib/script/generate_histogram.PLS
Changing sharpbang in blib/script/generate_histogram.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/generate_histogram.PLS.bak
blib/script/generate_histogram.PLS -> blib/script/bp_generate_histogram.pl
Copying scripts/popgen/heterogeneity_test.PLS -> blib/script/heterogeneity_test.PLS
Changing sharpbang in blib/script/heterogeneity_test.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/heterogeneity_test.PLS.bak
blib/script/heterogeneity_test.PLS -> blib/script/bp_heterogeneity_test.pl
Copying scripts/DB/flanks.PLS -> blib/script/flanks.PLS
Changing sharpbang in blib/script/flanks.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/flanks.PLS.bak
blib/script/flanks.PLS -> blib/script/bp_flanks.pl
Copying scripts/seq/split_seq.PLS -> blib/script/split_seq.PLS
Changing sharpbang in blib/script/split_seq.PLS to /home/fly1400/ap1400/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/load_gff.PLS -> blib/script/load_gff.PLS
Changing sharpbang in blib/script/load_gff.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/load_gff.PLS.bak
blib/script/load_gff.PLS -> blib/script/bp_load_gff.pl
Copying scripts/DB/biogetseq.PLS -> blib/script/biogetseq.PLS
Changing sharpbang in blib/script/biogetseq.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/biogetseq.PLS.bak
blib/script/biogetseq.PLS -> blib/script/bp_biogetseq.pl
Copying scripts/index/bp_fetch.PLS -> blib/script/bp_fetch.PLS
Changing sharpbang in blib/script/bp_fetch.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/bp_fetch.PLS.bak
blib/script/bp_fetch.PLS -> blib/script/bp_fetch.pl
Copying scripts/utilities/mutate.PLS -> blib/script/mutate.PLS
Changing sharpbang in blib/script/mutate.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/mutate.PLS.bak
blib/script/mutate.PLS -> blib/script/bp_mutate.pl
Copying scripts/Bio-DB-GFF/process_sgd.PLS -> blib/script/process_sgd.PLS
Changing sharpbang in blib/script/process_sgd.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/process_sgd.PLS.bak
blib/script/process_sgd.PLS -> blib/script/bp_process_sgd.pl
Copying scripts/index/bp_index.PLS -> blib/script/bp_index.PLS
Changing sharpbang in blib/script/bp_index.PLS to /home/fly1400/ap1400/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/fly1400/ap1400/bin/perl-static
Deleting blib/script/dbsplit.PLS.bak
blib/script/dbsplit.PLS -> blib/script/bp_dbsplit.pl
Copying scripts/seqstats/oligo_count.PLS -> blib/script/oligo_count.PLS
Changing sharpbang in blib/script/oligo_count.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/oligo_count.PLS.bak
blib/script/oligo_count.PLS -> blib/script/bp_oligo_count.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/fly1400/ap1400/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/Bio-DB-GFF/process_gadfly.PLS -> blib/script/process_gadfly.PLS
Changing sharpbang in blib/script/process_gadfly.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/process_gadfly.PLS.bak
blib/script/process_gadfly.PLS -> blib/script/bp_process_gadfly.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/fly1400/ap1400/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/searchio/fastam9_to_table.PLS -> blib/script/fastam9_to_table.PLS
Changing sharpbang in blib/script/fastam9_to_table.PLS to /home/fly1400/ap1400/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/DB/biofetch_genbank_proxy.PLS -> blib/script/biofetch_genbank_proxy.PLS
Changing sharpbang in blib/script/biofetch_genbank_proxy.PLS to /home/fly1400/ap1400/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/utilities/seq_length.PLS -> blib/script/seq_length.PLS
Changing sharpbang in blib/script/seq_length.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/seq_length.PLS.bak
blib/script/seq_length.PLS -> blib/script/bp_seq_length.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/fly1400/ap1400/bin/perl-static
Deleting blib/script/extract_feature_seq.PLS.bak
blib/script/extract_feature_seq.PLS -> blib/script/bp_extract_feature_seq.pl
Copying scripts/Bio-DB-GFF/genbank2gff.PLS -> blib/script/genbank2gff.PLS
Changing sharpbang in blib/script/genbank2gff.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/genbank2gff.PLS.bak
blib/script/genbank2gff.PLS -> blib/script/bp_genbank2gff.pl
Copying scripts/taxa/taxid4species.PLS -> blib/script/taxid4species.PLS
Changing sharpbang in blib/script/taxid4species.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/taxid4species.PLS.bak
blib/script/taxid4species.PLS -> blib/script/bp_taxid4species.pl
Copying scripts/Bio-DB-GFF/bulk_load_gff.PLS -> blib/script/bulk_load_gff.PLS
Changing sharpbang in blib/script/bulk_load_gff.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/bulk_load_gff.PLS.bak
blib/script/bulk_load_gff.PLS -> blib/script/bp_bulk_load_gff.pl
Copying scripts/utilities/search2gff.PLS -> blib/script/search2gff.PLS
Changing sharpbang in blib/script/search2gff.PLS to /home/fly1400/ap1400/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/fly1400/ap1400/bin/perl-static
Deleting blib/script/blast2tree.PLS.bak
blib/script/blast2tree.PLS -> blib/script/bp_blast2tree.pl
Copying scripts/seq/make_mrna_protein.PLS -> blib/script/make_mrna_protein.PLS
Changing sharpbang in blib/script/make_mrna_protein.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/make_mrna_protein.PLS.bak
blib/script/make_mrna_protein.PLS -> blib/script/bp_make_mrna_protein.pl
Copying scripts/seq/unflatten_seq.PLS -> blib/script/unflatten_seq.PLS
Changing sharpbang in blib/script/unflatten_seq.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/unflatten_seq.PLS.bak
blib/script/unflatten_seq.PLS -> blib/script/bp_unflatten_seq.pl
Copying scripts/utilities/search2tribe.PLS -> blib/script/search2tribe.PLS
Changing sharpbang in blib/script/search2tribe.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/search2tribe.PLS.bak
blib/script/search2tribe.PLS -> blib/script/bp_search2tribe.pl
Copying scripts/DB/bioflat_index.PLS -> blib/script/bioflat_index.PLS
Changing sharpbang in blib/script/bioflat_index.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/bioflat_index.PLS.bak
blib/script/bioflat_index.PLS -> blib/script/bp_bioflat_index.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/fly1400/ap1400/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/taxa/query_entrez_taxa.PLS -> blib/script/query_entrez_taxa.PLS
Changing sharpbang in blib/script/query_entrez_taxa.PLS to /home/fly1400/ap1400/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/pairwise_kaks.PLS -> blib/script/pairwise_kaks.PLS
Changing sharpbang in blib/script/pairwise_kaks.PLS to /home/fly1400/ap1400/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/fly1400/ap1400/bin/perl-static
Deleting blib/script/fast_load_gff.PLS.bak
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Copying scripts/seqstats/chaos_plot.PLS -> blib/script/chaos_plot.PLS
Changing sharpbang in blib/script/chaos_plot.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/chaos_plot.PLS.bak
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Copying scripts/taxa/taxonomy2tree.PLS -> blib/script/taxonomy2tree.PLS
Changing sharpbang in blib/script/taxonomy2tree.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/taxonomy2tree.PLS.bak
blib/script/taxonomy2tree.PLS -> blib/script/bp_taxonomy2tree.pl
Copying scripts/utilities/bp_mrtrans.PLS -> blib/script/bp_mrtrans.PLS
Changing sharpbang in blib/script/bp_mrtrans.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/bp_mrtrans.PLS.bak
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Copying scripts/utilities/search2alnblocks.PLS -> blib/script/search2alnblocks.PLS
Changing sharpbang in blib/script/search2alnblocks.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/search2alnblocks.PLS.bak
blib/script/search2alnblocks.PLS -> blib/script/bp_search2alnblocks.pl
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Deleting blib/script/download_query_genbank.PLS.bak
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Copying scripts/utilities/bp_nrdb.PLS -> blib/script/bp_nrdb.PLS
Changing sharpbang in blib/script/bp_nrdb.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/bp_nrdb.PLS.bak
blib/script/bp_nrdb.PLS -> blib/script/bp_nrdb.pl
Copying scripts/utilities/mask_by_search.PLS -> blib/script/mask_by_search.PLS
Changing sharpbang in blib/script/mask_by_search.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/mask_by_search.PLS.bak
blib/script/mask_by_search.PLS -> blib/script/bp_mask_by_search.pl
Copying scripts/seqstats/gccalc.PLS -> blib/script/gccalc.PLS
Changing sharpbang in blib/script/gccalc.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/gccalc.PLS.bak
blib/script/gccalc.PLS -> blib/script/bp_gccalc.pl
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Changing sharpbang in blib/script/composite_LD.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/composite_LD.PLS.bak
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Changing sharpbang in blib/script/classify_hits_kingdom.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/classify_hits_kingdom.PLS.bak
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Deleting blib/script/aacomp.PLS.bak
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Deleting blib/script/process_wormbase.PLS.bak
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Copying scripts/taxa/local_taxonomydb_query.PLS -> blib/script/local_taxonomydb_query.PLS
Changing sharpbang in blib/script/local_taxonomydb_query.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/local_taxonomydb_query.PLS.bak
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Copying scripts/biblio/biblio.PLS -> blib/script/biblio.PLS
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Deleting blib/script/biblio.PLS.bak
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Changing sharpbang in blib/script/seqretsplit.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/seqretsplit.PLS.bak
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Copying scripts/utilities/remote_blast.PLS -> blib/script/remote_blast.PLS
Changing sharpbang in blib/script/remote_blast.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/remote_blast.PLS.bak
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Copying scripts/Bio-DB-GFF/genbank2gff3.PLS -> blib/script/genbank2gff3.PLS
Changing sharpbang in blib/script/genbank2gff3.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/genbank2gff3.PLS.bak
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Copying scripts/searchio/search2table.PLS -> blib/script/search2table.PLS
Changing sharpbang in blib/script/search2table.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/search2table.PLS.bak
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Changing sharpbang in blib/script/search2BSML.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/search2BSML.PLS.bak
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Copying scripts/seq/translate_seq.PLS -> blib/script/translate_seq.PLS
Changing sharpbang in blib/script/translate_seq.PLS to /home/fly1400/ap1400/bin/perl-static
Deleting blib/script/translate_seq.PLS.bak
blib/script/translate_seq.PLS -> blib/script/bp_translate_seq.pl
Replacement list is longer than search list at Bio/Range.pm line 238.
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 238.
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 238.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN4> line 120.
t/Align/SimpleAlign.t ........................ 
1..152
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 - no_sequences
ok 11 - no_sequences
ok 12 - select_noncont
ok 13 - select_noncont
ok 14 - no_sequences
ok 15 - select_noncont
ok 16 - select_noncont
ok 17 - each_seq
ok 18 - get_nse
ok 19 - id
ok 20 - no_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 - no_residues
ok 34 - no_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 - added 3 seqs
ok 86 - first 2 features added
ok 87 - 3rd feature added
ok 88 - slice 1 len
ok 89 - slice 2 len
ok 90 - slice 3 len
ok 91 - slice 4 len
ok 92 - initial display id ok
ok 93 - safe display id ok
ok 94 - restored display id ok
ok 95 - sort by list ok
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102 - BIC:GGATCCATT[C/C]CTACT
ok 103 - BIC:GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT
ok 104 - BIC:G[G/C]ATCCATT[C/G]CTACT
ok 105 - BIC:GGATCCATT[C/G]CTACT
ok 106 - BIC:GGATCCATT[C/G]CTAC[T/A]
ok 107 - BIC:GGATCCATT[C/G]CTA[C/G][T/A]
ok 108 - BIC:GGATCCATT[C/G]CTACT
ok 109 - BIC:GGATCCATT{C.C}CTACT
ok 110 - BIC:GGAT{C.-}{C.-}ATT{C.C}CT{A.C}CT
ok 111 - BIC:G{G.C}ATCCATT{C.G}CTACT
ok 112 - BIC:GGATCCATT{C.G}CTACT
ok 113 - BIC:GGATCCATT{C.G}CTAC{T.A}
ok 114 - BIC:GGATCCATT{C.G}CTA{C.G}{T.A}
ok 115 - BIC:GGATCCATT{C.G}CTACT
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
Replacement list is longer than search list at Bio/Range.pm line 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
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 238.
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 238.
t/AlignIO/AlignIO.t .......................... 
1..28
ok 1 - use Bio::AlignIO;
ok 2 - input filehandle method test : metafasta
ok 3 - input filehandle method test : po
ok 4 - input filehandle method test : nexus
ok 5 - input filehandle method test : clustalw
ok 6 - input filehandle method test : prodom
ok 7 - input filehandle method test : fasta
ok 8 - input filehandle method test : arp
ok 9 - input filehandle method test : xmfa
ok 10 - input filehandle method test : mase
ok 11 - input filehandle method test : psi
ok 12 - input filehandle method test : phylip
ok 13 - input filehandle method test : pfam
ok 14 - input filehandle method test : selex
ok 15 - input filehandle method test : stockholm
ok 16 - input filehandle method test : msf
ok 17 - filehandle output test : metafasta
ok 18 - filehandle output test : po
ok 19 - filehandle output test : nexus
ok 20 - filehandle output test : clustalw
ok 21 - filehandle output test : fasta
ok 22 - filehandle output test : xmfa
ok 23 - filehandle output test : psi
ok 24 - filehandle output test : phylip
ok 25 - filehandle output test : pfam
ok 26 - filehandle output test : selex
ok 27 - filehandle output test : stockholm
ok 28 - filehandle output test : msf
ok
Replacement list is longer than search list at Bio/Range.pm line 238.
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 no_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 no_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 no_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 no_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 238.
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 238.
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 238.
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 238.
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 238.
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 238.
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 238.
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 238.
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 238.
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 238.
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 238.
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 238.
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 238.
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 238.
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 238.
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 238.
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 238.
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 238.
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 238.
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 238.
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 238.
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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
t/Annotation/Annotation.t .................... 
1..159
ok 1 - use Bio::Annotation::Collection;
ok 2 - use Bio::Annotation::DBLink;
ok 3 - use Bio::Annotation::Comment;
ok 4 - use Bio::Annotation::Reference;
ok 5 - use Bio::Annotation::SimpleValue;
ok 6 - use Bio::Annotation::Target;
ok 7 - use Bio::Annotation::AnnotationFactory;
ok 8 - use Bio::Annotation::StructuredValue;
ok 9 - use Bio::Annotation::TagTree;
ok 10 - use Bio::Annotation::Tree;
ok 11 - use Bio::Seq;
ok 12 - use Bio::SeqFeature::Annotated;
ok 13 - use Bio::SimpleAlign;
ok 14 - use Bio::Cluster::UniGene;
ok 15 - The object isa Bio::AnnotationI
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22 - The object isa Bio::AnnotationI
ok 23
ok 24
ok 25
ok 26 - The object isa Bio::AnnotationCollectionI
ok 27
ok 28
ok 29 - The object isa Bio::AnnotationI
ok 30
ok 31 - The object isa Bio::AnnotationI
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 - The object isa Bio::AnnotationI
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 - The object isa Bio::AnnotationCollectionI
ok 70
ok 71
ok 72
ok 73
ok 74 - The object isa Bio::Annotation::StructuredValue
ok 75
ok 76
ok 77
ok 78
ok 79 - use Bio::Annotation::OntologyTerm;
ok 80 - The object isa Bio::Ontology::Term
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86 - The object isa Bio::AnnotatableI
ok 87 - isa SeqFeatureI isa Bio::SeqFeatureI
ok 88 - isa AnnotatableI isa Bio::AnnotatableI
ok 89 - isa SeqFeatureI isa Bio::SeqFeatureI
ok 90 - isa AnnotatableI isa Bio::AnnotatableI
ok 91 - The object isa Bio::AnnotatableI
ok 92 - The object isa Bio::AnnotatableI
ok 93 - The object isa Bio::Factory::ObjectFactoryI
ok 94 - The object isa Bio::Annotation::SimpleValue
ok 95
ok 96 - The object isa Bio::Annotation::OntologyTerm
ok 97 - Bio::Annotation::Comment
ok 98 - The object isa Bio::Annotation::Comment
ok 99
ok 100 - Bio::Annotation::Comment
ok 101 - The object isa Bio::Annotation::Comment
ok 102 - Bio::Annotation::Comment
ok 103 - The object isa Bio::Annotation::Comment
ok 104
ok 105 - The object isa Bio::Annotation::Target
ok 106
ok 107
ok 108 - The object isa Bio::AnnotationI
ok 109 - tree_id()
ok 110 - tagname()
ok 111 - The object isa Bio::AnnotatableI
ok 112 - add tree to AlignI
ok 113 - get seq from node id
ok 114
ok 115 - The object isa Bio::Annotation::Tree
ok 116 - The object isa Bio::AnnotationI
ok 117 - default itext
ok 118 - roundtrip
ok 119 - itext
ok 120 - spxr
ok 121 - indent
ok 122 - xml
ok 123 - The object isa Data::Stag::StagI
ok 124
ok 125 - child changes
ok 126 - The object isa Data::Stag::StagI
ok 127
ok 128 - child changes
ok 129 - The object isa Data::Stag::StagI
ok 130
ok 131 - child changes
ok 132 - child changes in parent node
ok 133 - no tags
ok 134 - before Stag node
ok 135 - after Stag node
ok 136 - both stag nodes
ok 137 - different instances
ok 138 - before TagTree
ok 139 - after TagTree
ok 140 - both stag nodes
ok 141 - different instances
ok 142 - before TagTree
ok 143 - after TagTree
ok 144 - stag nodes
ok 145 - same instance
ok 146 - before TagTree
ok 147 - after TagTree
ok 148 - stag nodes
ok 149 - different instance
ok 150 - The object isa Bio::AnnotationI
ok 151 - The object isa Data::Stag::StagI
ok 152 - child changes
ok 153 - The object isa Data::Stag::StagI
ok 154 - child changes
ok 155 - The object isa Data::Stag::StagI
ok 156 - child changes
ok 157
ok 158
ok 159 - The object isa Bio::Annotation::TagTree
ok
Replacement list is longer than search list at Bio/Range.pm line 238.
t/Annotation/AnnotationAdaptor.t ............. 
1..23
ok 1 - use Bio::SeqFeature::Generic;
ok 2 - use Bio::SeqFeature::AnnotationAdaptor;
ok 3 - use Bio::Annotation::DBLink;
ok 4 - use Bio::Annotation::Comment;
ok 5 - use Bio::Annotation::SimpleValue;
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok
t/Assembly/Assembly.t ........................ skipped: The optional module DB_File (or dependencies thereof) was not installed
Replacement list is longer than search list at Bio/Range.pm line 238.
Bio::Assembly::IO: could not load tigr - for more details on supported formats please see the Assembly::IO docs
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::Assembly::IO::tigr. Can't load '/home/fly1400/ap1400/lib/auto/DB_File/DB_File.so' for module DB_File: libdb-4.3.so: cannot open shared object file: No such file or directory at /home/fly1400/var/megalib/XSLoader.pm line 71.
 at /home/fly1400/ap1400/lib/DB_File.pm line 252
Compilation failed in require at Bio/SeqFeature/Collection.pm line 134.
BEGIN failed--compilation aborted at Bio/SeqFeature/Collection.pm line 134.
Compilation failed in require at Bio/Assembly/Contig.pm line 210.
BEGIN failed--compilation aborted at Bio/Assembly/Contig.pm line 210.
Compilation failed in require at Bio/Assembly/IO/tigr.pm line 224.
BEGIN failed--compilation aborted at Bio/Assembly/IO/tigr.pm line 224.
Compilation failed in require at Bio/Root/Root.pm line 420.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422
STACK: Bio::Assembly::IO::_load_format_module Bio/Assembly/IO.pm:181
STACK: Bio::Assembly::IO::new Bio/Assembly/IO.pm:122
STACK: t/Assembly/ContigSpectrum.t:11
-----------------------------------------------------------


#   Failed test 'The thing isa Bio::Assembly::IO'
#   at t/Assembly/ContigSpectrum.t line 15.
#     The thing isn't defined
Can't call method "next_assembly" on an undefined value at t/Assembly/ContigSpectrum.t line 16.
# Looks like you planned 134 tests but ran 3.
# Looks like you failed 1 test of 3 run.
# Looks like your test exited with 2 just after 3.
t/Assembly/ContigSpectrum.t .................. 
1..134
ok 1 - use Bio::Assembly::IO;
ok 2 - use Bio::Assembly::Tools::ContigSpectrum;
not ok 3 - The thing isa Bio::Assembly::IO
Dubious, test returned 2 (wstat 512, 0x200)
Failed 132/134 subtests 
Use of tied on a handle without * is deprecated at /home/fly1400/var/megalib/XML/Parser/Expat.pm line 447.
Use of tied on a handle without * is deprecated at /home/fly1400/var/megalib/XML/Parser/Expat.pm line 447.
Use of tied on a handle without * is deprecated at /home/fly1400/var/megalib/XML/Parser/Expat.pm line 447.
Use of tied on a handle without * is deprecated at /home/fly1400/var/megalib/XML/Parser/Expat.pm line 447.
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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
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 81
Replacement list is longer than search list at Bio/Range.pm line 238, <GEN0> 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 238.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
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 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 74.
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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 67.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 90.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> 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 238.
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 238.
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 238.
t/LocalDB/DBFasta.t .......................... 
1..15
ok 1 - use Bio::Root::IO;
ok 2 - use File::Copy;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok
t/LocalDB/DBQual.t ........................... 
1..38
ok 1 - use Bio::Root::IO;
ok 2 - use File::Copy;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13 - The object isa Bio::Seq::PrimaryQual
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25 - The object isa Bio::Seq::PrimaryQual
ok 26
ok 27
ok 28 - The object isa Bio::Seq::PrimaryQual
ok 29
ok 30
ok 31
ok 32 - The object isa Bio::Seq::PrimaryQual
ok 33
ok 34 - The object isa Bio::Seq::PrimaryQual
ok 35
ok 36
ok 37
ok 38
ok
t/LocalDB/Flat.t ............................. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/LocalDB/Index.t ............................ skipped: The optional module DB_File (or dependencies thereof) was not installed
Replacement list is longer than search list at Bio/Range.pm line 238.
t/LocalDB/Registry.t ......................... 
1..14
ok 1 - use Bio::DB::Registry;
ok 2 - use Bio::DB::Flat;
ok 3
ok 4 # skip The optional module DB_File (or dependencies thereof) was not installed
ok 5 # skip The optional module DB_File (or dependencies thereof) was not installed
ok 6 # skip Network tests have not been requested
ok 7 # skip Network tests have not been requested
ok 8 # skip Network tests have not been requested
ok 9 # skip Network tests have not been requested
ok 10 # skip Network tests have not been requested
ok 11 # skip Network tests have not been requested
ok 12 # skip Network tests have not been requested
ok 13 # skip Network tests have not been requested
ok 14 # skip Network tests have not been requested
ok
Replacement list is longer than search list at Bio/Range.pm line 238.

#   Failed test 'use Bio::DB::SeqFeature::Store::GFF3Loader;'
#   at t/LocalDB/SeqFeature.t line 16.
#     Tried to use 'Bio::DB::SeqFeature::Store::GFF3Loader'.
#     Error:  Can't load '/home/fly1400/ap1400/lib/auto/DB_File/DB_File.so' for module DB_File: libdb-4.3.so: cannot open shared object file: No such file or directory at /home/fly1400/var/megalib/XSLoader.pm line 71.
#  at /home/fly1400/ap1400/lib/DB_File.pm line 252
# Compilation failed in require at Bio/DB/SeqFeature/Store/LoadHelper.pm line 39.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/LoadHelper.pm line 39.
# Compilation failed in require at Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72.
# Compilation failed in require at (eval 50) line 2.
# BEGIN failed--compilation aborted at (eval 50) line 2.
# Looks like you failed 1 test of 59.
t/LocalDB/SeqFeature.t ....................... 
1..59
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
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 52) line 2.
#  at t/LocalDB/SeqFeature.t line 27
# 
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/59 subtests 
	(less 57 skipped subtests: 1 okay)
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't load '/home/fly1400/ap1400/lib/auto/DB_File/DB_File.so' for module DB_File: libdb-4.3.so: cannot open shared object file: No such file or directory at /home/fly1400/var/megalib/XSLoader.pm line 71.
 at /home/fly1400/ap1400/lib/DB_File.pm line 252
Compilation failed in require at Bio/DB/Taxonomy/flatfile.pm line 77.
BEGIN failed--compilation aborted at Bio/DB/Taxonomy/flatfile.pm line 77.
Compilation failed in require at Bio/Root/Root.pm line 420.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422
STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:251
STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:102
STACK: t/LocalDB/transfac_pro.t:18
-----------------------------------------------------------
Bio::DB::Taxonomy: flatfile cannot be found
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't load '/home/fly1400/ap1400/lib/auto/DB_File/DB_File.so' for module DB_File: libdb-4.3.so: cannot open shared object file: No such file or directory at /home/fly1400/var/megalib/XSLoader.pm line 71.
 at /home/fly1400/ap1400/lib/DB_File.pm line 252
Compilation failed in require at Bio/DB/Taxonomy/flatfile.pm line 77.
BEGIN failed--compilation aborted at Bio/DB/Taxonomy/flatfile.pm line 77.
Compilation failed in require at Bio/Root/Root.pm line 420.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422
STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:251
STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:102
STACK: t/LocalDB/transfac_pro.t:18
-----------------------------------------------------------

For more information about the Bio::DB::Taxonomy system please see
the Bio::DB::Taxonomy docs.  This includes ways of checking for 
formats at compile time, not run time.
Replacement list is longer than search list at Bio/Range.pm line 238.
Use of qw(...) as parentheses is deprecated at Bio/Matrix/PSM/SiteMatrix.pm line 335.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::TFBS::transfac_pro. Attempt to reload DB_File.pm aborted.
Compilation failed in require at Bio/DB/TFBS/transfac_pro.pm line 105.
BEGIN failed--compilation aborted at Bio/DB/TFBS/transfac_pro.pm line 105.
Compilation failed in require at Bio/Root/Root.pm line 420.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422
STACK: Bio::DB::TFBS::_load_tax_module Bio/DB/TFBS.pm:138
STACK: Bio::DB::TFBS::new Bio/DB/TFBS.pm:117
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. Attempt to reload DB_File.pm aborted.
Compilation failed in require at Bio/DB/TFBS/transfac_pro.pm line 105.
BEGIN failed--compilation aborted at Bio/DB/TFBS/transfac_pro.pm line 105.
Compilation failed in require at Bio/Root/Root.pm line 420.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422
STACK: Bio::DB::TFBS::_load_tax_module Bio/DB/TFBS.pm:138
STACK: Bio::DB::TFBS::new Bio/DB/TFBS.pm:117
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 238.
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 238.
t/Map/Map.t .................................. 
1..267
ok 1 - use Bio::Map::SimpleMap;
ok 2 - use Bio::Map::Marker;
ok 3 - use Bio::Map::Position;
ok 4 - use Bio::Map::Relative;
ok 5 - use Bio::Map::Mappable;
ok 6
ok 7
ok 8
ok 9
ok 10 - Length is 0
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151 - use Bio::Map::Gene;
ok 152 - use Bio::Map::GeneMap;
ok 153 - use Bio::Map::TranscriptionFactor;
ok 154 - use Bio::Map::GeneRelative;
ok 155 - use Bio::Map::GenePosition;
ok 156 - use Bio::Map::Prediction;
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok 176
ok 177
ok 178
ok 179
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ok 181
ok 182
ok 183
ok 184
ok 185
ok 186
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ok 192
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ok 201
ok 202
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ok 204
ok 205
ok 206
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ok 211
ok 212
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ok 214
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ok 217
ok 218
ok 219
ok 220
ok 221
ok 222
ok 223
ok 224
ok 225
ok 226
ok 227
ok 228
ok 229
ok 230
ok 231
ok 232
ok 233
ok 234
ok 235
ok 236
ok 237
ok 238
ok 239
ok 240
ok 241
ok 242
ok 243
ok 244
ok 245
ok 246
ok 247
ok 248
ok 249 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 250 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 251 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 252 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 253 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 254 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 255 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 256 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 257 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 258 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 259 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 260 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 261 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 262 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 263 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 264 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 265 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 266 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 267 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok
Replacement list is longer than search list at Bio/Range.pm line 238, <GEN1> 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 238.
t/Map/Physical.t ............................. 
1..39
ok 1 - use Bio::Map::Physical;
ok 2 - use Bio::MapIO;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12 - code holds and returns a string, definition requires a boolean
ok 13 - code holds and returns a string, definition requires a boolean
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok
Use of qw(...) as parentheses is deprecated at Bio/Matrix/PSM/SiteMatrix.pm line 335.
t/Matrix/IO/masta.t .......................... 
1..16
ok 1 - use Bio::Matrix::PSM::IO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok
Replacement list is longer than search list at Bio/Range.pm line 238.
Use of qw(...) as parentheses is deprecated at Bio/Matrix/PSM/SiteMatrix.pm line 335.
t/Matrix/IO/psm.t ............................ 
1..63
ok 1 - use Bio::Matrix::PSM::IO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok
Replacement list is longer than search list at Bio/Range.pm line 238.
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 238.
Use of qw(...) as parentheses is deprecated at Bio/Matrix/PSM/SiteMatrix.pm line 335.
t/Matrix/ProtPsm.t ........................... 
1..14
ok 1 - use Bio::Matrix::PSM::IO;
ok 2
ok 3
ok 4
ok 5 # skip TODO: Module incomplete
ok 6 # skip TODO: Module incomplete
ok 7 # skip TODO: Module incomplete
ok 8 # skip TODO: Module incomplete
ok 9 # skip TODO: Module incomplete
ok 10 # skip TODO: Module incomplete
ok 11 # skip TODO: Module incomplete
ok 12 # skip TODO: Module incomplete
ok 13 # skip TODO: Module incomplete
ok 14 # skip TODO: Module incomplete
ok
Use of qw(...) as parentheses is deprecated at Bio/Matrix/PSM/SiteMatrix.pm line 335.
t/Matrix/SiteMatrix.t ........................ 
1..14
ok 1 - use Bio::Matrix::PSM::SiteMatrix;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok
t/Ontology/GOterm.t .......................... 
1..62
ok 1 - use Bio::Ontology::GOterm;
ok 2 - use Bio::Ontology::Ontology;
ok 3 - use Bio::Annotation::DBLink;
ok 4 - The object isa Bio::Ontology::GOterm
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok
t/Ontology/GraphAdaptor.t .................... 
1..28
ok 1 - use Bio::Ontology::SimpleGOEngine::GraphAdaptor;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok
t/Ontology/IO/go.t ........................... 
1..102
ok 1 - use Bio::OntologyIO;
ok 2
ok 3 - The object isa Bio::Ontology::OntologyI
ok 4
ok 5 - The object isa Bio::Ontology::OntologyEngineI
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok
Use of tied on a handle without * is deprecated at /home/fly1400/var/megalib/XML/Parser/Expat.pm line 447.
t/Ontology/IO/interpro.t ..................... 
1..47
ok 1 - use Bio::OntologyIO;
ok 2
ok 3
ok 4
ok 5
ok 6 - term Integrins alpha chain in ontology InterPro
ok 7
ok 8 - term post-translational modification in ontology InterPro
ok 9
ok 10 - term Repeat in ontology InterPro
ok 11
ok 12 - term Binding Site in ontology InterPro
ok 13
ok 14 - term Cdc20/Fizzy in ontology InterPro
ok 15
ok 16 - term Kringle in ontology InterPro
ok 17
ok 18 - term Helix-turn-helix, AraC type  in ontology InterPro
ok 19
ok 20 - term Active Site in ontology InterPro
ok 21
ok 22 - term Active Site in ontology InterPro
ok 23
ok 24 - term Binding Site in ontology InterPro
ok 25
ok 26 - term Domain in ontology InterPro
ok 27
ok 28 - term Family in ontology InterPro
ok 29
ok 30 - term Repeat in ontology InterPro
ok 31
ok 32 - term post-translational modification in ontology InterPro
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok
t/Ontology/IO/obo.t .......................... 
1..83
ok 1 - use Bio::OntologyIO;
ok 2 - use Bio::Ontology::RelationshipType;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46 - got a ontology IO handler isa Bio::OntologyIO
ok 47 - got ontology parser2 isa Bio::Ontology::Ontology
ok 48 - got OBO engine object isa Bio::Ontology::OBOEngine
ok 49 - got ontology parser2 isa Bio::Ontology::Ontology
ok 50 - got OBO engine object isa Bio::Ontology::OBOEngine
ok 51 - got ontology parser2 isa Bio::Ontology::Ontology
ok 52 - got OBO engine object isa Bio::Ontology::OBOEngine
ok 53 - Gene ontology
ok 54 - biological process
ok 55 - molecular function
ok 56 - Got root
ok 57 - Got root
ok 58 - Got regulates
# 	 from gene_ontology
ok 59 - Got
# 	 positively regulates from gene_ontology
ok 60 - Got
# 	  regulates from biological_process
ok 61 - Got
# 	 positively regulates from biological_process
ok 62 - Got predicates for gene_ontology
ok 63 - Got predicates for biological_process
ok 64 - Got regulates predicate
ok 65 - Got positively regulates predicate
ok 66 - Got relationships for biological_process
ok 67 - Got relationships for molecular_function
ok 68 - Got is a relationship from
# 	 molecular_function
ok 69 - Got term object isa Bio::Ontology::Term
ok 70 - Got term id
ok 71 - Got term name
ok 72 - Got regulated object isa Bio::Ontology::Term
ok 73 - Got regulated term1 id
ok 74 - Got term1 object isa Bio::Ontology::Term
ok 75 - Got back the child
ok 76 - Got term object isa Bio::Ontology::Term
ok 77 - Got term id
ok 78 - Got term name
ok 79 - Got regulated object isa Bio::Ontology::Term
ok 80 - Got regulated term1 id
ok 81 - Got identical regulation
ok 82 - Got term1 object isa Bio::Ontology::Term
ok 83 - Got back the child
ok
t/Ontology/Ontology.t ........................ 
1..52
ok 1 - use Bio::OntologyIO;
ok 2 - use Bio::Ontology::RelationshipType;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok
t/Ontology/OntologyEngine.t .................. 
1..27
ok 1 - use Bio::Ontology::Term;
ok 2 - use Bio::Ontology::Relationship;
ok 3 - use Bio::Ontology::RelationshipType;
ok 4 - use Bio::Ontology::SimpleOntologyEngine;
ok 5 - use Bio::Ontology::Ontology;
ok 6 - The object isa Bio::Ontology::OntologyEngineI
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
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ok 15
ok 16
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ok 22
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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
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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
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ok 14
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ok 37
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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 238.
Replacement list is longer than search list at Bio/Perl.pm line 614.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 42.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 46.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 54.
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 81
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
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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 81
Replacement list is longer than search list at Bio/Range.pm line 238.
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
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ok 99
ok 100
ok 101
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ok 121
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ok 123
ok 124
ok 125
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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 81
Replacement list is longer than search list at Bio/Range.pm line 238.
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
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ok 61
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ok 63
ok 64
ok 65
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ok 69
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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
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ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
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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 81
Replacement list is longer than search list at Bio/Range.pm line 238.
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
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ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
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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
t/PodSyntax.t ................................ 
1..2252
ok 1 - POD test for ./Build.PL (no pod)
ok 2 - POD test for ./Makefile.PL (no pod)
ok 3 - POD test for ./Build (no pod)
ok 4 - POD test for Bio/AlignIO.pm
ok 5 - POD test for Bio/AnalysisI.pm
ok 6 - POD test for Bio/AnalysisParserI.pm
ok 7 - POD test for Bio/AnalysisResultI.pm
ok 8 - POD test for Bio/AnnotatableI.pm
ok 9 - POD test for Bio/AnnotationCollectionI.pm
ok 10 - POD test for Bio/AnnotationI.pm
ok 11 - POD test for Bio/Biblio.pm
ok 12 - POD test for Bio/ClusterI.pm
ok 13 - POD test for Bio/ClusterIO.pm
ok 14 - POD test for Bio/DasI.pm
ok 15 - POD test for Bio/DBLinkContainerI.pm
ok 16 - POD test for Bio/DescribableI.pm
ok 17 - POD test for Bio/FeatureHolderI.pm
ok 18 - POD test for Bio/FeatureIO.pm
ok 19 - POD test for Bio/HandlerBaseI.pm
ok 20 - POD test for Bio/IdCollectionI.pm
ok 21 - POD test for Bio/IdentifiableI.pm
ok 22 - POD test for Bio/LocatableSeq.pm
ok 23 - POD test for Bio/LocationI.pm
ok 24 - POD test for Bio/MapIO.pm
ok 25 - POD test for Bio/OntologyIO.pm
ok 26 - POD test for Bio/ParameterBaseI.pm
ok 27 - POD test for Bio/Perl.pm
ok 28 - POD test for Bio/PhyloNetwork.pm
ok 29 - POD test for Bio/PrimarySeq.pm
ok 30 - POD test for Bio/PrimarySeqI.pm
ok 31 - POD test for Bio/PullParserI.pm
ok 32 - POD test for Bio/Range.pm
ok 33 - POD test for Bio/RangeI.pm
ok 34 - POD test for Bio/SearchDist.pm
ok 35 - POD test for Bio/SearchIO.pm
ok 36 - POD test for Bio/Seq.pm
ok 37 - POD test for Bio/SeqAnalysisParserI.pm
ok 38 - POD test for Bio/SeqFeatureI.pm
ok 39 - POD test for Bio/SeqI.pm
ok 40 - POD test for Bio/SeqIO.pm
ok 41 - POD test for Bio/SeqUtils.pm
ok 42 - POD test for Bio/SimpleAlign.pm
ok 43 - POD test for Bio/SimpleAnalysisI.pm
ok 44 - POD test for Bio/Species.pm
ok 45 - POD test for Bio/Taxon.pm
ok 46 - POD test for Bio/Taxonomy.pm
ok 47 - POD test for Bio/TreeIO.pm
ok 48 - POD test for Bio/UpdateableSeqI.pm
ok 49 - POD test for Bio/WebAgent.pm
ok 50 - POD test for doc/makedoc.PL (no pod)
ok 51 - POD test for examples/bioperl.pl (no pod)
ok 52 - POD test for examples/generate_random_seq.pl (no pod)
ok 53 - POD test for examples/longorf.pl
ok 54 - POD test for examples/make_primers.pl (no pod)
ok 55 - POD test for examples/rev_and_trans.pl (no pod)
ok 56 - POD test for examples/revcom_dir.pl (no pod)
ok 57 - POD test for examples/subsequence.cgi (no pod)
ok 58 - POD test for maintenance/authors.pl
ok 59 - POD test for maintenance/check_NAME.pl
ok 60 - POD test for maintenance/check_URLs.pl
ok 61 - POD test for maintenance/cvs2cl_by_file.pl
ok 62 - POD test for maintenance/dependencies.pl
ok 63 - POD test for maintenance/deprecated.pl
ok 64 - POD test for maintenance/module_usage.pl (no pod)
ok 65 - POD test for maintenance/modules.pl
ok 66 - POD test for maintenance/ncbi_blast_switches.pl (no pod)
ok 67 - POD test for maintenance/pod.pl
ok 68 - POD test for maintenance/symlink_script.pl
ok 69 - POD test for maintenance/version.pl
ok 70 - POD test for t/Alphabet.t (no pod)
ok 71 - POD test for t/Perl.t (no pod)
ok 72 - POD test for t/PodSyntax.t (no pod)
ok 73 - POD test for t/SearchDist.t (no pod)
ok 74 - POD test for t/SeqEvolution.t (no pod)
ok 75 - POD test for t/SeqIO.t (no pod)
ok 76 - POD test for t/Species.t (no pod)
ok 77 - POD test for t/Symbol.t (no pod)
ok 78 - POD test for t/TaxonTree.t (no pod)
ok 79 - POD test for Bio/Align/AlignI.pm
ok 80 - POD test for Bio/Align/DNAStatistics.pm
ok 81 - POD test for Bio/Align/PairwiseStatistics.pm
ok 82 - POD test for Bio/Align/ProteinStatistics.pm
ok 83 - POD test for Bio/Align/StatisticsI.pm
ok 84 - POD test for Bio/Align/Utilities.pm
ok 85 - POD test for Bio/AlignIO/arp.pm
ok 86 - POD test for Bio/AlignIO/bl2seq.pm
ok 87 - POD test for Bio/AlignIO/clustalw.pm
ok 88 - POD test for Bio/AlignIO/emboss.pm
ok 89 - POD test for Bio/AlignIO/fasta.pm
ok 90 - POD test for Bio/AlignIO/largemultifasta.pm
ok 91 - POD test for Bio/AlignIO/maf.pm
ok 92 - POD test for Bio/AlignIO/mase.pm
ok 93 - POD test for Bio/AlignIO/mega.pm
ok 94 - POD test for Bio/AlignIO/meme.pm
ok 95 - POD test for Bio/AlignIO/metafasta.pm
ok 96 - POD test for Bio/AlignIO/msf.pm
ok 97 - POD test for Bio/AlignIO/nexus.pm
ok 98 - POD test for Bio/AlignIO/pfam.pm
ok 99 - POD test for Bio/AlignIO/phylip.pm
ok 100 - POD test for Bio/AlignIO/po.pm
ok 101 - POD test for Bio/AlignIO/proda.pm
ok 102 - POD test for Bio/AlignIO/prodom.pm
ok 103 - POD test for Bio/AlignIO/psi.pm
ok 104 - POD test for Bio/AlignIO/selex.pm
ok 105 - POD test for Bio/AlignIO/stockholm.pm
ok 106 - POD test for Bio/AlignIO/xmfa.pm
ok 107 - POD test for Bio/Annotation/AnnotationFactory.pm
ok 108 - POD test for Bio/Annotation/Collection.pm
ok 109 - POD test for Bio/Annotation/Comment.pm
ok 110 - POD test for Bio/Annotation/DBLink.pm
ok 111 - POD test for Bio/Annotation/OntologyTerm.pm
ok 112 - POD test for Bio/Annotation/Reference.pm
ok 113 - POD test for Bio/Annotation/Relation.pm
ok 114 - POD test for Bio/Annotation/SimpleValue.pm
ok 115 - POD test for Bio/Annotation/StructuredValue.pm
ok 116 - POD test for Bio/Annotation/TagTree.pm
ok 117 - POD test for Bio/Annotation/Target.pm
ok 118 - POD test for Bio/Annotation/Tree.pm
ok 119 - POD test for Bio/Annotation/TypeManager.pm
ok 120 - POD test for Bio/Assembly/Contig.pm
ok 121 - POD test for Bio/Assembly/ContigAnalysis.pm
ok 122 - POD test for Bio/Assembly/IO.pm
ok 123 - POD test for Bio/Assembly/Scaffold.pm
ok 124 - POD test for Bio/Assembly/ScaffoldI.pm
ok 125 - POD test for Bio/Assembly/Singlet.pm
ok 126 - POD test for Bio/Biblio/Article.pm
ok 127 - POD test for Bio/Biblio/BiblioBase.pm
ok 128 - POD test for Bio/Biblio/Book.pm
ok 129 - POD test for Bio/Biblio/BookArticle.pm
ok 130 - POD test for Bio/Biblio/IO.pm
ok 131 - POD test for Bio/Biblio/Journal.pm
ok 132 - POD test for Bio/Biblio/JournalArticle.pm
ok 133 - POD test for Bio/Biblio/MedlineArticle.pm
ok 134 - POD test for Bio/Biblio/MedlineBook.pm
ok 135 - POD test for Bio/Biblio/MedlineBookArticle.pm
ok 136 - POD test for Bio/Biblio/MedlineJournal.pm
ok 137 - POD test for Bio/Biblio/MedlineJournalArticle.pm
ok 138 - POD test for Bio/Biblio/Organisation.pm
ok 139 - POD test for Bio/Biblio/Patent.pm
ok 140 - POD test for Bio/Biblio/Person.pm
ok 141 - POD test for Bio/Biblio/Proceeding.pm
ok 142 - POD test for Bio/Biblio/Provider.pm
ok 143 - POD test for Bio/Biblio/PubmedArticle.pm
ok 144 - POD test for Bio/Biblio/PubmedBookArticle.pm
ok 145 - POD test for Bio/Biblio/PubmedJournalArticle.pm
ok 146 - POD test for Bio/Biblio/Ref.pm
ok 147 - POD test for Bio/Biblio/Service.pm
ok 148 - POD test for Bio/Biblio/TechReport.pm
ok 149 - POD test for Bio/Biblio/Thesis.pm
ok 150 - POD test for Bio/Biblio/WebResource.pm
ok 151 - POD test for Bio/Cluster/ClusterFactory.pm
ok 152 - POD test for Bio/Cluster/FamilyI.pm
ok 153 - POD test for Bio/Cluster/SequenceFamily.pm
ok 154 - POD test for Bio/Cluster/UniGene.pm
ok 155 - POD test for Bio/Cluster/UniGeneI.pm
ok 156 - POD test for Bio/ClusterIO/dbsnp.pm
ok 157 - POD test for Bio/ClusterIO/unigene.pm
ok 158 - POD test for Bio/CodonUsage/IO.pm
ok 159 - POD test for Bio/CodonUsage/Table.pm
ok 160 - POD test for Bio/Coordinate/Chain.pm
ok 161 - POD test for Bio/Coordinate/Collection.pm
ok 162 - POD test for Bio/Coordinate/ExtrapolatingPair.pm
ok 163 - POD test for Bio/Coordinate/GeneMapper.pm
ok 164 - POD test for Bio/Coordinate/Graph.pm
ok 165 - POD test for Bio/Coordinate/MapperI.pm
ok 166 - POD test for Bio/Coordinate/Pair.pm
ok 167 - POD test for Bio/Coordinate/Result.pm
ok 168 - POD test for Bio/Coordinate/ResultI.pm
ok 169 - POD test for Bio/Coordinate/Utils.pm
ok 170 - POD test for Bio/Das/FeatureTypeI.pm
ok 171 - POD test for Bio/Das/SegmentI.pm
ok 172 - POD test for Bio/DB/Ace.pm
ok 173 - POD test for Bio/DB/BiblioI.pm
ok 174 - POD test for Bio/DB/BioFetch.pm
ok 175 - POD test for Bio/DB/CUTG.pm
ok 176 - POD test for Bio/DB/DBFetch.pm
ok 177 - POD test for Bio/DB/EMBL.pm
ok 178 - POD test for Bio/DB/EntrezGene.pm
ok 179 - POD test for Bio/DB/EUtilities.pm
ok 180 - POD test for Bio/DB/Expression.pm
ok 181 - POD test for Bio/DB/Failover.pm
ok 182 - POD test for Bio/DB/Fasta.pm
ok 183 - POD test for Bio/DB/FileCache.pm
ok 184 - POD test for Bio/DB/Flat.pm
ok 185 - POD test for Bio/DB/GenBank.pm
ok 186 - POD test for Bio/DB/GenericWebAgent.pm
ok 187 - POD test for Bio/DB/GenPept.pm
ok 188 - POD test for Bio/DB/GFF.pm
ok 189 - POD test for Bio/DB/HIV.pm
ok 190 - POD test for Bio/DB/InMemoryCache.pm
ok 191 - POD test for Bio/DB/LocationI.pm
ok 192 - POD test for Bio/DB/MeSH.pm
ok 193 - POD test for Bio/DB/NCBIHelper.pm
ok 194 - POD test for Bio/DB/Qual.pm
ok 195 - POD test for Bio/DB/QueryI.pm
ok 196 - POD test for Bio/DB/RandomAccessI.pm
ok 197 - POD test for Bio/DB/ReferenceI.pm
ok 198 - POD test for Bio/DB/RefSeq.pm
ok 199 - POD test for Bio/DB/Registry.pm
ok 200 - POD test for Bio/DB/SeqFeature.pm
ok 201 - POD test for Bio/DB/SeqHound.pm
ok 202 - POD test for Bio/DB/SeqI.pm
ok 203 - POD test for Bio/DB/SeqVersion.pm
ok 204 - POD test for Bio/DB/SwissProt.pm
ok 205 - POD test for Bio/DB/Taxonomy.pm
ok 206 - POD test for Bio/DB/TFBS.pm
ok 207 - POD test for Bio/DB/Universal.pm
ok 208 - POD test for Bio/DB/UpdateableSeqI.pm
ok 209 - POD test for Bio/DB/WebDBSeqI.pm
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ok 650 - POD test for examples/tools/gb_to_gff.pl (no pod)
ok 651 - POD test for examples/tools/gff2ps.pl
ok 652 - POD test for examples/tools/parse_codeml.pl (no pod)
ok 653 - POD test for examples/tools/psw.pl (no pod)
ok 654 - POD test for examples/tools/reverse-translate.pl
ok 655 - POD test for examples/tools/run_genscan.pl (no pod)
ok 656 - POD test for examples/tools/run_primer3.pl
ok 657 - POD test for examples/tools/seq_pattern.pl (no pod)
ok 658 - POD test for examples/tools/standaloneblast.pl (no pod)
ok 659 - POD test for examples/tree/paup2phylip.pl (no pod)
ok 660 - POD test for scripts/biblio/biblio.PLS
ok 661 - POD test for scripts/Bio-DB-GFF/bulk_load_gff.PLS
ok 662 - POD test for scripts/Bio-DB-GFF/fast_load_gff.PLS
ok 663 - POD test for scripts/Bio-DB-GFF/genbank2gff.PLS
ok 664 - POD test for scripts/Bio-DB-GFF/genbank2gff3.PLS
ok 665 - POD test for scripts/Bio-DB-GFF/generate_histogram.PLS
ok 666 - POD test for scripts/Bio-DB-GFF/load_gff.PLS
ok 667 - POD test for scripts/Bio-DB-GFF/meta_gff.PLS
ok 668 - POD test for scripts/Bio-DB-GFF/process_gadfly.PLS
ok 669 - POD test for scripts/Bio-DB-GFF/process_sgd.PLS
ok 670 - POD test for scripts/Bio-DB-GFF/process_wormbase.PLS
ok 671 - POD test for scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS (no pod)
ok 672 - POD test for scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS (no pod)
ok 673 - POD test for scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS (no pod)
ok 674 - POD test for scripts/DB/biofetch_genbank_proxy.PLS
ok 675 - POD test for scripts/DB/bioflat_index.PLS
ok 676 - POD test for scripts/DB/biogetseq.PLS
ok 677 - POD test for scripts/DB/flanks.PLS
ok 678 - POD test for scripts/index/bp_fetch.PLS
ok 679 - POD test for scripts/index/bp_index.PLS
ok 680 - POD test for scripts/index/bp_seqret.PLS
ok 681 - POD test for scripts/popgen/composite_LD.PLS
ok 682 - POD test for scripts/popgen/heterogeneity_test.PLS
ok 683 - POD test for scripts/searchio/fastam9_to_table.PLS
ok 684 - POD test for scripts/searchio/filter_search.PLS
ok 685 - POD test for scripts/searchio/hmmer_to_table.PLS
ok 686 - POD test for scripts/searchio/parse_hmmsearch.PLS
ok 687 - POD test for scripts/searchio/search2table.PLS
ok 688 - POD test for scripts/seq/extract_feature_seq.PLS
ok 689 - POD test for scripts/seq/make_mrna_protein.PLS
ok 690 - POD test for scripts/seq/seqconvert.PLS
ok 691 - POD test for scripts/seq/seqretsplit.PLS
ok 692 - POD test for scripts/seq/split_seq.PLS
ok 693 - POD test for scripts/seq/translate_seq.PLS
ok 694 - POD test for scripts/seq/unflatten_seq.PLS
ok 695 - POD test for scripts/seqstats/aacomp.PLS
ok 696 - POD test for scripts/seqstats/chaos_plot.PLS
ok 697 - POD test for scripts/seqstats/gccalc.PLS
ok 698 - POD test for scripts/seqstats/oligo_count.PLS
ok 699 - POD test for scripts/taxa/classify_hits_kingdom.PLS
ok 700 - POD test for scripts/taxa/local_taxonomydb_query.PLS
ok 701 - POD test for scripts/taxa/query_entrez_taxa.PLS
ok 702 - POD test for scripts/taxa/taxid4species.PLS
ok 703 - POD test for scripts/taxa/taxonomy2tree.PLS
ok 704 - POD test for scripts/tree/blast2tree.PLS
ok 705 - POD test for scripts/tree/nexus2nh.PLS
ok 706 - POD test for scripts/tree/tree2pag.PLS
ok 707 - POD test for scripts/utilities/bp_mrtrans.PLS
ok 708 - POD test for scripts/utilities/bp_nrdb.PLS
ok 709 - POD test for scripts/utilities/bp_sreformat.PLS
ok 710 - POD test for scripts/utilities/dbsplit.PLS
ok 711 - POD test for scripts/utilities/download_query_genbank.PLS
ok 712 - POD test for scripts/utilities/mask_by_search.PLS
ok 713 - POD test for scripts/utilities/mutate.PLS
ok 714 - POD test for scripts/utilities/pairwise_kaks.PLS
ok 715 - POD test for scripts/utilities/remote_blast.PLS
ok 716 - POD test for scripts/utilities/search2alnblocks.PLS
ok 717 - POD test for scripts/utilities/search2BSML.PLS
ok 718 - POD test for scripts/utilities/search2gff.PLS
ok 719 - POD test for scripts/utilities/search2tribe.PLS
ok 720 - POD test for scripts/utilities/seq_length.PLS
ok 721 - POD test for t/Align/AlignStats.t (no pod)
ok 722 - POD test for t/Align/AlignUtil.t (no pod)
ok 723 - POD test for t/Align/SimpleAlign.t (no pod)
ok 724 - POD test for t/Align/TreeBuild.t (no pod)
ok 725 - POD test for t/Align/Utilities.t (no pod)
ok 726 - POD test for t/AlignIO/AlignIO.t (no pod)
ok 727 - POD test for t/AlignIO/arp.t (no pod)
ok 728 - POD test for t/AlignIO/bl2seq.t (no pod)
ok 729 - POD test for t/AlignIO/clustalw.t (no pod)
ok 730 - POD test for t/AlignIO/emboss.t (no pod)
ok 731 - POD test for t/AlignIO/fasta.t (no pod)
ok 732 - POD test for t/AlignIO/largemultifasta.t (no pod)
ok 733 - POD test for t/AlignIO/maf.t (no pod)
ok 734 - POD test for t/AlignIO/mase.t (no pod)
ok 735 - POD test for t/AlignIO/mega.t (no pod)
ok 736 - POD test for t/AlignIO/meme.t (no pod)
ok 737 - POD test for t/AlignIO/metafasta.t (no pod)
ok 738 - POD test for t/AlignIO/msf.t (no pod)
ok 739 - POD test for t/AlignIO/nexus.t (no pod)
ok 740 - POD test for t/AlignIO/pfam.t (no pod)
ok 741 - POD test for t/AlignIO/phylip.t (no pod)
ok 742 - POD test for t/AlignIO/po.t (no pod)
ok 743 - POD test for t/AlignIO/prodom.t (no pod)
ok 744 - POD test for t/AlignIO/psi.t (no pod)
ok 745 - POD test for t/AlignIO/selex.t (no pod)
ok 746 - POD test for t/AlignIO/stockholm.t (no pod)
ok 747 - POD test for t/AlignIO/xmfa.t (no pod)
ok 748 - POD test for t/Annotation/Annotation.t (no pod)
ok 749 - POD test for t/Annotation/AnnotationAdaptor.t (no pod)
ok 750 - POD test for t/Assembly/Assembly.t (no pod)
ok 751 - POD test for t/Assembly/ContigSpectrum.t (no pod)
ok 752 - POD test for t/Biblio/Biblio.t (no pod)
ok 753 - POD test for t/Biblio/biofetch.t (no pod)
ok 754 - POD test for t/Biblio/eutils.t (no pod)
ok 755 - POD test for t/Biblio/References.t (no pod)
ok 756 - POD test for t/ClusterIO/ClusterIO.t (no pod)
ok 757 - POD test for t/ClusterIO/SequenceFamily.t (no pod)
ok 758 - POD test for t/ClusterIO/unigene.t (no pod)
ok 759 - POD test for t/Coordinate/CoordinateGraph.t (no pod)
ok 760 - POD test for t/Coordinate/CoordinateMapper.t (no pod)
ok 761 - POD test for t/Coordinate/GeneCoordinateMapper.t (no pod)
ok 762 - POD test for t/lib/Error.pm
ok 763 - POD test for t/LiveSeq/Chain.t (no pod)
ok 764 - POD test for t/LiveSeq/LiveSeq.t (no pod)
ok 765 - POD test for t/LiveSeq/Mutation.t (no pod)
ok 766 - POD test for t/LiveSeq/Mutator.t (no pod)
ok 767 - POD test for t/LocalDB/BioDBGFF.t (no pod)
ok 768 - POD test for t/LocalDB/BlastIndex.t (no pod)
ok 769 - POD test for t/LocalDB/DBFasta.t (no pod)
ok 770 - POD test for t/LocalDB/DBQual.t (no pod)
ok 771 - POD test for t/LocalDB/Flat.t (no pod)
ok 772 - POD test for t/LocalDB/Index.t (no pod)
ok 773 - POD test for t/LocalDB/Registry.t (no pod)
ok 774 - POD test for t/LocalDB/SeqFeature.t (no pod)
ok 775 - POD test for t/LocalDB/transfac_pro.t (no pod)
ok 776 - POD test for t/Map/Cyto.t (no pod)
ok 777 - POD test for t/Map/Linkage.t (no pod)
ok 778 - POD test for t/Map/Map.t (no pod)
ok 779 - POD test for t/Map/MapIO.t (no pod)
ok 780 - POD test for t/Map/MicrosatelliteMarker.t (no pod)
ok 781 - POD test for t/Map/Physical.t (no pod)
ok 782 - POD test for t/Matrix/InstanceSite.t (no pod)
ok 783 - POD test for t/Matrix/Matrix.t (no pod)
ok 784 - POD test for t/Matrix/ProtMatrix.t (no pod)
ok 785 - POD test for t/Matrix/ProtPsm.t (no pod)
ok 786 - POD test for t/Matrix/SiteMatrix.t (no pod)
ok 787 - POD test for t/Ontology/GOterm.t (no pod)
ok 788 - POD test for t/Ontology/GraphAdaptor.t (no pod)
ok 789 - POD test for t/Ontology/Ontology.t (no pod)
ok 790 - POD test for t/Ontology/OntologyEngine.t (no pod)
ok 791 - POD test for t/Ontology/OntologyStore.t (no pod)
ok 792 - POD test for t/Ontology/Relationship.t (no pod)
ok 793 - POD test for t/Ontology/RelationshipType.t (no pod)
ok 794 - POD test for t/Ontology/Term.t (no pod)
ok 795 - POD test for t/Phenotype/Correlate.t (no pod)
ok 796 - POD test for t/Phenotype/Measure.t (no pod)
ok 797 - POD test for t/Phenotype/MeSH.t (no pod)
ok 798 - POD test for t/Phenotype/MiniMIMentry.t (no pod)
ok 799 - POD test for t/Phenotype/OMIMentry.t (no pod)
ok 800 - POD test for t/Phenotype/OMIMentryAllelicVariant.t (no pod)
ok 801 - POD test for t/Phenotype/OMIMparser.t (no pod)
ok 802 - POD test for t/Phenotype/Phenotype.t (no pod)
ok 803 - POD test for t/PopGen/Coalescent.t (no pod)
ok 804 - POD test for t/PopGen/HtSNP.t (no pod)
ok 805 - POD test for t/PopGen/MK.t (no pod)
ok 806 - POD test for t/PopGen/PopGen.t (no pod)
ok 807 - POD test for t/PopGen/PopGenSims.t (no pod)
ok 808 - POD test for t/PopGen/TagHaplotype.t (no pod)
ok 809 - POD test for t/RemoteDB/BioFetch.t (no pod)
ok 810 - POD test for t/RemoteDB/CUTG.t (no pod)
ok 811 - POD test for t/RemoteDB/DB.t (no pod)
ok 812 - POD test for t/RemoteDB/EMBL.t (no pod)
ok 813 - POD test for t/RemoteDB/EUtilities.t (no pod)
ok 814 - POD test for t/RemoteDB/RefSeq.t (no pod)
ok 815 - POD test for t/RemoteDB/SeqHound.t (no pod)
ok 816 - POD test for t/RemoteDB/SeqRead_fail.t (no pod)
ok 817 - POD test for t/RemoteDB/SeqVersion.t (no pod)
ok 818 - POD test for t/RemoteDB/Taxonomy.t (no pod)
ok 819 - POD test for t/Restriction/Analysis.t (no pod)
ok 820 - POD test for t/Restriction/Gel.t (no pod)
ok 821 - POD test for t/Restriction/IO.t (no pod)
ok 822 - POD test for t/Root/Exception.t (no pod)
ok 823 - POD test for t/Root/RootI.t (no pod)
ok 824 - POD test for t/Root/RootIO.t (no pod)
ok 825 - POD test for t/Root/Storable.t (no pod)
ok 826 - POD test for t/Root/Tempfile.t (no pod)
ok 827 - POD test for t/Root/Utilities.t (no pod)
ok 828 - POD test for t/SearchIO/blast.t (no pod)
ok 829 - POD test for t/SearchIO/blast_pull.t (no pod)
ok 830 - POD test for t/SearchIO/blasttable.t (no pod)
ok 831 - POD test for t/SearchIO/blastxml.t (no pod)
ok 832 - POD test for t/SearchIO/CigarString.t (no pod)
ok 833 - POD test for t/SearchIO/cross_match.t (no pod)
ok 834 - POD test for t/SearchIO/erpin.t (no pod)
ok 835 - POD test for t/SearchIO/exonerate.t (no pod)
ok 836 - POD test for t/SearchIO/fasta.t (no pod)
ok 837 - POD test for t/SearchIO/GbrowseGFF.t (no pod)
ok 838 - POD test for t/SearchIO/hmmer.t (no pod)
ok 839 - POD test for t/SearchIO/hmmer_pull.t (no pod)
ok 840 - POD test for t/SearchIO/infernal.t (no pod)
ok 841 - POD test for t/SearchIO/megablast.t (no pod)
ok 842 - POD test for t/SearchIO/psl.t (no pod)
ok 843 - POD test for t/SearchIO/rnamotif.t (no pod)
ok 844 - POD test for t/SearchIO/SearchIO.t (no pod)
ok 845 - POD test for t/SearchIO/sim4.t (no pod)
ok 846 - POD test for t/SearchIO/SimilarityPair.t (no pod)
ok 847 - POD test for t/SearchIO/waba.t (no pod)
ok 848 - POD test for t/SearchIO/wise.t (no pod)
ok 849 - POD test for t/Seq/DBLink.t (no pod)
ok 850 - POD test for t/Seq/EncodedSeq.t (no pod)
ok 851 - POD test for t/Seq/LargeLocatableSeq.t (no pod)
ok 852 - POD test for t/Seq/LargePSeq.t (no pod)
ok 853 - POD test for t/Seq/LocatableSeq.t (no pod)
ok 854 - POD test for t/Seq/MetaSeq.t (no pod)
ok 855 - POD test for t/Seq/PrimaryQual.t (no pod)
ok 856 - POD test for t/Seq/PrimarySeq.t (no pod)
ok 857 - POD test for t/Seq/PrimedSeq.t (no pod)
ok 858 - POD test for t/Seq/Quality.t (no pod)
ok 859 - POD test for t/Seq/Seq.t (no pod)
ok 860 - POD test for t/Seq/WithQuality.t (no pod)
ok 861 - POD test for t/SeqFeature/FeatureIO.t (no pod)
ok 862 - POD test for t/SeqFeature/Location.t (no pod)
ok 863 - POD test for t/SeqFeature/LocationFactory.t (no pod)
ok 864 - POD test for t/SeqFeature/Primer.t (no pod)
ok 865 - POD test for t/SeqFeature/Range.t (no pod)
ok 866 - POD test for t/SeqFeature/RangeI.t (no pod)
ok 867 - POD test for t/SeqFeature/SeqAnalysisParser.t (no pod)
ok 868 - POD test for t/SeqFeature/SeqFeatAnnotated.t (no pod)
ok 869 - POD test for t/SeqFeature/SeqFeatCollection.t (no pod)
ok 870 - POD test for t/SeqFeature/SeqFeature.t (no pod)
ok 871 - POD test for t/SeqFeature/SeqFeaturePrimer.t (no pod)
ok 872 - POD test for t/SeqFeature/Unflattener.t (no pod)
ok 873 - POD test for t/SeqFeature/Unflattener2.t (no pod)
ok 874 - POD test for t/SeqIO/abi.t (no pod)
ok 875 - POD test for t/SeqIO/ace.t (no pod)
ok 876 - POD test for t/SeqIO/agave.t (no pod)
ok 877 - POD test for t/SeqIO/alf.t (no pod)
ok 878 - POD test for t/SeqIO/asciitree.t (no pod)
ok 879 - POD test for t/SeqIO/bsml.t (no pod)
ok 880 - POD test for t/SeqIO/bsml_sax.t (no pod)
ok 881 - POD test for t/SeqIO/chadoxml.t (no pod)
ok 882 - POD test for t/SeqIO/chaos.t (no pod)
ok 883 - POD test for t/SeqIO/chaosxml.t (no pod)
ok 884 - POD test for t/SeqIO/ctf.t (no pod)
ok 885 - POD test for t/SeqIO/embl.t (no pod)
ok 886 - POD test for t/SeqIO/entrezgene.t (no pod)
ok 887 - POD test for t/SeqIO/excel.t (no pod)
ok 888 - POD test for t/SeqIO/exp.t (no pod)
ok 889 - POD test for t/SeqIO/fasta.t (no pod)
ok 890 - POD test for t/SeqIO/fastq.t (no pod)
ok 891 - POD test for t/SeqIO/flybase_chadoxml.t (no pod)
ok 892 - POD test for t/SeqIO/game.t (no pod)
ok 893 - POD test for t/SeqIO/gcg.t (no pod)
ok 894 - POD test for t/SeqIO/genbank.t (no pod)
ok 895 - POD test for t/SeqIO/Handler.t (no pod)
ok 896 - POD test for t/SeqIO/interpro.t (no pod)
ok 897 - POD test for t/SeqIO/kegg.t (no pod)
ok 898 - POD test for t/SeqIO/largefasta.t (no pod)
ok 899 - POD test for t/SeqIO/lasergene.t (no pod)
ok 900 - POD test for t/SeqIO/locuslink.t (no pod)
ok 901 - POD test for t/SeqIO/metafasta.t (no pod)
ok 902 - POD test for t/SeqIO/MultiFile.t (no pod)
ok 903 - POD test for t/SeqIO/Multiple_fasta.t (no pod)
ok 904 - POD test for t/SeqIO/phd.t (no pod)
ok 905 - POD test for t/SeqIO/pir.t (no pod)
ok 906 - POD test for t/SeqIO/pln.t (no pod)
ok 907 - POD test for t/SeqIO/qual.t (no pod)
ok 908 - POD test for t/SeqIO/raw.t (no pod)
ok 909 - POD test for t/SeqIO/scf.t (no pod)
ok 910 - POD test for t/SeqIO/SeqBuilder.t (no pod)
ok 911 - POD test for t/SeqIO/Splicedseq.t (no pod)
ok 912 - POD test for t/SeqIO/strider.t (no pod)
ok 913 - POD test for t/SeqIO/swiss.t (no pod)
ok 914 - POD test for t/SeqIO/tab.t (no pod)
ok 915 - POD test for t/SeqIO/table.t (no pod)
ok 916 - POD test for t/SeqIO/tigr.t (no pod)
ok 917 - POD test for t/SeqIO/tigrxml.t (no pod)
ok 918 - POD test for t/SeqIO/tinyseq.t (no pod)
ok 919 - POD test for t/SeqIO/ztr.t (no pod)
ok 920 - POD test for t/SeqTools/CodonTable.t (no pod)
ok 921 - POD test for t/SeqTools/ECnumber.t (no pod)
ok 922 - POD test for t/SeqTools/GuessSeqFormat.t (no pod)
ok 923 - POD test for t/SeqTools/OddCodes.t (no pod)
ok 924 - POD test for t/SeqTools/SeqPattern.t (no pod)
ok 925 - POD test for t/SeqTools/SeqStats.t (no pod)
ok 926 - POD test for t/SeqTools/SeqUtils.t (no pod)
ok 927 - POD test for t/SeqTools/SeqWords.t (no pod)
ok 928 - POD test for t/Structure/IO.t (no pod)
ok 929 - POD test for t/Structure/Structure.t (no pod)
ok 930 - POD test for t/Tools/ePCR.t (no pod)
ok 931 - POD test for t/Tools/Est2Genome.t (no pod)
ok 932 - POD test for t/Tools/FootPrinter.t (no pod)
ok 933 - POD test for t/Tools/Geneid.t (no pod)
ok 934 - POD test for t/Tools/Genewise.t (no pod)
ok 935 - POD test for t/Tools/Genomewise.t (no pod)
ok 936 - POD test for t/Tools/Genpred.t (no pod)
ok 937 - POD test for t/Tools/GFF.t (no pod)
ok 938 - POD test for t/Tools/Hmmer.t (no pod)
ok 939 - POD test for t/Tools/IUPAC.t (no pod)
ok 940 - POD test for t/Tools/Lucy.t (no pod)
ok 941 - POD test for t/Tools/Match.t (no pod)
ok 942 - POD test for t/Tools/pICalculator.t (no pod)
ok 943 - POD test for t/Tools/Primer3.t (no pod)
ok 944 - POD test for t/Tools/Promoterwise.t (no pod)
ok 945 - POD test for t/Tools/Pseudowise.t (no pod)
ok 946 - POD test for t/Tools/QRNA.t (no pod)
ok 947 - POD test for t/Tools/RandDistFunctions.t (no pod)
ok 948 - POD test for t/Tools/RepeatMasker.t (no pod)
ok 949 - POD test for t/Tools/rnamotif.t (no pod)
ok 950 - POD test for t/Tools/Seg.t (no pod)
ok 951 - POD test for t/Tools/Sigcleave.t (no pod)
ok 952 - POD test for t/Tools/Signalp.t (no pod)
ok 953 - POD test for t/Tools/Sim4.t (no pod)
ok 954 - POD test for t/Tools/SiRNA.t (no pod)
ok 955 - POD test for t/Tools/TandemRepeatsFinder.t (no pod)
ok 956 - POD test for t/Tools/TargetP.t (no pod)
ok 957 - POD test for t/Tools/Tmhmm.t (no pod)
ok 958 - POD test for t/Tools/tRNAscanSE.t (no pod)
ok 959 - POD test for t/Tree/Compatible.t (no pod)
ok 960 - POD test for t/Tree/Node.t (no pod)
ok 961 - POD test for t/Tree/RandomTreeFactory.t (no pod)
ok 962 - POD test for t/Tree/Tree.t (no pod)
ok 963 - POD test for t/Tree/TreeIO.t (no pod)
ok 964 - POD test for t/Tree/TreeStatistics.t (no pod)
ok 965 - POD test for t/Variation/AAChange.t (no pod)
ok 966 - POD test for t/Variation/AAReverseMutate.t (no pod)
ok 967 - POD test for t/Variation/Allele.t (no pod)
ok 968 - POD test for t/Variation/DNAMutation.t (no pod)
ok 969 - POD test for t/Variation/RNAChange.t (no pod)
ok 970 - POD test for t/Variation/SeqDiff.t (no pod)
ok 971 - POD test for t/Variation/SNP.t (no pod)
ok 972 - POD test for t/Variation/Variation_IO.t (no pod)
ok 973 - POD test for blib/script/bp_sreformat.pl
ok 974 - POD test for blib/script/bp_seqconvert.pl
ok 975 - POD test for blib/script/bp_seqret.pl
ok 976 - POD test for blib/script/bp_parse_hmmsearch.pl
ok 977 - POD test for blib/script/bp_tree2pag.pl
ok 978 - POD test for blib/script/bp_meta_gff.pl
ok 979 - POD test for blib/script/bp_nexus2nh.pl
ok 980 - POD test for blib/script/bp_flanks.pl
ok 981 - POD test for blib/script/bp_filter_search.pl
ok 982 - POD test for blib/script/bp_split_seq.pl
ok 983 - POD test for blib/script/bp_seqfeature_gff3.pl (no pod)
ok 984 - POD test for blib/script/bp_generate_histogram.pl
ok 985 - POD test for blib/script/bp_heterogeneity_test.pl
ok 986 - POD test for blib/script/bp_load_gff.pl
ok 987 - POD test for blib/script/bp_biogetseq.pl
ok 988 - POD test for blib/script/bp_fetch.pl
ok 989 - POD test for blib/script/bp_mutate.pl
ok 990 - POD test for blib/script/bp_process_sgd.pl
ok 991 - POD test for blib/script/bp_index.pl
ok 992 - POD test for blib/script/bp_dbsplit.pl
ok 993 - POD test for blib/script/bp_oligo_count.pl
ok 994 - POD test for blib/script/bp_seq_length.pl
ok 995 - POD test for blib/script/bp_seqfeature_load.pl (no pod)
ok 996 - POD test for blib/script/bp_process_gadfly.pl
ok 997 - POD test for blib/script/bp_hmmer_to_table.pl
ok 998 - POD test for blib/script/bp_fastam9_to_table.pl
ok 999 - POD test for blib/script/bp_genbank2gff.pl
ok 1000 - POD test for blib/script/bp_biofetch_genbank_proxy.pl
ok 1001 - POD test for blib/script/bp_extract_feature_seq.pl
ok 1002 - POD test for blib/script/bp_search2gff.pl
ok 1003 - POD test for blib/script/bp_taxid4species.pl
ok 1004 - POD test for blib/script/bp_bulk_load_gff.pl
ok 1005 - POD test for blib/script/bp_blast2tree.pl
ok 1006 - POD test for blib/script/bp_search2tribe.pl
ok 1007 - POD test for blib/script/bp_make_mrna_protein.pl
ok 1008 - POD test for blib/script/bp_unflatten_seq.pl
ok 1009 - POD test for blib/script/bp_chaos_plot.pl
ok 1010 - POD test for blib/script/bp_bioflat_index.pl
ok 1011 - POD test for blib/script/bp_pairwise_kaks.pl
ok 1012 - POD test for blib/script/bp_seqfeature_delete.pl (no pod)
ok 1013 - POD test for blib/script/bp_query_entrez_taxa.pl
ok 1014 - POD test for blib/script/bp_fast_load_gff.pl
ok 1015 - POD test for blib/script/bp_mrtrans.pl
ok 1016 - POD test for blib/script/bp_taxonomy2tree.pl
ok 1017 - POD test for blib/script/bp_nrdb.pl
ok 1018 - POD test for blib/script/bp_search2alnblocks.pl
ok 1019 - POD test for blib/script/bp_gccalc.pl
ok 1020 - POD test for blib/script/bp_download_query_genbank.pl
ok 1021 - POD test for blib/script/bp_mask_by_search.pl
ok 1022 - POD test for blib/script/bp_composite_LD.pl
ok 1023 - POD test for blib/script/bp_aacomp.pl
ok 1024 - POD test for blib/script/bp_classify_hits_kingdom.pl
ok 1025 - POD test for blib/script/bp_biblio.pl
ok 1026 - POD test for blib/script/bp_process_wormbase.pl
ok 1027 - POD test for blib/script/bp_seqretsplit.pl
ok 1028 - POD test for blib/script/bp_local_taxonomydb_query.pl
ok 1029 - POD test for blib/script/bp_remote_blast.pl
ok 1030 - POD test for blib/script/bp_genbank2gff3.pl
ok 1031 - POD test for blib/script/bp_search2table.pl
ok 1032 - POD test for blib/script/bp_search2BSML.pl
ok 1033 - POD test for blib/script/bp_translate_seq.pl
ok 1034 - POD test for Bio/AlignIO/Handler/GenericAlignHandler.pm
ok 1035 - POD test for Bio/Assembly/IO/ace.pm
ok 1036 - POD test for Bio/Assembly/IO/phrap.pm
ok 1037 - POD test for Bio/Assembly/IO/tigr.pm
ok 1038 - POD test for Bio/Assembly/Tools/ContigSpectrum.pm
ok 1039 - POD test for Bio/Biblio/IO/medline2ref.pm
ok 1040 - POD test for Bio/Biblio/IO/medlinexml.pm
ok 1041 - POD test for Bio/Biblio/IO/pubmed2ref.pm
ok 1042 - POD test for Bio/Biblio/IO/pubmedxml.pm
ok 1043 - POD test for Bio/Coordinate/Result/Gap.pm
ok 1044 - POD test for Bio/Coordinate/Result/Match.pm
ok 1045 - POD test for Bio/DB/Biblio/biofetch.pm
ok 1046 - POD test for Bio/DB/Biblio/eutils.pm
ok 1047 - POD test for Bio/DB/Biblio/soap.pm
ok 1048 - POD test for Bio/DB/Expression/geo.pm
ok 1049 - POD test for Bio/DB/Flat/BDB.pm
ok 1050 - POD test for Bio/DB/Flat/BinarySearch.pm
ok 1051 - POD test for Bio/DB/GFF/Aggregator.pm
ok 1052 - POD test for Bio/DB/GFF/Featname.pm
ok 1053 - POD test for Bio/DB/GFF/Feature.pm
ok 1054 - POD test for Bio/DB/GFF/Homol.pm
ok 1055 - POD test for Bio/DB/GFF/RelSegment.pm
ok 1056 - POD test for Bio/DB/GFF/Segment.pm
ok 1057 - POD test for Bio/DB/GFF/Typename.pm
ok 1058 - POD test for Bio/DB/HIV/HIVAnnotProcessor.pm
ok 1059 - POD test for Bio/DB/HIV/HIVQueryHelper.pm
ok 1060 - POD test for Bio/DB/Query/GenBank.pm
ok 1061 - POD test for Bio/DB/Query/HIVQuery.pm
ok 1062 - POD test for Bio/DB/Query/WebQuery.pm
ok 1063 - POD test for Bio/DB/SeqFeature/NormalizedFeature.pm
ok 1064 - POD test for Bio/DB/SeqFeature/NormalizedFeatureI.pm
ok 1065 - POD test for Bio/DB/SeqFeature/NormalizedTableFeatureI.pm
ok 1066 - POD test for Bio/DB/SeqFeature/Segment.pm
ok 1067 - POD test for Bio/DB/SeqFeature/Store.pm
ok 1068 - POD test for Bio/DB/SeqVersion/gi.pm
ok 1069 - POD test for Bio/DB/Taxonomy/entrez.pm
ok 1070 - POD test for Bio/DB/Taxonomy/flatfile.pm
ok 1071 - POD test for Bio/DB/Taxonomy/list.pm
ok 1072 - POD test for Bio/DB/TFBS/transfac_pro.pm
ok 1073 - POD test for Bio/Expression/FeatureGroup/FeatureGroupMas50.pm
ok 1074 - POD test for Bio/Expression/FeatureSet/FeatureSetMas50.pm
ok 1075 - POD test for Bio/LiveSeq/IO/BioPerl.pm
ok 1076 - POD test for Bio/LiveSeq/IO/Loader.pm
ok 1077 - POD test for Bio/Matrix/IO/mlagan.pm
ok 1078 - POD test for Bio/Matrix/IO/phylip.pm
ok 1079 - POD test for Bio/Matrix/IO/scoring.pm
ok 1080 - POD test for Bio/Matrix/PSM/InstanceSite.pm
ok 1081 - POD test for Bio/Matrix/PSM/InstanceSiteI.pm
ok 1082 - POD test for Bio/Matrix/PSM/IO.pm
ok 1083 - POD test for Bio/Matrix/PSM/ProtMatrix.pm
ok 1084 - POD test for Bio/Matrix/PSM/ProtPsm.pm
ok 1085 - POD test for Bio/Matrix/PSM/Psm.pm
ok 1086 - POD test for Bio/Matrix/PSM/PsmHeader.pm
ok 1087 - POD test for Bio/Matrix/PSM/PsmHeaderI.pm
ok 1088 - POD test for Bio/Matrix/PSM/PsmI.pm
ok 1089 - POD test for Bio/Matrix/PSM/SiteMatrix.pm
ok 1090 - POD test for Bio/Matrix/PSM/SiteMatrixI.pm
ok 1091 - POD test for Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm
ok 1092 - POD test for Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm
ok 1093 - POD test for Bio/OntologyIO/Handlers/BaseSAXHandler.pm
ok 1094 - POD test for Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
ok 1095 - POD test for Bio/OntologyIO/Handlers/InterProHandler.pm
ok 1096 - POD test for Bio/Phenotype/MeSH/Term.pm
ok 1097 - POD test for Bio/Phenotype/MeSH/Twig.pm
ok 1098 - POD test for Bio/Phenotype/OMIM/MiniMIMentry.pm
ok 1099 - POD test for Bio/Phenotype/OMIM/OMIMentry.pm
ok 1100 - POD test for Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm
ok 1101 - POD test for Bio/Phenotype/OMIM/OMIMparser.pm
ok 1102 - POD test for Bio/PopGen/IO/csv.pm
ok 1103 - POD test for Bio/PopGen/IO/hapmap.pm
ok 1104 - POD test for Bio/PopGen/IO/phase.pm
ok 1105 - POD test for Bio/PopGen/IO/prettybase.pm
ok 1106 - POD test for Bio/PopGen/Simulation/Coalescent.pm
ok 1107 - POD test for Bio/PopGen/Simulation/GeneticDrift.pm
ok 1108 - POD test for Bio/Restriction/Enzyme/MultiCut.pm
ok 1109 - POD test for Bio/Restriction/Enzyme/MultiSite.pm
ok 1110 - POD test for Bio/Restriction/IO/bairoch.pm
ok 1111 - POD test for Bio/Restriction/IO/base.pm
ok 1112 - POD test for Bio/Restriction/IO/itype2.pm
ok 1113 - POD test for Bio/Restriction/IO/prototype.pm
ok 1114 - POD test for Bio/Restriction/IO/withrefm.pm
ok 1115 - POD test for Bio/Root/Test/Warn.pm
ok 1116 - POD test for Bio/Search/Hit/BlastHit.pm
ok 1117 - POD test for Bio/Search/Hit/BlastPullHit.pm
ok 1118 - POD test for Bio/Search/Hit/Fasta.pm
ok 1119 - POD test for Bio/Search/Hit/GenericHit.pm
ok 1120 - POD test for Bio/Search/Hit/HitFactory.pm
ok 1121 - POD test for Bio/Search/Hit/HitI.pm
ok 1122 - POD test for Bio/Search/Hit/HMMERHit.pm
ok 1123 - POD test for Bio/Search/Hit/HmmpfamHit.pm
ok 1124 - POD test for Bio/Search/Hit/ModelHit.pm
ok 1125 - POD test for Bio/Search/Hit/PsiBlastHit.pm
ok 1126 - POD test for Bio/Search/Hit/PullHitI.pm
ok 1127 - POD test for Bio/Search/HSP/BlastHSP.pm
ok 1128 - POD test for Bio/Search/HSP/BlastPullHSP.pm
ok 1129 - POD test for Bio/Search/HSP/FastaHSP.pm
ok 1130 - POD test for Bio/Search/HSP/GenericHSP.pm
ok 1131 - POD test for Bio/Search/HSP/HMMERHSP.pm
ok 1132 - POD test for Bio/Search/HSP/HmmpfamHSP.pm
ok 1133 - POD test for Bio/Search/HSP/HSPFactory.pm
ok 1134 - POD test for Bio/Search/HSP/HSPI.pm
ok 1135 - POD test for Bio/Search/HSP/ModelHSP.pm
ok 1136 - POD test for Bio/Search/HSP/PsiBlastHSP.pm
ok 1137 - POD test for Bio/Search/HSP/PSLHSP.pm
ok 1138 - POD test for Bio/Search/HSP/PullHSPI.pm
ok 1139 - POD test for Bio/Search/HSP/WABAHSP.pm
ok 1140 - POD test for Bio/Search/Iteration/GenericIteration.pm
ok 1141 - POD test for Bio/Search/Iteration/IterationI.pm
ok 1142 - POD test for Bio/Search/Result/BlastPullResult.pm
ok 1143 - POD test for Bio/Search/Result/BlastResult.pm
ok 1144 - POD test for Bio/Search/Result/CrossMatchResult.pm
ok 1145 - POD test for Bio/Search/Result/GenericResult.pm
ok 1146 - POD test for Bio/Search/Result/HMMERResult.pm
ok 1147 - POD test for Bio/Search/Result/HmmpfamResult.pm
ok 1148 - POD test for Bio/Search/Result/PullResultI.pm
ok 1149 - POD test for Bio/Search/Result/ResultFactory.pm
ok 1150 - POD test for Bio/Search/Result/ResultI.pm
ok 1151 - POD test for Bio/Search/Result/WABAResult.pm
ok 1152 - POD test for Bio/SearchIO/Writer/BSMLResultWriter.pm
ok 1153 - POD test for Bio/SearchIO/Writer/GbrowseGFF.pm
ok 1154 - POD test for Bio/SearchIO/Writer/HitTableWriter.pm
ok 1155 - POD test for Bio/SearchIO/Writer/HSPTableWriter.pm
ok 1156 - POD test for Bio/SearchIO/Writer/HTMLResultWriter.pm
ok 1157 - POD test for Bio/SearchIO/Writer/ResultTableWriter.pm
ok 1158 - POD test for Bio/SearchIO/Writer/TextResultWriter.pm
ok 1159 - POD test for Bio/SearchIO/XML/BlastHandler.pm
ok 1160 - POD test for Bio/SearchIO/XML/PsiBlastHandler.pm
ok 1161 - POD test for Bio/Seq/Meta/Array.pm
ok 1162 - POD test for Bio/SeqFeature/Gene/Exon.pm
ok 1163 - POD test for Bio/SeqFeature/Gene/ExonI.pm
ok 1164 - POD test for Bio/SeqFeature/Gene/GeneStructure.pm
ok 1165 - POD test for Bio/SeqFeature/Gene/GeneStructureI.pm
ok 1166 - POD test for Bio/SeqFeature/Gene/Intron.pm
ok 1167 - POD test for Bio/SeqFeature/Gene/NC_Feature.pm
ok 1168 - POD test for Bio/SeqFeature/Gene/Poly_A_site.pm
ok 1169 - POD test for Bio/SeqFeature/Gene/Promoter.pm
ok 1170 - POD test for Bio/SeqFeature/Gene/Transcript.pm
ok 1171 - POD test for Bio/SeqFeature/Gene/TranscriptI.pm
ok 1172 - POD test for Bio/SeqFeature/Gene/UTR.pm
ok 1173 - POD test for Bio/SeqFeature/SiRNA/Oligo.pm
ok 1174 - POD test for Bio/SeqFeature/SiRNA/Pair.pm
ok 1175 - POD test for Bio/SeqFeature/Tools/FeatureNamer.pm
ok 1176 - POD test for Bio/SeqFeature/Tools/IDHandler.pm
ok 1177 - POD test for Bio/SeqFeature/Tools/TypeMapper.pm
ok 1178 - POD test for Bio/SeqFeature/Tools/Unflattener.pm
ok 1179 - POD test for Bio/SeqIO/game/featHandler.pm
ok 1180 - POD test for Bio/SeqIO/game/gameHandler.pm
ok 1181 - POD test for Bio/SeqIO/game/gameSubs.pm
ok 1182 - POD test for Bio/SeqIO/game/gameWriter.pm
ok 1183 - POD test for Bio/SeqIO/game/seqHandler.pm
ok 1184 - POD test for Bio/SeqIO/Handler/GenericRichSeqHandler.pm
ok 1185 - POD test for Bio/SeqIO/tinyseq/tinyseqHandler.pm
ok 1186 - POD test for Bio/Structure/IO/pdb.pm
ok 1187 - POD test for Bio/Tools/Alignment/Consed.pm
ok 1188 - POD test for Bio/Tools/Alignment/Trim.pm
ok 1189 - POD test for Bio/Tools/Analysis/SimpleAnalysisBase.pm
ok 1190 - POD test for Bio/Tools/EMBOSS/Palindrome.pm
ok 1191 - POD test for Bio/Tools/EUtilities/Cookie.pm
ok 1192 - POD test for Bio/Tools/EUtilities/EUtilDataI.pm
ok 1193 - POD test for Bio/Tools/EUtilities/EUtilParameters.pm
ok 1194 - POD test for Bio/Tools/EUtilities/History.pm
ok 1195 - POD test for Bio/Tools/EUtilities/HistoryI.pm
ok 1196 - POD test for Bio/Tools/EUtilities/Info.pm
ok 1197 - POD test for Bio/Tools/EUtilities/Link.pm
ok 1198 - POD test for Bio/Tools/EUtilities/Query.pm
ok 1199 - POD test for Bio/Tools/EUtilities/Summary.pm
ok 1200 - POD test for Bio/Tools/HMMER/Domain.pm
ok 1201 - POD test for Bio/Tools/HMMER/Results.pm
ok 1202 - POD test for Bio/Tools/HMMER/Set.pm
ok 1203 - POD test for Bio/Tools/Phylo/Gerp.pm
ok 1204 - POD test for Bio/Tools/Phylo/Gumby.pm
ok 1205 - POD test for Bio/Tools/Phylo/Molphy.pm
ok 1206 - POD test for Bio/Tools/Phylo/PAML.pm
ok 1207 - POD test for Bio/Tools/Prediction/Exon.pm
ok 1208 - POD test for Bio/Tools/Prediction/Gene.pm
ok 1209 - POD test for Bio/Tools/Primer/AssessorI.pm
ok 1210 - POD test for Bio/Tools/Primer/Feature.pm
ok 1211 - POD test for Bio/Tools/Primer/Pair.pm
ok 1212 - POD test for Bio/Tools/Run/GenericParameters.pm
ok 1213 - POD test for Bio/Tools/Run/ParametersI.pm
ok 1214 - POD test for Bio/Tools/Run/RemoteBlast.pm
ok 1215 - POD test for Bio/Tools/Run/StandAloneBlast.pm
ok 1216 - POD test for Bio/Tools/Run/StandAloneNCBIBlast.pm
ok 1217 - POD test for Bio/Tools/Run/StandAloneWUBlast.pm
ok 1218 - POD test for Bio/Tools/Run/WrapperBase.pm
ok 1219 - POD test for Bio/Tools/Signalp/ExtendedSignalp.pm
ok 1220 - POD test for Bio/Tools/Sim4/Exon.pm
ok 1221 - POD test for Bio/Tools/Sim4/Results.pm
ok 1222 - POD test for Bio/Tools/Spidey/Exon.pm
ok 1223 - POD test for Bio/Tools/Spidey/Results.pm
ok 1224 - POD test for Bio/Tree/Draw/Cladogram.pm
ok 1225 - POD test for Bio/Variation/IO/flat.pm
ok 1226 - POD test for Bio/Variation/IO/xml.pm
ok 1227 - POD test for doc/Deobfuscator/bin/deob_index.pl
ok 1228 - POD test for doc/Deobfuscator/cgi-bin/deob_detail.cgi
ok 1229 - POD test for doc/Deobfuscator/cgi-bin/deob_interface.cgi
ok 1230 - POD test for doc/Deobfuscator/lib/Deobfuscator.pm
ok 1231 - POD test for doc/Deobfuscator/t/00.load.t (no pod)
ok 1232 - POD test for doc/Deobfuscator/t/pod.t (no pod)
ok 1233 - POD test for examples/root/lib/TestInterface.pm
ok 1234 - POD test for examples/root/lib/TestObject.pm
ok 1235 - POD test for t/lib/Array/Compare.pm
ok 1236 - POD test for t/lib/Sub/Uplevel.pm
ok 1237 - POD test for t/lib/Test/Builder.pm
ok 1238 - POD test for t/lib/Test/Exception.pm
ok 1239 - POD test for t/lib/Test/Harness.pm
ok 1240 - POD test for t/lib/Test/More.pm
ok 1241 - POD test for t/lib/Test/Simple.pm
ok 1242 - POD test for t/lib/Test/Tutorial.pod
ok 1243 - POD test for t/lib/Test/Warn.pm
ok 1244 - POD test for t/lib/Tree/DAG_Node.pm
ok 1245 - POD test for t/Matrix/IO/masta.t (no pod)
ok 1246 - POD test for t/Matrix/IO/psm.t (no pod)
ok 1247 - POD test for t/Ontology/IO/go.t (no pod)
ok 1248 - POD test for t/Ontology/IO/interpro.t (no pod)
ok 1249 - POD test for t/Ontology/IO/obo.t (no pod)
ok 1250 - POD test for t/RemoteDB/HIV/HIV.t (no pod)
ok 1251 - POD test for t/RemoteDB/HIV/HIVAnnotProcessor.t (no pod)
ok 1252 - POD test for t/RemoteDB/HIV/HIVQuery.t (no pod)
ok 1253 - POD test for t/RemoteDB/HIV/HIVQueryHelper.t (no pod)
ok 1254 - POD test for t/SearchIO/Writer/HitTableWriter.t (no pod)
ok 1255 - POD test for t/SearchIO/Writer/HTMLWriter.t (no pod)
ok 1256 - POD test for t/Tools/Alignment/Consed.t (no pod)
ok 1257 - POD test for t/Tools/EMBOSS/Palindrome.t (no pod)
ok 1258 - POD test for t/Tools/EUtilities/egquery.t (no pod)
ok 1259 - POD test for t/Tools/EUtilities/einfo.t (no pod)
ok 1260 - POD test for t/Tools/EUtilities/elink_acheck.t (no pod)
ok 1261 - POD test for t/Tools/EUtilities/elink_lcheck.t (no pod)
ok 1262 - POD test for t/Tools/EUtilities/elink_llinks.t (no pod)
ok 1263 - POD test for t/Tools/EUtilities/elink_ncheck.t (no pod)
ok 1264 - POD test for t/Tools/EUtilities/elink_neighbor.t (no pod)
ok 1265 - POD test for t/Tools/EUtilities/elink_neighbor_history.t (no pod)
ok 1266 - POD test for t/Tools/EUtilities/elink_scores.t (no pod)
ok 1267 - POD test for t/Tools/EUtilities/epost.t (no pod)
ok 1268 - POD test for t/Tools/EUtilities/esearch.t (no pod)
ok 1269 - POD test for t/Tools/EUtilities/espell.t (no pod)
ok 1270 - POD test for t/Tools/EUtilities/esummary.t (no pod)
ok 1271 - POD test for t/Tools/EUtilities/EUtilParameters.t (no pod)
ok 1272 - POD test for t/Tools/Phylo/Gerp.t (no pod)
ok 1273 - POD test for t/Tools/Phylo/Molphy.t (no pod)
ok 1274 - POD test for t/Tools/Phylo/PAML.t (no pod)
ok 1275 - POD test for t/Tools/Run/RemoteBlast.t (no pod)
ok 1276 - POD test for t/Tools/Run/StandAloneBlast.t (no pod)
ok 1277 - POD test for t/Tools/Run/WrapperBase.t (no pod)
ok 1278 - POD test for t/Tools/Signalp/ExtendedSignalp.t (no pod)
ok 1279 - POD test for t/Tools/Spidey/Spidey.t (no pod)
ok 1280 - POD test for t/Tree/PhyloNetwork/Factory.t (no pod)
ok 1281 - POD test for t/Tree/PhyloNetwork/GraphViz.t (no pod)
ok 1282 - POD test for t/Tree/PhyloNetwork/MuVector.t (no pod)
ok 1283 - POD test for t/Tree/PhyloNetwork/PhyloNetwork.t (no pod)
ok 1284 - POD test for t/Tree/PhyloNetwork/RandomFactory.t (no pod)
ok 1285 - POD test for t/Tree/PhyloNetwork/TreeFactory.t (no pod)
ok 1286 - POD test for t/Tree/TreeIO/lintree.t (no pod)
ok 1287 - POD test for t/Tree/TreeIO/newick.t (no pod)
ok 1288 - POD test for t/Tree/TreeIO/nexus.t (no pod)
ok 1289 - POD test for t/Tree/TreeIO/nhx.t (no pod)
ok 1290 - POD test for t/Tree/TreeIO/phyloxml.t (no pod)
ok 1291 - POD test for t/Tree/TreeIO/svggraph.t (no pod)
ok 1292 - POD test for t/Tree/TreeIO/tabtree.t (no pod)
ok 1293 - POD test for blib/lib/Bio/WebAgent.pm
ok 1294 - POD test for blib/lib/Bio/TreeIO.pm
ok 1295 - POD test for blib/lib/Bio/LocationI.pm
ok 1296 - POD test for blib/lib/Bio/Taxonomy.pm
ok 1297 - POD test for blib/lib/Bio/DBLinkContainerI.pm
ok 1298 - POD test for blib/lib/Bio/SeqIO.pm
ok 1299 - POD test for blib/lib/Bio/AnalysisI.pm
ok 1300 - POD test for blib/lib/Bio/FeatureIO.pm
ok 1301 - POD test for blib/lib/Bio/MapIO.pm
ok 1302 - POD test for blib/lib/Bio/PullParserI.pm
ok 1303 - POD test for blib/lib/Bio/SimpleAnalysisI.pm
ok 1304 - POD test for blib/lib/Bio/IdCollectionI.pm
ok 1305 - POD test for blib/lib/Bio/UpdateableSeqI.pm
ok 1306 - POD test for blib/lib/Bio/Biblio.pm
ok 1307 - POD test for blib/lib/Bio/AlignIO.pm
ok 1308 - POD test for blib/lib/Bio/Seq.pm
ok 1309 - POD test for blib/lib/Bio/DescribableI.pm
ok 1310 - POD test for blib/lib/Bio/RangeI.pm
ok 1311 - POD test for blib/lib/Bio/OntologyIO.pm
ok 1312 - POD test for blib/lib/Bio/FeatureHolderI.pm
ok 1313 - POD test for blib/lib/Bio/AnalysisResultI.pm
ok 1314 - POD test for blib/lib/Bio/Taxon.pm
ok 1315 - POD test for blib/lib/Bio/SeqAnalysisParserI.pm
ok 1316 - POD test for blib/lib/Bio/SearchIO.pm
ok 1317 - POD test for blib/lib/Bio/AnalysisParserI.pm
ok 1318 - POD test for blib/lib/Bio/SearchDist.pm
ok 1319 - POD test for blib/lib/Bio/AnnotationCollectionI.pm
ok 1320 - POD test for blib/lib/Bio/SeqFeatureI.pm
ok 1321 - POD test for blib/lib/Bio/ParameterBaseI.pm
ok 1322 - POD test for blib/lib/Bio/PrimarySeq.pm
ok 1323 - POD test for blib/lib/Bio/AnnotationI.pm
ok 1324 - POD test for blib/lib/Bio/PrimarySeqI.pm
ok 1325 - POD test for blib/lib/Bio/SimpleAlign.pm
ok 1326 - POD test for blib/lib/Bio/ClusterIO.pm
ok 1327 - POD test for blib/lib/Bio/SeqI.pm
ok 1328 - POD test for blib/lib/Bio/HandlerBaseI.pm
ok 1329 - POD test for blib/lib/Bio/IdentifiableI.pm
ok 1330 - POD test for blib/lib/Bio/Species.pm
ok 1331 - POD test for blib/lib/Bio/LocatableSeq.pm
ok 1332 - POD test for blib/lib/Bio/ClusterI.pm
ok 1333 - POD test for blib/lib/Bio/DasI.pm
ok 1334 - POD test for blib/lib/Bio/SeqUtils.pm
ok 1335 - POD test for blib/lib/Bio/PhyloNetwork.pm
ok 1336 - POD test for blib/lib/Bio/Range.pm
ok 1337 - POD test for blib/lib/Bio/Perl.pm
ok 1338 - POD test for blib/lib/Bio/AnnotatableI.pm
ok 1339 - POD test for blib/lib/Bio/ConfigData.pm
ok 1340 - POD test for Bio/DB/Flat/BDB/embl.pm
ok 1341 - POD test for Bio/DB/Flat/BDB/fasta.pm
ok 1342 - POD test for Bio/DB/Flat/BDB/genbank.pm
ok 1343 - POD test for Bio/DB/Flat/BDB/swiss.pm
ok 1344 - POD test for Bio/DB/GFF/Adaptor/ace.pm
ok 1345 - POD test for Bio/DB/GFF/Adaptor/berkeleydb.pm
ok 1346 - POD test for Bio/DB/GFF/Adaptor/biofetch.pm
ok 1347 - POD test for Bio/DB/GFF/Adaptor/biofetch_oracle.pm
ok 1348 - POD test for Bio/DB/GFF/Adaptor/dbi.pm
ok 1349 - POD test for Bio/DB/GFF/Adaptor/memory.pm
ok 1350 - POD test for Bio/DB/GFF/Aggregator/alignment.pm
ok 1351 - POD test for Bio/DB/GFF/Aggregator/clone.pm
ok 1352 - POD test for Bio/DB/GFF/Aggregator/coding.pm
ok 1353 - POD test for Bio/DB/GFF/Aggregator/gene.pm
ok 1354 - POD test for Bio/DB/GFF/Aggregator/match.pm
ok 1355 - POD test for Bio/DB/GFF/Aggregator/none.pm
ok 1356 - POD test for Bio/DB/GFF/Aggregator/orf.pm
ok 1357 - POD test for Bio/DB/GFF/Aggregator/processed_transcript.pm
ok 1358 - POD test for Bio/DB/GFF/Aggregator/so_transcript.pm
ok 1359 - POD test for Bio/DB/GFF/Aggregator/transcript.pm
ok 1360 - POD test for Bio/DB/GFF/Aggregator/ucsc_acembly.pm
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ok 2037 - POD test for blib/lib/Bio/SeqIO/game/seqHandler.pm
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ok 2039 - POD test for blib/lib/Bio/SeqIO/game/gameWriter.pm
ok 2040 - POD test for blib/lib/Bio/SeqIO/game/gameHandler.pm
ok 2041 - POD test for blib/lib/Bio/SeqIO/game/featHandler.pm
ok 2042 - POD test for blib/lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm
ok 2043 - POD test for blib/lib/Bio/DB/GFF/Feature.pm
ok 2044 - POD test for blib/lib/Bio/DB/GFF/Typename.pm
ok 2045 - POD test for blib/lib/Bio/DB/GFF/Homol.pm
ok 2046 - POD test for blib/lib/Bio/DB/GFF/Segment.pm
ok 2047 - POD test for blib/lib/Bio/DB/GFF/Featname.pm
ok 2048 - POD test for blib/lib/Bio/DB/GFF/Aggregator.pm
ok 2049 - POD test for blib/lib/Bio/DB/GFF/RelSegment.pm
ok 2050 - POD test for blib/lib/Bio/DB/Biblio/biofetch.pm
ok 2051 - POD test for blib/lib/Bio/DB/Biblio/eutils.pm
ok 2052 - POD test for blib/lib/Bio/DB/Biblio/soap.pm
ok 2053 - POD test for blib/lib/Bio/DB/Expression/geo.pm
ok 2054 - POD test for blib/lib/Bio/DB/Query/WebQuery.pm
ok 2055 - POD test for blib/lib/Bio/DB/Query/HIVQuery.pm
ok 2056 - POD test for blib/lib/Bio/DB/Query/GenBank.pm
ok 2057 - POD test for blib/lib/Bio/DB/SeqFeature/NormalizedFeatureI.pm
ok 2058 - POD test for blib/lib/Bio/DB/SeqFeature/Store.pm
ok 2059 - POD test for blib/lib/Bio/DB/SeqFeature/NormalizedTableFeatureI.pm
ok 2060 - POD test for blib/lib/Bio/DB/SeqFeature/Segment.pm
ok 2061 - POD test for blib/lib/Bio/DB/SeqFeature/NormalizedFeature.pm
ok 2062 - POD test for blib/lib/Bio/DB/SeqVersion/gi.pm
ok 2063 - POD test for blib/lib/Bio/DB/HIV/HIVAnnotProcessor.pm
ok 2064 - POD test for blib/lib/Bio/DB/HIV/HIVQueryHelper.pm
ok 2065 - POD test for blib/lib/Bio/DB/Flat/BDB.pm
ok 2066 - POD test for blib/lib/Bio/DB/Flat/BinarySearch.pm
ok 2067 - POD test for blib/lib/Bio/DB/Taxonomy/list.pm
ok 2068 - POD test for blib/lib/Bio/DB/Taxonomy/entrez.pm
ok 2069 - POD test for blib/lib/Bio/DB/Taxonomy/flatfile.pm
ok 2070 - POD test for blib/lib/Bio/DB/TFBS/transfac_pro.pm
ok 2071 - POD test for blib/lib/Bio/SearchIO/Writer/HSPTableWriter.pm
ok 2072 - POD test for blib/lib/Bio/SearchIO/Writer/GbrowseGFF.pm
ok 2073 - POD test for blib/lib/Bio/SearchIO/Writer/BSMLResultWriter.pm
ok 2074 - POD test for blib/lib/Bio/SearchIO/Writer/ResultTableWriter.pm
ok 2075 - POD test for blib/lib/Bio/SearchIO/Writer/HitTableWriter.pm
ok 2076 - POD test for blib/lib/Bio/SearchIO/Writer/TextResultWriter.pm
ok 2077 - POD test for blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm
ok 2078 - POD test for blib/lib/Bio/SearchIO/XML/BlastHandler.pm
ok 2079 - POD test for blib/lib/Bio/SearchIO/XML/PsiBlastHandler.pm
ok 2080 - POD test for blib/lib/Bio/Search/HSP/PSLHSP.pm
ok 2081 - POD test for blib/lib/Bio/Search/HSP/WABAHSP.pm
ok 2082 - POD test for blib/lib/Bio/Search/HSP/ModelHSP.pm
ok 2083 - POD test for blib/lib/Bio/Search/HSP/PsiBlastHSP.pm
ok 2084 - POD test for blib/lib/Bio/Search/HSP/FastaHSP.pm
ok 2085 - POD test for blib/lib/Bio/Search/HSP/GenericHSP.pm
ok 2086 - POD test for blib/lib/Bio/Search/HSP/HmmpfamHSP.pm
ok 2087 - POD test for blib/lib/Bio/Search/HSP/HSPFactory.pm
ok 2088 - POD test for blib/lib/Bio/Search/HSP/PullHSPI.pm
ok 2089 - POD test for blib/lib/Bio/Search/HSP/HMMERHSP.pm
ok 2090 - POD test for blib/lib/Bio/Search/HSP/HSPI.pm
ok 2091 - POD test for blib/lib/Bio/Search/HSP/BlastHSP.pm
ok 2092 - POD test for blib/lib/Bio/Search/HSP/BlastPullHSP.pm
ok 2093 - POD test for blib/lib/Bio/Search/Result/HmmpfamResult.pm
ok 2094 - POD test for blib/lib/Bio/Search/Result/HMMERResult.pm
ok 2095 - POD test for blib/lib/Bio/Search/Result/BlastPullResult.pm
ok 2096 - POD test for blib/lib/Bio/Search/Result/ResultI.pm
ok 2097 - POD test for blib/lib/Bio/Search/Result/BlastResult.pm
ok 2098 - POD test for blib/lib/Bio/Search/Result/WABAResult.pm
ok 2099 - POD test for blib/lib/Bio/Search/Result/ResultFactory.pm
ok 2100 - POD test for blib/lib/Bio/Search/Result/GenericResult.pm
ok 2101 - POD test for blib/lib/Bio/Search/Result/CrossMatchResult.pm
ok 2102 - POD test for blib/lib/Bio/Search/Result/PullResultI.pm
ok 2103 - POD test for blib/lib/Bio/Search/Hit/PsiBlastHit.pm
ok 2104 - POD test for blib/lib/Bio/Search/Hit/BlastPullHit.pm
ok 2105 - POD test for blib/lib/Bio/Search/Hit/HitFactory.pm
ok 2106 - POD test for blib/lib/Bio/Search/Hit/HitI.pm
ok 2107 - POD test for blib/lib/Bio/Search/Hit/PullHitI.pm
ok 2108 - POD test for blib/lib/Bio/Search/Hit/BlastHit.pm
ok 2109 - POD test for blib/lib/Bio/Search/Hit/HMMERHit.pm
ok 2110 - POD test for blib/lib/Bio/Search/Hit/HmmpfamHit.pm
ok 2111 - POD test for blib/lib/Bio/Search/Hit/GenericHit.pm
ok 2112 - POD test for blib/lib/Bio/Search/Hit/ModelHit.pm
ok 2113 - POD test for blib/lib/Bio/Search/Hit/Fasta.pm
ok 2114 - POD test for blib/lib/Bio/Search/Iteration/GenericIteration.pm
ok 2115 - POD test for blib/lib/Bio/Search/Iteration/IterationI.pm
ok 2116 - POD test for blib/lib/Bio/Biblio/IO/medline2ref.pm
ok 2117 - POD test for blib/lib/Bio/Biblio/IO/pubmedxml.pm
ok 2118 - POD test for blib/lib/Bio/Biblio/IO/pubmed2ref.pm
ok 2119 - POD test for blib/lib/Bio/Biblio/IO/medlinexml.pm
ok 2120 - POD test for blib/lib/Bio/Expression/FeatureGroup/FeatureGroupMas50.pm
ok 2121 - POD test for blib/lib/Bio/Expression/FeatureSet/FeatureSetMas50.pm
ok 2122 - POD test for blib/lib/Bio/SeqFeature/Gene/Exon.pm
ok 2123 - POD test for blib/lib/Bio/SeqFeature/Gene/NC_Feature.pm
ok 2124 - POD test for blib/lib/Bio/SeqFeature/Gene/TranscriptI.pm
ok 2125 - POD test for blib/lib/Bio/SeqFeature/Gene/Transcript.pm
ok 2126 - POD test for blib/lib/Bio/SeqFeature/Gene/GeneStructureI.pm
ok 2127 - POD test for blib/lib/Bio/SeqFeature/Gene/Poly_A_site.pm
ok 2128 - POD test for blib/lib/Bio/SeqFeature/Gene/ExonI.pm
ok 2129 - POD test for blib/lib/Bio/SeqFeature/Gene/Promoter.pm
ok 2130 - POD test for blib/lib/Bio/SeqFeature/Gene/Intron.pm
ok 2131 - POD test for blib/lib/Bio/SeqFeature/Gene/UTR.pm
ok 2132 - POD test for blib/lib/Bio/SeqFeature/Gene/GeneStructure.pm
ok 2133 - POD test for blib/lib/Bio/SeqFeature/Tools/TypeMapper.pm
ok 2134 - POD test for blib/lib/Bio/SeqFeature/Tools/Unflattener.pm
ok 2135 - POD test for blib/lib/Bio/SeqFeature/Tools/IDHandler.pm
ok 2136 - POD test for blib/lib/Bio/SeqFeature/Tools/FeatureNamer.pm
ok 2137 - POD test for blib/lib/Bio/SeqFeature/SiRNA/Oligo.pm
ok 2138 - POD test for blib/lib/Bio/SeqFeature/SiRNA/Pair.pm
ok 2139 - POD test for blib/lib/Bio/Coordinate/Result/Gap.pm
ok 2140 - POD test for blib/lib/Bio/Coordinate/Result/Match.pm
ok 2141 - POD test for blib/lib/Bio/Tree/Draw/Cladogram.pm
ok 2142 - POD test for blib/lib/Bio/Root/Test/Warn.pm
ok 2143 - POD test for blib/lib/Bio/Seq/Meta/Array.pm
ok 2144 - POD test for blib/lib/Bio/Restriction/IO/prototype.pm
ok 2145 - POD test for blib/lib/Bio/Restriction/IO/base.pm
ok 2146 - POD test for blib/lib/Bio/Restriction/IO/itype2.pm
ok 2147 - POD test for blib/lib/Bio/Restriction/IO/withrefm.pm
ok 2148 - POD test for blib/lib/Bio/Restriction/IO/bairoch.pm
ok 2149 - POD test for blib/lib/Bio/Restriction/Enzyme/MultiCut.pm
ok 2150 - POD test for blib/lib/Bio/Restriction/Enzyme/MultiSite.pm
ok 2151 - POD test for blib/lib/Bio/Phenotype/OMIM/MiniMIMentry.pm
ok 2152 - POD test for blib/lib/Bio/Phenotype/OMIM/OMIMparser.pm
ok 2153 - POD test for blib/lib/Bio/Phenotype/OMIM/OMIMentry.pm
ok 2154 - POD test for blib/lib/Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm
ok 2155 - POD test for blib/lib/Bio/Phenotype/MeSH/Twig.pm
ok 2156 - POD test for blib/lib/Bio/Phenotype/MeSH/Term.pm
ok 2157 - POD test for blib/lib/Bio/Variation/IO/xml.pm
ok 2158 - POD test for blib/lib/Bio/Variation/IO/flat.pm
ok 2159 - POD test for blib/lib/Bio/Structure/IO/pdb.pm
ok 2160 - POD test for blib/lib/Bio/Assembly/Tools/ContigSpectrum.pm
ok 2161 - POD test for blib/lib/Bio/Assembly/IO/phrap.pm
ok 2162 - POD test for blib/lib/Bio/Assembly/IO/tigr.pm
ok 2163 - POD test for blib/lib/Bio/Assembly/IO/ace.pm
ok 2164 - POD test for blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm
ok 2165 - POD test for blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm
ok 2166 - POD test for blib/lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
ok 2167 - POD test for blib/lib/Bio/OntologyIO/Handlers/InterProHandler.pm
ok 2168 - POD test for blib/lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm
ok 2169 - POD test for blib/lib/Bio/Matrix/PSM/IO/transfac.pm
ok 2170 - POD test for blib/lib/Bio/Matrix/PSM/IO/masta.pm
ok 2171 - POD test for blib/lib/Bio/Matrix/PSM/IO/psiblast.pm
ok 2172 - POD test for blib/lib/Bio/Matrix/PSM/IO/mast.pm
ok 2173 - POD test for blib/lib/Bio/Matrix/PSM/IO/meme.pm
ok 2174 - POD test for blib/lib/Bio/Tools/EUtilities/Info/LinkInfo.pm
ok 2175 - POD test for blib/lib/Bio/Tools/EUtilities/Info/FieldInfo.pm
ok 2176 - POD test for blib/lib/Bio/Tools/EUtilities/Query/GlobalQuery.pm
ok 2177 - POD test for blib/lib/Bio/Tools/EUtilities/Link/UrlLink.pm
ok 2178 - POD test for blib/lib/Bio/Tools/EUtilities/Link/LinkSet.pm
ok 2179 - POD test for blib/lib/Bio/Tools/EUtilities/Summary/DocSum.pm
ok 2180 - POD test for blib/lib/Bio/Tools/EUtilities/Summary/Item.pm
ok 2181 - POD test for blib/lib/Bio/Tools/Analysis/Protein/ELM.pm
ok 2182 - POD test for blib/lib/Bio/Tools/Analysis/Protein/GOR4.pm
ok 2183 - POD test for blib/lib/Bio/Tools/Analysis/Protein/HNN.pm
ok 2184 - POD test for blib/lib/Bio/Tools/Analysis/Protein/Sopma.pm
ok 2185 - POD test for blib/lib/Bio/Tools/Analysis/Protein/NetPhos.pm
ok 2186 - POD test for blib/lib/Bio/Tools/Analysis/Protein/Scansite.pm
ok 2187 - POD test for blib/lib/Bio/Tools/Analysis/Protein/Domcut.pm
ok 2188 - POD test for blib/lib/Bio/Tools/Analysis/Protein/Mitoprot.pm
ok 2189 - POD test for blib/lib/Bio/Tools/Analysis/DNA/ESEfinder.pm
ok 2190 - POD test for blib/lib/Bio/Tools/Phylo/PAML/ModelResult.pm
ok 2191 - POD test for blib/lib/Bio/Tools/Phylo/PAML/Result.pm
ok 2192 - POD test for blib/lib/Bio/Tools/Phylo/Molphy/Result.pm
ok 2193 - POD test for blib/lib/Bio/Tools/Phylo/Phylip/ProtDist.pm
ok 2194 - POD test for blib/lib/Bio/Tools/Primer/Assessor/Base.pm
ok 2195 - POD test for blib/lib/Bio/Tools/SiRNA/Ruleset/tuschl.pm
ok 2196 - POD test for blib/lib/Bio/Tools/SiRNA/Ruleset/saigo.pm
ok 2197 - POD test for blib/lib/Bio/DB/GFF/Aggregator/so_transcript.pm
ok 2198 - POD test for blib/lib/Bio/DB/GFF/Aggregator/ucsc_unigene.pm
ok 2199 - POD test for blib/lib/Bio/DB/GFF/Aggregator/ucsc_acembly.pm
ok 2200 - POD test for blib/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm
ok 2201 - POD test for blib/lib/Bio/DB/GFF/Aggregator/gene.pm
ok 2202 - POD test for blib/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm
ok 2203 - POD test for blib/lib/Bio/DB/GFF/Aggregator/alignment.pm
ok 2204 - POD test for blib/lib/Bio/DB/GFF/Aggregator/match.pm
ok 2205 - POD test for blib/lib/Bio/DB/GFF/Aggregator/ucsc_softberry.pm
ok 2206 - POD test for blib/lib/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
ok 2207 - POD test for blib/lib/Bio/DB/GFF/Aggregator/transcript.pm
ok 2208 - POD test for blib/lib/Bio/DB/GFF/Aggregator/none.pm
ok 2209 - POD test for blib/lib/Bio/DB/GFF/Aggregator/ucsc_refgene.pm
ok 2210 - POD test for blib/lib/Bio/DB/GFF/Aggregator/clone.pm
ok 2211 - POD test for blib/lib/Bio/DB/GFF/Aggregator/coding.pm
ok 2212 - POD test for blib/lib/Bio/DB/GFF/Aggregator/ucsc_genscan.pm
ok 2213 - POD test for blib/lib/Bio/DB/GFF/Aggregator/processed_transcript.pm
ok 2214 - POD test for blib/lib/Bio/DB/GFF/Aggregator/orf.pm
ok 2215 - POD test for blib/lib/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
ok 2216 - POD test for blib/lib/Bio/DB/GFF/Adaptor/memory.pm
ok 2217 - POD test for blib/lib/Bio/DB/GFF/Adaptor/berkeleydb.pm
ok 2218 - POD test for blib/lib/Bio/DB/GFF/Adaptor/dbi.pm
ok 2219 - POD test for blib/lib/Bio/DB/GFF/Adaptor/biofetch_oracle.pm
ok 2220 - POD test for blib/lib/Bio/DB/GFF/Adaptor/biofetch.pm
ok 2221 - POD test for blib/lib/Bio/DB/GFF/Adaptor/ace.pm
ok 2222 - POD test for blib/lib/Bio/DB/GFF/Util/Rearrange.pm
ok 2223 - POD test for blib/lib/Bio/DB/GFF/Util/Binning.pm
ok 2224 - POD test for blib/lib/Bio/DB/SeqFeature/Store/bdb.pm
ok 2225 - POD test for blib/lib/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm
ok 2226 - POD test for blib/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm
ok 2227 - POD test for blib/lib/Bio/DB/SeqFeature/Store/Loader.pm
ok 2228 - POD test for blib/lib/Bio/DB/SeqFeature/Store/GFF2Loader.pm
ok 2229 - POD test for blib/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm
ok 2230 - POD test for blib/lib/Bio/DB/SeqFeature/Store/memory.pm
ok 2231 - POD test for blib/lib/Bio/DB/SeqFeature/Store/berkeleydb.pm
ok 2232 - POD test for blib/lib/Bio/DB/Flat/BDB/swiss.pm
ok 2233 - POD test for blib/lib/Bio/DB/Flat/BDB/genbank.pm
ok 2234 - POD test for blib/lib/Bio/DB/Flat/BDB/fasta.pm
ok 2235 - POD test for blib/lib/Bio/DB/Flat/BDB/embl.pm
ok 2236 - POD test for blib/lib/Bio/Structure/SecStr/DSSP/Res.pm
ok 2237 - POD test for blib/lib/Bio/Structure/SecStr/STRIDE/Res.pm
ok 2238 - POD test for blib/lib/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
ok 2239 - POD test for blib/lib/Bio/DB/GFF/Adaptor/memory/iterator.pm
ok 2240 - POD test for blib/lib/Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
ok 2241 - POD test for blib/lib/Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
ok 2242 - POD test for blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm
ok 2243 - POD test for blib/lib/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
ok 2244 - POD test for blib/lib/Bio/DB/GFF/Adaptor/dbi/pg.pm
ok 2245 - POD test for blib/lib/Bio/DB/GFF/Adaptor/dbi/mysql.pm
ok 2246 - POD test for blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm
ok 2247 - POD test for blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm
ok 2248 - POD test for blib/lib/Bio/DB/GFF/Adaptor/dbi/iterator.pm
ok 2249 - POD test for blib/lib/Bio/DB/GFF/Adaptor/dbi/oracleace.pm
ok 2250 - POD test for blib/lib/Bio/DB/GFF/Adaptor/dbi/oracle.pm
ok 2251 - POD test for blib/lib/Bio/DB/SeqFeature/Store/DBI/mysql.pm
ok 2252 - POD test for blib/lib/Bio/DB/SeqFeature/Store/DBI/Iterator.pm
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
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 238.
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 238.
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 238.
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/DB.t .............................. skipped: Network tests have not been requested
t/RemoteDB/EMBL.t ............................ skipped: Network tests have not been requested
t/RemoteDB/EUtilities.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/fly1400/var/cpan/build/BioPerl-1.6.0-D8UZwJ/blib/lib/Bio/Range.pm line 238.
t/RemoteDB/HIV/HIVAnnotProcessor.t ........... 
1..11
ok 1 - use Bio::Seq;
ok 2 - use Bio::SeqIO;
ok 3 - use Bio::DB::HIV::HIVAnnotProcessor;
ok 4 - The object isa Bio::DB::HIV::HIVAnnotProcessor
ok 5 - The object isa Bio::Root::Root
ok 6 - Bio::DB::HIV::HIVAnnotProcessor->can(...)
ok 7 - Bio::DB::HIV::HIVAnnotProcessor->can('hiv_query')
ok 8 - bad type set exception
ok 9 - attach stream
ok 10 - write exception
ok 11 - access stream
ok
t/RemoteDB/HIV/HIVQuery.t .................... 
1..41
ok 1 - use Bio::DB::Query::HIVQuery;
ok 2 - use Bio::DB::HIV;
ok 3 - use Bio::Annotation::Collection;
ok 4 - use Bio::Annotation::Comment;
ok 5 - use Bio::Annotation::Reference;
ok 6 - use Bio::DB::HIV::HIVQueryHelper;
ok 7 - The object isa Bio::DB::Query::HIVQuery
ok 8 - The object isa Bio::Root::Root
ok 9 - Bio::DB::Query::HIVQuery->can(...)
ok 10 - Bio::DB::Query::HIVQuery->can(...)
ok 11 - Bio::DB::Query::HIVQuery->can(...)
ok 12 - _map_db_uri set in default object
ok 13 - _make_search_if_uri set in default object
ok 14 - _search_uri set in default object
ok 15 - _schema_file set in default object
ok 16 - _run_option set in default object
ok 17 - annotations container available
ok 18 - query syntax check 1
ok 19 - query syntax check 2
ok 20 - query syntax check 3
ok 21 - query parser check
ok 22 - multiquery parse check
ok 23 - use HTML::Parser;
ok 24 - help html to file
ok 25 - help html parsed
ok 26 - bad field exception check
ok 27 - bad match data exception check
ok 28 - empty field not ok exception check
ok 29 - uninitialized schema exception check
ok 30 - query not run (level 1) warning check
ok 31 - query not run (level 2) warning check
ok 32 # skip Network tests have not been requested
ok 33 # skip Network tests have not been requested
ok 34 # skip Network tests have not been requested
ok 35 # skip Network tests have not been requested
ok 36 # skip Network tests have not been requested
ok 37 # skip Network tests have not been requested
ok 38 # skip Network tests have not been requested
ok 39 # skip Network tests have not been requested
ok 40 # skip Network tests have not been requested
ok 41 # skip Network tests have not been requested
ok
t/RemoteDB/HIV/HIVQueryHelper.t .............. 
1..40
ok 1 - use Bio::DB::HIV::HIVQueryHelper;
ok 2 - The object isa HIVSchema
ok 3 - The object isa QRY
ok 4 - The object isa R
ok 5 - The object isa Q
ok 6 - schema load
ok 7 - HIVSchema->can(...)
ok 8 - fields complete
ok 9 - tables complete
ok 10 - aliases complete
ok 11
ok 12 - test field syntax ok
ok 13 - test field syntax ok
ok 14 - test alias by field name
ok 15 - correct primary key for SequenceEntry
ok 16 - correct number of foreign keys for AUthor
ok 17 - correct foreign table for au_pub_id
ok 18 - correct annotation key hash
ok 19 - QRY->can(...)
ok 20 - R->can(...)
ok 21 - Q->can(...)
ok 22 - null QRY
ok 23 - null R (request object)
ok 24 - null Q (atomic query object)
ok 25 - R obj create and init (1)
ok 26 - R obj create and init (2)
ok 27 - R::In
ok 28 - !R::In
ok 29 - R::Eq
ok 30 - QRY obj create and init (1)
ok 31 - QRY obj create and init (2)
ok 32 - QRY obj create and init (3)
ok 33 - QRY overload |
ok 34 - QRY overload &
ok 35 - QRY nontrivial &
ok 36 - parse: ('odds bodkins', a)[X] m[Y] u[Z] OR 'b'[X] {A B [C] [D]} 
ok 37 - make: 2 queries returned
ok 38 - {annotation fields} parsed correctly
ok 39 - parse: ('odds bodkins', a)[X] m[Y] u[Z] AND b[X] {A B [C] [D]} 
ok 40 - above query is null
ok
t/RemoteDB/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
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't load '/home/fly1400/ap1400/lib/auto/DB_File/DB_File.so' for module DB_File: libdb-4.3.so: cannot open shared object file: No such file or directory at /home/fly1400/var/megalib/XSLoader.pm line 71.
 at /home/fly1400/ap1400/lib/DB_File.pm line 252
Compilation failed in require at Bio/DB/Taxonomy/flatfile.pm line 77.
BEGIN failed--compilation aborted at Bio/DB/Taxonomy/flatfile.pm line 77.
Compilation failed in require at Bio/Root/Root.pm line 420.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422
STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:251
STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:102
STACK: t/RemoteDB/Taxonomy.t:24
-----------------------------------------------------------
Bio::DB::Taxonomy: flatfile cannot be found
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't load '/home/fly1400/ap1400/lib/auto/DB_File/DB_File.so' for module DB_File: libdb-4.3.so: cannot open shared object file: No such file or directory at /home/fly1400/var/megalib/XSLoader.pm line 71.
 at /home/fly1400/ap1400/lib/DB_File.pm line 252
Compilation failed in require at Bio/DB/Taxonomy/flatfile.pm line 77.
BEGIN failed--compilation aborted at Bio/DB/Taxonomy/flatfile.pm line 77.
Compilation failed in require at Bio/Root/Root.pm line 420.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:422
STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:251
STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:102
STACK: t/RemoteDB/Taxonomy.t:24
-----------------------------------------------------------

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

#   Failed test at t/RemoteDB/Taxonomy.t line 24.
Use of uninitialized value $db in string eq at t/RemoteDB/Taxonomy.t line 32.
Can't call method "get_taxon" on an undefined value at t/RemoteDB/Taxonomy.t line 124.
# Looks like you planned 103 tests but ran 82.
# Looks like you failed 1 test of 82 run.
# Looks like your test exited with 255 just after 82.
t/RemoteDB/Taxonomy.t ........................ 
1..103
ok 1 - use Bio::DB::Taxonomy;
ok 2 - use Bio::Tree::Tree;
ok 3
not 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 # skip Unable to connect to entrez database; no network or server busy?
ok 44 # skip Unable to connect to entrez database; no network or server busy?
ok 45 # skip Unable to connect to entrez database; no network or server busy?
ok 46 # skip Unable to connect to entrez database; no network or server busy?
ok 47 # skip Unable to connect to entrez database; no network or server busy?
ok 48 # skip Unable to connect to entrez database; no network or server busy?
ok 49 # skip Unable to connect to entrez database; no network or server busy?
ok 50 # skip Unable to connect to entrez database; no network or server busy?
ok 51 # skip Unable to connect to entrez database; no network or server busy?
ok 52 # skip Unable to connect to entrez database; no network or server busy?
ok 53 # skip Unable to connect to entrez database; no network or server busy?
ok 54 # skip Unable to connect to entrez database; no network or server busy?
ok 55 # skip Unable to connect to entrez database; no network or server busy?
ok 56 # skip Unable to connect to entrez database; no network or server busy?
ok 57 # skip Unable to connect to entrez database; no network or server busy?
ok 58 # skip Unable to connect to entrez database; no network or server busy?
ok 59 # skip Unable to connect to entrez database; no network or server busy?
ok 60 # skip Unable to connect to entrez database; no network or server busy?
ok 61 # skip Unable to connect to entrez database; no network or server busy?
ok 62 # skip Unable to connect to entrez database; no network or server busy?
ok 63 # skip Unable to connect to entrez database; no network or server busy?
ok 64 # skip Unable to connect to entrez database; no network or server busy?
ok 65 # skip Unable to connect to entrez database; no network or server busy?
ok 66 # skip Unable to connect to entrez database; no network or server busy?
ok 67 # skip Unable to connect to entrez database; no network or server busy?
ok 68 # skip Unable to connect to entrez database; no network or server busy?
ok 69 # skip Unable to connect to entrez database; no network or server busy?
ok 70 # skip Unable to connect to entrez database; no network or server busy?
ok 71 # skip Unable to connect to entrez database; no network or server busy?
ok 72 # skip Unable to connect to entrez database; no network or server busy?
ok 73 # skip Unable to connect to entrez database; no network or server busy?
ok 74 # skip Unable to connect to entrez database; no network or server busy?
ok 75 # skip Unable to connect to entrez database; no network or server busy?
ok 76 # skip Unable to connect to entrez database; no network or server busy?
ok 77 # skip Unable to connect to entrez database; no network or server busy?
ok 78 # skip Unable to connect to entrez database; no network or server busy?
ok 79 # skip Unable to connect to entrez database; no network or server busy?
ok 80 # skip Unable to connect to entrez database; no network or server busy?
ok 81
ok 82
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 22/103 subtests 
	(less 76 skipped subtests: 5 okay)
Replacement list is longer than search list at Bio/Range.pm line 238.
Use of uninitialized value $opt in uc at Bio/Restriction/Analysis.pm line 355, <DATA> line 1064.
Use of uninitialized value $opt in uc at Bio/Restriction/Analysis.pm line 355, <DATA> 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 TG
ok 150 - start at 41
ok 151 - end at 42
ok 152 - sequence for GATTAAAAAAAGAGTG
ok 153 - start at 43
ok 154 - end at 58
ok 155 - sequence for TCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTG
ok 156 - start at 59
ok 157 - end at 93
ok 158 - sequence for AGTAAATTAAAATTTTATTGACTTAGGTCA
ok 159 - start at 94
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 CCAGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTG
ok 174 - start at 209
ok 175 - end at 40
ok 176
ok 177 - bug 2139
ok
Replacement list is longer than search list at Bio/Range.pm line 238.
Use of uninitialized value $opt in uc at Bio/Restriction/Analysis.pm line 355, <DATA> 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 238.
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 238.
t/Root/RootI.t ............................... 
1..50
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 1.006
ok 18 - warns for versions below current version 1.006
ok 19 - throws for versions above 1.006
ok 20 - throws for versions above 1.006
ok 21 - throws for versions equal to 1.006
ok 22 - simple
ok 23 - simple
ok 24 - warns for versions below current version 1.006
ok 25 - warns for versions below current version 1.006
ok 26 - throws for versions above 1.006
ok 27 - throws for versions above 1.006
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
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 first.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gzip' found. Using first.
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gunzip' found. Using first.
---------------------------------------------------
t/Root/Utilities.t ........................... 
1..50
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
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 238.
t/SearchIO/CigarString.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 238.
t/SearchIO/GbrowseGFF.t ...................... 
1..3
ok 1 - use Bio::SearchIO;
ok 2
ok 3
ok
t/SearchIO/SearchIO.t ........................ 
1..19
ok 1 - use Bio::SearchIO;
ok 2 - blastxml for f.blastxml
ok 3 - fasta for f.fy
ok 4 - exonerate for f.exonerate
ok 5 - blast for f.tblx
ok 6 - fasta for f.fx
ok 7 - fasta for f.osearch
ok 8 - blast for filename.bls
ok 9 - exonerate for f.exon
ok 10 - fasta for f.SSEARCH.m9
ok 11 - blast for filename.blast
ok 12 - fasta for f.m9
ok 13 - blast for f.blx
ok 14 - blastxml for f.xml
ok 15 - fasta for f.fasta
ok 16 - fasta for f.fa
ok 17 - blast for fast.bls
ok 18 - fasta for f.ssearch
ok 19 - fasta for f.psearch
ok
Replacement list is longer than search list at Bio/Range.pm line 238.
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
Replacement list is longer than search list at Bio/Range.pm line 238.
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 238.
Use of uninitialized value within @col_spec in lc at Bio/SearchIO/Writer/ResultTableWriter.pm line 200, <GEN1> 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 238.
t/SearchIO/blast.t ........................... 
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ok 1 - use Bio::SearchIO;
ok 2 - database_name()
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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 527.
#     '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 528.
#     '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
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ok 865 - The object isa Bio::Search::Result::ResultI
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ok 885 - The object isa Bio::Search::Result::ResultI
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ok 907 - The object isa Bio::Search::Result::ResultI
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ok 930 - The object isa Bio::Search::Result::ResultI
ok 931
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ok 943 - blastxml for f.blastxml
ok 944 - fasta for f.fy
ok 945 - exonerate for f.exonerate
ok 946 - blast for f.tblx
ok 947 - fasta for f.fx
ok 948 - fasta for f.osearch
ok 949 - blast for filename.bls
ok 950 - exonerate for f.exon
ok 951 - fasta for f.SSEARCH.m9
ok 952 - blast for filename.blast
ok 953 - fasta for f.m9
ok 954 - blast for f.blx
ok 955 - blastxml for f.xml
ok 956 - fasta for f.fasta
ok 957 - fasta for f.fa
ok 958 - blast for fast.bls
ok 959 - fasta for f.ssearch
ok 960 - fasta for f.psearch
ok 961
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ok 969
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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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ok
Replacement list is longer than search list at Bio/Range.pm line 238.
t/SearchIO/blast_pull.t ...................... 
1..289
ok 1 - use Bio::SearchIO;
ok 2
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ok 59 - database_name()
ok 60
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ok 190
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
ok 201
ok 202
ok 203 - full hit name
ok 204 - hit accession
ok 205
ok 206 - query start
ok 207 - query start
ok 208
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ok
Replacement list is longer than search list at Bio/Range.pm line 238.
t/SearchIO/blasttable.t ...................... 
1..154
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
ok 13 - hsp1_qe
ok 14 - hsp1_qs
ok 15 - hsp1_qstr
ok 16 - hsp2_bits
ok 17 - hsp2_gaps
ok 18 - hsp2_he
ok 19 - hsp2_hs
ok 20 - hsp2_hstr
ok 21 - hsp2_qe
ok 22 - hsp2_qs
ok 23 - hsp2_qstr
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
ok 32 - hsp4_bits
ok 33 - hsp4_gaps
ok 34 - hsp4_he
ok 35 - hsp4_hs
ok 36 - hsp4_hstr
ok 37 - hsp4_qe
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
ok 47 - hsp5_qstr
ok 48 - hsp6_bits
ok 49 - hsp6_gaps
ok 50 - hsp6_he
ok 51 - hsp6_hs
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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Replacement list is longer than search list at Bio/Range.pm line 238.
t/SearchIO/blastxml.t ........................ 
1..298
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
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 - query name on HSP
ok 23 - query desc on HSP
ok 24 - hitname
ok 25 - hitdesc
ok 26
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ok 51
ok 52 - The object isa Bio::Search::Hit::HitI
ok 53
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ok 100
ok 101 - query name on HSP
ok 102 - query desc on HSP
ok 103 - hitname
ok 104 - hitdesc
ok 105
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ok 133
ok 134 - query name on HSP
ok 135 - query desc on HSP
ok 136 - hitname
ok 137 - hitdesc
ok 138
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ok 160
not ok 161 # TODO Some stats not working
#   Failed (TODO) test at t/SearchIO/blastxml.t line 258.
#          got: undef
#     expected: '31984247'
not ok 162 # TODO Some stats not working
#   Failed (TODO) test at t/SearchIO/blastxml.t line 259.
#          got: undef
#     expected: '88780'
not ok 163 # TODO Some stats not working
#   Failed (TODO) test at t/SearchIO/blastxml.t line 260.
#          got: undef
#     expected: '49'
ok 164
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ok
Replacement list is longer than search list at Bio/Range.pm line 238.
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 238.
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 238.
t/SearchIO/exonerate.t ....................... 
1..45
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
Replacement list is longer than search list at Bio/Range.pm line 238.
t/SearchIO/fasta.t ........................... 
1..287
ok 1 - use Bio::SearchIO;
ok 2
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ok 4
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ok
Replacement list is longer than search list at Bio/Range.pm line 238.
t/SearchIO/hmmer.t ........................... 
1..116
ok 1 - use Bio::SearchIO;
ok 2
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ok
Replacement list is longer than search list at Bio/Range.pm line 238.
t/SearchIO/hmmer_pull.t ...................... 
1..290
ok 1 - use Bio::SearchIO;
ok 2
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ok 4
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ok
Replacement list is longer than search list at Bio/Range.pm line 238.
t/SearchIO/infernal.t ........................ 
1..316
ok 1 - use Bio::SearchIO;
ok 2 - The object isa Bio::Search::Result::ResultI
ok 3 - Result CMSEARCH
ok 4 - Result CMSEARCH reference
ok 5 - Result CMSEARCH 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 - No p values
ok 45 - Hit length
ok 46 - Hit overlap
ok 47 - Hit query_length
ok 48 - Hit rank
ok 49 - Hit raw_score
ok 50 - Hit score
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::Hit::HitI
ok 125 - Hit accession
ok 126 - Hit GI
ok 127 - Hit algorithm
ok 128 - Hit bits
ok 129 - Hit description
ok 130 - Hit length
ok 131 - Hit locus
ok 132 - Hit n
ok 133 - Hit name
ok 134 - Hit num_hsps
ok 135 - Hit overlap
ok 136 - Hit query_length
ok 137 - Hit rank
ok 138 - Hit raw_score
ok 139 - Hit score
ok 140
ok 141 - The object isa Bio::Search::HSP::HSPI
ok 142 - HSP algorithm
ok 143
ok 144 - The object isa Bio::SeqFeature::Similarity
ok 145 - The object isa Bio::SeqFeature::Similarity
ok 146 - HSP frame
ok 147 - HSP gaps
ok 148 - The object isa Bio::Align::AlignI
ok 149 - HSP hit isa Bio::SeqFeature::Similarity
ok 150 - HSP hit_string
ok 151 - HSP homology_string
ok 152 - HSP hsp_group
ok 153 - HSP hsp_length
ok 154 - HSP length
ok 155 - HSP links
ok 156 - HSP n
ok 157 - HSP query isa Bio::SeqFeature::Similarity
ok 158 - HSP query_string
ok 159 - HSP range
ok 160 - HSP rank
ok 161
ok 162 - HSP end
ok 163 - HSP expect
ok 164 - The object isa Bio::LocatableSeq
ok 165 - HSP seq_str
ok 166 - HSP start
ok 167 - HSP custom_score
ok 168 - HSP meta
ok 169 - HSP strand
ok 170 - HSP meta gap bug
ok 171 - HSP meta
ok 172 - HSP meta
ok 173
ok 174
ok 175 - The object isa Bio::Search::Result::ResultI
ok 176 - Result CMSEARCH
ok 177 - Result CMSEARCH reference
ok 178 - Result CMSEARCH version
ok 179 - Result parameters
ok 180 - Result statistics
ok 181 - Result entries
ok 182 - Result letters
ok 183 - Result database_name
ok 184 - Result num_hits
ok 185 - Result program_reference
ok 186 - Result query_accession
ok 187 - Result query_description
ok 188 - Result query_length
ok 189 - Result query_name
ok 190 - The object isa Bio::Search::Hit::HitI
ok 191 - Hit GI
ok 192 - Hit accession
ok 193 - Hit algorithm
ok 194 - Hit bits
ok 195 - Hit description
ok 196 - Hit locus
ok 197 - Hit n
ok 198 - Hit name
ok 199 - Hit num_hsps
ok 200 - No p values
ok 201 - Hit length
ok 202 - Hit overlap
ok 203 - Hit query_length
ok 204 - Hit rank
ok 205 - Hit raw_score
ok 206 - Hit score
ok 207
ok 208 - The object isa Bio::Search::HSP::HSPI
ok 209 - HSP algorithm
ok 210
ok 211 - The object isa Bio::SeqFeature::Similarity
ok 212 - The object isa Bio::SeqFeature::Similarity
ok 213
ok 214
ok 215 - HSP frame
ok 216 - HSP gaps
ok 217 - Hit length
ok 218 - The object isa Bio::Align::AlignI
ok 219 - HSP hit isa Bio::SeqFeature::Similarity
ok 220 - HSP hit_string
ok 221 - HSP homology_string
ok 222 - HSP hsp_group
ok 223 - HSP hsp_length
ok 224 - HSP length
ok 225 - HSP links
ok 226 - HSP n
ok 227 - HSP pvalue
ok 228 - HSP query isa Bio::SeqFeature::Similarity
ok 229 - HSP query_string
ok 230 - HSP range
ok 231 - HSP rank
ok 232
ok 233 - HSP end
ok 234 - HSP expect
ok 235 - The object isa Bio::LocatableSeq
ok 236 - HSP seq_str
ok 237 - HSP start
ok 238 - HSP custom_score
ok 239 - HSP meta
ok 240 - HSP strand
ok 241 - The object isa Bio::Search::HSP::HSPI
ok 242 - HSP algorithm
ok 243
ok 244 - The object isa Bio::SeqFeature::Similarity
ok 245 - The object isa Bio::SeqFeature::Similarity
ok 246 - HSP frame
ok 247 - HSP gaps
ok 248 - The object isa Bio::Align::AlignI
ok 249 - HSP hit isa Bio::SeqFeature::Similarity
ok 250 - HSP hit_string
ok 251 - HSP homology_string
ok 252 - HSP hsp_group
ok 253 - HSP hsp_length
ok 254 - HSP length
ok 255 - HSP links
ok 256 - HSP n
ok 257 - HSP pvalue
ok 258 - HSP query isa Bio::SeqFeature::Similarity
ok 259 - HSP query_string
ok 260 - HSP range
ok 261 - HSP rank
ok 262
ok 263 - HSP end
ok 264 - HSP expect
ok 265 - The object isa Bio::LocatableSeq
ok 266 - HSP seq_str
ok 267 - HSP start
ok 268 - HSP custom_score
ok 269 - HSP meta
ok 270 - HSP strand
ok 271 - The object isa Bio::Search::Hit::HitI
ok 272 - Hit accession
ok 273 - Hit GI
ok 274 - Hit algorithm
ok 275 - Hit bits
ok 276 - Hit description
ok 277 - Hit length
ok 278 - Hit locus
ok 279 - Hit n
ok 280 - Hit name
ok 281 - Hit num_hsps
ok 282 - Hit overlap
ok 283 - Hit query_length
ok 284 - Hit rank
ok 285 - Hit raw_score
ok 286 - Hit score
ok 287
ok 288 - The object isa Bio::Search::HSP::HSPI
ok 289 - HSP algorithm
ok 290
ok 291 - The object isa Bio::SeqFeature::Similarity
ok 292 - The object isa Bio::SeqFeature::Similarity
ok 293 - HSP frame
ok 294 - HSP gaps
ok 295 - The object isa Bio::Align::AlignI
ok 296 - HSP hit isa Bio::SeqFeature::Similarity
ok 297 - HSP hit_string
ok 298 - HSP homology_string
ok 299 - HSP hsp_group
ok 300 - HSP hsp_length
ok 301 - HSP length
ok 302 - HSP links
ok 303 - HSP n
ok 304 - HSP query isa Bio::SeqFeature::Similarity
ok 305 - HSP query_string
ok 306 - HSP range
ok 307 - HSP rank
ok 308
ok 309 - HSP end
ok 310 - HSP expect
ok 311 - The object isa Bio::LocatableSeq
ok 312 - HSP seq_str
ok 313 - HSP start
ok 314 - HSP custom_score
ok 315 - HSP meta
ok 316 - HSP strand
ok
Replacement list is longer than search list at Bio/Range.pm line 238.
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 238.
t/SearchIO/psl.t ............................. 
1..49
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
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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
Replacement list is longer than search list at Bio/Range.pm line 238.
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 238.
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
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
Replacement list is longer than search list at Bio/Range.pm line 238.
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 238.
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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
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 238.
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 238.
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 238.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
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 238.
t/Seq/LocatableSeq.t ......................... 
1..116
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(0x81942f8)'
#     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
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
not ok 115 # TODO Bio::LocatableSeq global variables have scoping issues
#   Failed (TODO) test at t/Seq/LocatableSeq.t line 284.
#          got: '\-\.=~'
#     expected: '-\?'
not ok 116 # TODO Bio::LocatableSeq global variables have scoping issues
#   Failed (TODO) test at t/Seq/LocatableSeq.t line 286.
#          got: '19'
#     expected: anything else
ok
Replacement list is longer than search list at Bio/Range.pm line 238.
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 238.
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 238.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
t/Seq/PrimarySeq.t ........................... 
1..53
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 - The object isa Bio::PrimarySeqI
ok 27
ok 28 - The object isa Bio::PrimarySeqI
ok 29
ok 30 - The object isa Bio::PrimarySeqI
ok 31
ok 32 - The object isa Bio::PrimarySeqI
ok 33
ok 34 - Translation: LVAST
ok 35 - Translation: MVAST
ok 36 - Translation: MVAST
ok 37 - Translation: MVAST*
ok 38 - Translation: M*
ok 39 - Translation: M
ok 40
ok 41 - Translation: MWP
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
Replacement list is longer than search list at Bio/Range.pm line 238.
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 238.
t/Seq/Quality.t .............................. 
1..52
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
Replacement list is longer than search list at Bio/Range.pm line 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
t/Seq/Seq.t .................................. 
1..61
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
Replacement list is longer than search list at Bio/Range.pm line 238.
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 238.
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 238.
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 238.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
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 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
t/SeqFeature/LocationFactory.t ............... 
1..271
ok 1 - use Bio::Factory::FTLocationFactory;
ok 2 - The object isa Bio::Factory::LocationFactoryI
ok 3 - Bio::Location::Simple
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12 - Location String: J00194:100..202
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: 1..?
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: (122.133)..(204.221)
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::Simple
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56 - Location String: 340..565
ok 57
ok 58 - Bio::Location::Split
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67 - Location String: join(12..78,134..202)
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: ?..?
ok 79
ok 80 - Bio::Location::Fuzzy
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89 - Location String: <345..500
ok 90
ok 91 - Bio::Location::Fuzzy
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100 - Location String: ?22..?64
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: J00194:100..202
ok 112
ok 113 - Bio::Location::Simple
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122 - Location String: 467
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: (23.45)..600
ok 134
ok 135 - Bio::Location::Simple
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144 - Location String: 123^124
ok 145
ok 146 - Bio::Location::Fuzzy
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155 - Location String: <1..?
ok 156
ok 157 - Bio::Location::Fuzzy
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166 - Location String: 145^177
ok 167
ok 168 - Bio::Location::Fuzzy
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok 176
ok 177 - Location String: 22..?64
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: complement(34..(122.126))
ok 189
ok 190 - Bio::Location::Split
ok 191
ok 192
ok 193
ok 194
ok 195
ok 196
ok 197
ok 198
ok 199 - Location String: complement(join(4918..5163,2691..4571))
ok 200
ok 201 - Bio::Location::Split
ok 202
ok 203
ok 204
ok 205
ok 206
ok 207
ok 208
ok 209
ok 210 - Location String: join(AY016290.1:108..185,AY016291.1:1546..1599)
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: ?..>393
ok 222
ok 223 - Bio::Location::Fuzzy
ok 224
ok 225
ok 226
ok 227
ok 228
ok 229
ok 230
ok 231
ok 232 - Location String: ?2465..2774
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: (122.133)..(204.221)
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: <1..888
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
Replacement list is longer than search list at Bio/Range.pm line 238.
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 238.
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 238.
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 238.
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
t/SeqFeature/SeqFeatCollection.t ............. skipped: The optional module DB_File (or dependencies thereof) was not installed
Replacement list is longer than search list at Bio/Range.pm line 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 33.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 38.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 63.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN18> line 32.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN18> line 41.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN35> line 72.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN35> line 129.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN35> line 152.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN35> line 256.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN35> line 275.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN35> line 498.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN35> line 512.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN35> line 572.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN35> line 590.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN35> line 829.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN35> line 1153.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN35> line 1172.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN35> line 1348.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN35> line 1364.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN35> line 1483.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN35> line 1499.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN35> line 1607.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN35> line 1627.
t/SeqFeature/SeqFeature.t .................... 
1..214
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
Replacement list is longer than search list at Bio/Range.pm line 238.
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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 117.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 136.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 189.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 204.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 262.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 302.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 313.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 318.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 322.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 327.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 332.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 337.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 342.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 346.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 359.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 372.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 385.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 398.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 411.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 424.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 437.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 450.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 473.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 484.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 496.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 525.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 117.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 136.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 189.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 204.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 262.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 302.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 313.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 318.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 322.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 327.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 332.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 337.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 342.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 346.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 359.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 372.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 385.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 398.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 411.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 424.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 437.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 450.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 473.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 484.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 496.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 525.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN5> line 39.
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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 52.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 96.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 144.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 186.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 204.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 226.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 276.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 370.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 387.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 402.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 437.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 571.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 590.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 638.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 678.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 701.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 760.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 795.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 825.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 842.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 866.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 890.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 906.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 974.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 1088.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 1103.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 1114.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 1129.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 1142.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 1163.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 45.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 55.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 79.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 92.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN2> line 115.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN2> line 165.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN2> line 215.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN2> line 265.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN2> line 316.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN2> line 370.
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 238.
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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 54.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 72.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN11> line 42.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN11> line 46.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN11> line 54.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN12> line 35.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN12> line 178.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN12> line 241.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN13> line 35.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN13> line 151.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN13> line 208.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN14> line 61.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN14> line 63.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN14> line 65.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN14> line 67.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN14> line 69.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN14> line 70.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN19> line 66.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN19> line 97.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN19> line 107.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN19> line 403.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN19> line 459.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN50> line 135.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN50> line 138.
t/SeqIO/Handler.t ............................ 
1..550
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
Replacement list is longer than search list at Bio/Range.pm line 238.
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 238.
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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 35.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 178.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 241.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 178.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 241.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN2> line 178.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN2> line 241.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN3> line 35.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN3> line 241.
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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 101.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 116.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 138.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 162.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 189.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 214.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 250.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 49.
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 238.
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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 117.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 136.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 189.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 204.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 262.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 302.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 313.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 318.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 322.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 327.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 332.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 337.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 342.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 346.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 359.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 372.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 385.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 398.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 411.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 424.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 437.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 450.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 473.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 484.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 496.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 525.

#   Failed test at t/SeqIO/asciitree.t line 30.
# Looks like you failed 1 test of 2.
t/SeqIO/asciitree.t .......................... 
1..2
ok 1 - use Bio::SeqIO;
not ok 2
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/2 subtests 
Replacement list is longer than search list at Bio/Range.pm line 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
Use of tied on a handle without * is deprecated at /home/fly1400/var/megalib/XML/Parser/Expat.pm line 447.
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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 117.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 136.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 189.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 204.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 262.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 302.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 313.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 318.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 322.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 327.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 332.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 337.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 342.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 346.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 359.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 372.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 385.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 398.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 411.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 424.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 437.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 450.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 473.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 484.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 496.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 525.
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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN9> line 135.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN9> line 138.
t/SeqIO/embl.t ............................... 
1..56
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
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 81
Replacement list is longer than search list at Bio/Range.pm line 238.
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 238.
t/SeqIO/fasta.t .............................. 
1..18
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
Replacement list is longer than search list at Bio/Range.pm line 238.
t/SeqIO/fastq.t .............................. 
1..5
ok 1 - use Bio::SeqIO::fastq;
ok 2 - The object isa Bio::SeqIO
ok 3 - The object isa Bio::Seq::Quality
ok 4 - number of qual values
ok 5 - qual slice
ok
Replacement list is longer than search list at Bio/Range.pm line 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN0> line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN4> line 880.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN4> line 880.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN4> 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 238.
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(0x890b298)'
#     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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 54.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN1> line 72.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN11> line 42.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN11> line 46.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN11> line 54.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN12> line 35.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN12> line 178.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN12> line 241.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN13> line 35.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN13> line 151.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN13> line 208.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN14> line 61.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN14> line 63.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN14> line 65.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN14> line 67.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN14> line 69.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN14> line 70.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN19> line 66.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN19> line 97.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN19> line 107.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN19> line 403.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN19> line 459.
t/SeqIO/genbank.t ............................ 
1..249
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
Replacement list is longer than search list at Bio/Range.pm line 238.
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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
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 238.
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 238.
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 81
Replacement list is longer than search list at Bio/Range.pm line 238.
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
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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 238.
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 238.
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 238.
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 238.
t/SeqIO/raw.t ................................ 
1..14
ok 1 - use Bio::SeqIO::raw;
ok 2 - The object isa Bio::SeqIO
ok 3 - Bio::SeqIO::raw->can('next_seq')
ok 4 - Bio::SeqIO::raw->can('write_seq')
ok 5 - The object isa Bio::Seq
ok 6 - sequence
ok 7 - length
ok 8 - The object isa Bio::Seq
ok 9 - sequence
ok 10 - length
ok 11 - use Algorithm::Diff;
ok 12 - use IO::ScalarArray;
ok 13 - use IO::String;
ok 14 - raw format can round-trip
ok
Replacement list is longer than search list at Bio/Range.pm line 238.
t/SeqIO/scf.t ................................ 
1..59
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(0x8964b68)'
#     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
t/SeqIO/strider.t ............................ 
1..8
ok 1 - use Bio::SeqIO::strider;
not ok 2 # TODO & SKIP No tests for strider format -- no sample file to test against
not ok 3 # TODO & SKIP No tests for strider format -- no sample file to test against
not ok 4 # TODO & SKIP No tests for strider format -- no sample file to test against
not ok 5 # TODO & SKIP No tests for strider format -- no sample file to test against
not ok 6 # TODO & SKIP No tests for strider format -- no sample file to test against
not ok 7 # TODO & SKIP No tests for strider format -- no sample file to test against
not ok 8 # TODO & SKIP No tests for strider format -- no sample file to test against
ok
Replacement list is longer than search list at Bio/Range.pm line 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
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
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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
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ok 192
ok 193
ok 194
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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
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ok 217
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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 238.
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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
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
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ok 31
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ok 34
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ok 445
ok 446
ok 447
ok 448
ok 449
ok 450
ok
Replacement list is longer than search list at Bio/Range.pm line 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
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 81
Replacement list is longer than search list at Bio/Range.pm line 238.
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
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
Replacement list is longer than search list at Bio/Range.pm line 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
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 Bio/Range.pm line 238.
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
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
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 238.
Use of uninitialized value $format in lc at Bio/SeqIO.pm line 369.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN4> line 35.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN9> line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN9> line 934.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN9> 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 238.
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
t/SeqTools/SeqPattern.t ...................... 
1..9
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
Replacement list is longer than search list at Bio/Range.pm line 238.
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
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
Replacement list is longer than search list at Bio/Range.pm line 238.
t/SeqTools/SeqUtils.t ........................ 
1..41
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
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok
Replacement list is longer than search list at Bio/Range.pm line 238.
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 81
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 238.
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
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/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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
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 238.
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 238.
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
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok
t/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
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
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
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 - 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
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
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..81
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
Replacement list is longer than search list at Bio/Range.pm line 238.
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
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 238.
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
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 238.
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
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
Replacement list is longer than search list at Bio/Range.pm line 238.
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
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 238.
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
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 238.
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
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 238.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN8> line 256.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 105, <GEN9> line 2.
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
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ok 140 - The object isa Bio::Location::SplitLocationI
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Replacement list is longer than search list at Bio/Range.pm line 238.
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
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Replacement list is longer than search list at Bio/Range.pm line 238.
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 238.
t/Tools/Lucy.t ............................... 
1..22
ok 1 - use Bio::Tools::Lucy;
ok 2 - The object isa Bio::Tools::Lucy
ok 3
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Replacement list is longer than search list at Bio/Range.pm line 238.
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 238.
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 81
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
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UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
Replacement list is longer than search list at Bio/Range.pm line 238.
t/Tools/Phylo/PAML.t ......................... 
1..202
ok 1 - use Bio::Tools::Phylo::PAML;
ok 2
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ok 163 - node\#8 reconstructed seq
ok 164 - ancestral AA
ok 165 - ancestral AA
ok 166 - derived AA
ok 167 - ancestral AA
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ok 170 - derived AA
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ok
t/Tools/Phylo/Phylip/ProtDist.t .............. 
1..47
ok 1 - use Bio::Tools::Phylo::Phylip::ProtDist;
ok 2
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Replacement list is longer than search list at Bio/Range.pm line 238.
t/Tools/Primer3.t ............................ 
1..12
ok 1 - use Bio::Tools::Primer3;
ok 2
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ok 10 - The object isa Bio::Seq::PrimedSeq
ok 11
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ok
Replacement list is longer than search list at Bio/Range.pm line 238.
t/Tools/Promoterwise.t ....................... 
1..7
ok 1 - use Bio::Tools::Promoterwise;
ok 2 - The object isa Bio::Tools::Promoterwise
ok 3
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Replacement list is longer than search list at Bio/Range.pm line 238.
t/Tools/Pseudowise.t ......................... 
1..21
ok 1 - use Bio::Tools::Pseudowise;
ok 2
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t/Tools/QRNA.t ............................... 
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ok 1 - use Bio::Tools::QRNA;
ok 2
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t/Tools/RandDistFunctions.t .................. 
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ok 1 - use Bio::Tools::RandomDistFunctions;
ok 2
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ok
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t/Tools/RepeatMasker.t ....................... 
1..14
ok 1 - use Bio::Tools::RepeatMasker;
ok 2
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ok
t/Tools/Run/RemoteBlast.t .................... skipped: Network tests have not been requested
Replacement list is longer than search list at Bio/Range.pm line 238.
t/Tools/Run/StandAloneBlast.t ................ 
1..45
ok 1 - use Bio::Tools::Run::StandAloneBlast;
ok 2 - use Bio::SeqIO;
ok 3
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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
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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
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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 238.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
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
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t/Tools/Sigcleave.t .......................... 
1..18
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::Tools::Sigcleave;
ok 3
ok 4
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ok 6
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ok 9
ok 10
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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 238.
t/Tools/Signalp.t ............................ 
1..11
ok 1 - use Bio::Tools::Signalp;
ok 2
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ok
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t/Tools/Signalp/ExtendedSignalp.t ............ 
1..185
ok 1 - use Bio::Tools::Signalp::ExtendedSignalp;
ok 2
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ok
Replacement list is longer than search list at Bio/Range.pm line 238.
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
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ok
Replacement list is longer than search list at Bio/Range.pm line 238.
t/Tools/Spidey/Spidey.t ...................... 
1..26
ok 1 - use Bio::Tools::Spidey::Results;
ok 2
ok 3
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ok 5
ok 6
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ok 12
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ok
Replacement list is longer than search list at Bio/Range.pm line 238.
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 238.
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 238.
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 238.
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 238.
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 238.
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 81
t/Tree/Compatible.t .......................... 
1..5
ok 1 - use Bio::Tree::Compatible;
ok 2 - use Bio::TreeIO;
ok 3
ok 4
ok 5
ok
t/Tree/Node.t ................................ 
1..34
ok 1 - use Bio::Tree::Node;
ok 2 - use Bio::Tree::AlleleNode;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10 - retrieve the first value
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
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
t/Tree/PhyloNetwork/Factory.t ................ skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
t/Tree/PhyloNetwork/GraphViz.t ............... skipped: The optional module Bio::PhyloNetwork (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 81
t/Tree/PhyloNetwork/PhyloNetwork.t ........... skipped: The optional module Algorithm::Munkres (or dependencies thereof) was not installed
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
t/Tree/PhyloNetwork/RandomFactory.t .......... skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
t/Tree/PhyloNetwork/TreeFactory.t ............ skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
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 81
t/Tree/Tree.t ................................ 
1..60
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 - Root node is A's ancestor
ok 34 - Can reroot with C's ancsestor
ok 35 - Check to see that node count is correct after an internal node was removed after this re-rooting
ok 36 - Total original branch length is what it is supposed to be
ok 37 - Updated total branch length after the reroot
ok 38 - Make sure root is really what we asked for
ok 39 - Testing for failed re-rerooting
ok 40 - Test that rooting succeeded
ok 41 - Test that re-rooted tree has proper number of nodes after re-rooting
ok 42 - Branch length before rerooting
ok 43 - Branch length after rerooting
ok 44 - Root is really the ancestor we asked for
ok 45 - BFS traversal order
ok 46 - DFS travfersal order
ok 47 - DFS traversal after removing H
ok 48 - DFS traversal after removing G
ok 49 - DFS traversal after removing F
ok 50 - DFS after removing all but 0,1,2,A,B,C,D
ok 51 - Testing bootstrap copy
ok 52 - Testing bootstrap copy
ok 53 - Testing bootstrap copy
ok 54 - Testing bootstrap copy
ok 55 - Testing bootstrap copy
ok 56 - Testing bootstrap copy
ok 57 - Testing auto-boostrap copy during parse
ok 58 - Testing auto-boostrap copy during parse
ok 59 - Testing auto-boostrap copy during parse
ok 60 - Testing auto-boostrap copy during parse
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
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 # skip The optional module SVG::Graph (or dependencies thereof) was not installed
ok 20 # skip The optional module SVG::Graph (or dependencies thereof) was not installed
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 81
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 81
t/Tree/TreeIO/newick.t ....................... 
1..20
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
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
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 81
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
t/Tree/TreeIO/phyloxml.t ..................... skipped: The optional module XML::LibXML (or dependencies thereof) was not installed
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
t/Tree/TreeIO/svggraph.t ..................... 
1..4
ok 1 - use Bio::TreeIO;
ok 2 # skip The optional module SVG::Graph (or dependencies thereof) was not installed
ok 3 # skip The optional module SVG::Graph (or dependencies thereof) was not installed
ok 4 # skip The optional module SVG::Graph (or dependencies thereof) was not installed
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 81
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 81
t/Tree/TreeStatistics.t ...................... 
1..13
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 - association index
ok 9 - subtree association index
ok 10 - monophyletic clade size
ok 11 - monophyletic clade size
ok 12 - monophyletic clade size
ok 13 - monophyletic clade size
ok
Replacement list is longer than search list at Bio/Range.pm line 238.
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 238.
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 238.
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 238.
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 238.
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 238.
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 238.
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 238.
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/Assembly/ContigSpectrum.t                (Wstat: 512 Tests: 3 Failed: 1)
  Failed test:  3
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 134 tests but ran 3.
t/LocalDB/SeqFeature.t                     (Wstat: 256 Tests: 59 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/RemoteDB/Taxonomy.t                      (Wstat: 65280 Tests: 82 Failed: 1)
  Failed test:  4
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 103 tests but ran 82.
t/SeqIO/asciitree.t                        (Wstat: 256 Tests: 2 Failed: 1)
  Failed test:  2
  Non-zero exit status: 1
Files=318, Tests=17530, 136 wallclock secs ( 3.24 usr  2.66 sys + 86.06 cusr 16.73 csys = 108.69 CPU)
Result: FAIL
Failed 5/318 test programs. 5/17530 subtests failed.
make: *** [test] Error 255
  CJFIELDS/BioPerl-1.6.0.tar.gz
  make test TEST_VERBOSE=1 -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
  reports CJFIELDS/BioPerl-1.6.0.tar.gz
Finished 2011-04-28T14:16:30